Daily Papers

The creation of high-fidelity, digital versions of human heads is an important stepping stone in the process of further integrating virtual components into our everyday lives. Constructing such avatars is a challenging research problem, due to a high demand for photo-realism and real-time rendering performance. In this work, we propose Neural Parametric Gaussian Avatars (NPGA), a data-driven approach to create high-fidelity, controllable avatars from multi-view video recordings. We build our method around 3D Gaussian Splatting for its highly efficient rendering and to inherit the topological flexibility of point clouds. In contrast to previous work, we condition our avatars' dynamics on the rich expression space of neural parametric head models (NPHM), instead of mesh-based 3DMMs. To this end, we distill the backward deformation field of our underlying NPHM into forward deformations which are compatible with rasterization-based rendering. All remaining fine-scale, expression-dependent details are learned from the multi-view videos. To increase the representational capacity of our avatars, we augment the canonical Gaussian point cloud using per-primitive latent features which govern its dynamic behavior. To regularize this increased dynamic expressivity, we propose Laplacian terms on the latent features and predicted dynamics. We evaluate our method on the public NeRSemble dataset, demonstrating that NPGA significantly outperforms the previous state-of-the-art avatars on the self-reenactment task by 2.6 PSNR. Furthermore, we demonstrate accurate animation capabilities from real-world monocular videos.

We propose a method to learn a high-quality implicit 3D head avatar from a monocular RGB video captured in the wild. The learnt avatar is driven by a parametric face model to achieve user-controlled facial expressions and head poses. Our hybrid pipeline combines the geometry prior and dynamic tracking of a 3DMM with a neural radiance field to achieve fine-grained control and photorealism. To reduce over-smoothing and improve out-of-model expressions synthesis, we propose to predict local features anchored on the 3DMM geometry. These learnt features are driven by 3DMM deformation and interpolated in 3D space to yield the volumetric radiance at a designated query point. We further show that using a Convolutional Neural Network in the UV space is critical in incorporating spatial context and producing representative local features. Extensive experiments show that we are able to reconstruct high-quality avatars, with more accurate expression-dependent details, good generalization to out-of-training expressions, and quantitatively superior renderings compared to other state-of-the-art approaches.

We introduce GaussianSpeech, a novel approach that synthesizes high-fidelity animation sequences of photo-realistic, personalized 3D human head avatars from spoken audio. To capture the expressive, detailed nature of human heads, including skin furrowing and finer-scale facial movements, we propose to couple speech signal with 3D Gaussian splatting to create realistic, temporally coherent motion sequences. We propose a compact and efficient 3DGS-based avatar representation that generates expression-dependent color and leverages wrinkle- and perceptually-based losses to synthesize facial details, including wrinkles that occur with different expressions. To enable sequence modeling of 3D Gaussian splats with audio, we devise an audio-conditioned transformer model capable of extracting lip and expression features directly from audio input. Due to the absence of high-quality datasets of talking humans in correspondence with audio, we captured a new large-scale multi-view dataset of audio-visual sequences of talking humans with native English accents and diverse facial geometry. GaussianSpeech consistently achieves state-of-the-art performance with visually natural motion at real time rendering rates, while encompassing diverse facial expressions and styles.

Recently, we have witnessed the explosive growth of various volumetric representations in modeling animatable head avatars. However, due to the diversity of frameworks, there is no practical method to support high-level applications like 3D head avatar editing across different representations. In this paper, we propose a generic avatar editing approach that can be universally applied to various 3DMM driving volumetric head avatars. To achieve this goal, we design a novel expression-aware modification generative model, which enables lift 2D editing from a single image to a consistent 3D modification field. To ensure the effectiveness of the generative modification process, we develop several techniques, including an expression-dependent modification distillation scheme to draw knowledge from the large-scale head avatar model and 2D facial texture editing tools, implicit latent space guidance to enhance model convergence, and a segmentation-based loss reweight strategy for fine-grained texture inversion. Extensive experiments demonstrate that our method delivers high-quality and consistent results across multiple expression and viewpoints. Project page: https://zju3dv.github.io/geneavatar/

3D head avatars built with neural implicit volumetric representations have achieved unprecedented levels of photorealism. However, the computational cost of these methods remains a significant barrier to their widespread adoption, particularly in real-time applications such as virtual reality and teleconferencing. While attempts have been made to develop fast neural rendering approaches for static scenes, these methods cannot be simply employed to support realistic facial expressions, such as in the case of a dynamic facial performance. To address these challenges, we propose a novel fast 3D neural implicit head avatar model that achieves real-time rendering while maintaining fine-grained controllability and high rendering quality. Our key idea lies in the introduction of local hash table blendshapes, which are learned and attached to the vertices of an underlying face parametric model. These per-vertex hash-tables are linearly merged with weights predicted via a CNN, resulting in expression dependent embeddings. Our novel representation enables efficient density and color predictions using a lightweight MLP, which is further accelerated by a hierarchical nearest neighbor search method. Extensive experiments show that our approach runs in real-time while achieving comparable rendering quality to state-of-the-arts and decent results on challenging expressions.

3D head animation has seen major quality and runtime improvements over the last few years, particularly empowered by the advances in differentiable rendering and neural radiance fields. Real-time rendering is a highly desirable goal for real-world applications. We propose HeadGaS, a model that uses 3D Gaussian Splats (3DGS) for 3D head reconstruction and animation. In this paper we introduce a hybrid model that extends the explicit 3DGS representation with a base of learnable latent features, which can be linearly blended with low-dimensional parameters from parametric head models to obtain expression-dependent color and opacity values. We demonstrate that HeadGaS delivers state-of-the-art results in real-time inference frame rates, surpassing baselines by up to 2dB, while accelerating rendering speed by over x10.

3D facial reconstruction from a single in-the-wild image is a crucial task in human-centered computer vision tasks. While existing methods can recover accurate facial shapes, there remains significant space for improvement in fine-grained expression capture. Current approaches struggle with irregular mouth shapes, exaggerated expressions, and asymmetrical facial movements. We present TEASER (Token EnhAnced Spatial modeling for Expressions Reconstruction), which addresses these challenges and enhances 3D facial geometry performance. TEASER tackles two main limitations of existing methods: insufficient photometric loss for self-reconstruction and inaccurate localization of subtle expressions. We introduce a multi-scale tokenizer to extract facial appearance information. Combined with a neural renderer, these tokens provide precise geometric guidance for expression reconstruction. Furthermore, TEASER incorporates a pose-dependent landmark loss to further improve geometric performances. Our approach not only significantly enhances expression reconstruction quality but also offers interpretable tokens suitable for various downstream applications, such as photorealistic facial video driving, expression transfer, and identity swapping. Quantitative and qualitative experimental results across multiple datasets demonstrate that TEASER achieves state-of-the-art performance in precise expression reconstruction.

Medical knowledge is context-dependent and requires consistent reasoning across various natural language expressions of semantically equivalent phrases. This is particularly crucial for drug names, where patients often use brand names like Advil or Tylenol instead of their generic equivalents. To study this, we create a new robustness dataset, RABBITS, to evaluate performance differences on medical benchmarks after swapping brand and generic drug names using physician expert annotations. We assess both open-source and API-based LLMs on MedQA and MedMCQA, revealing a consistent performance drop ranging from 1-10\%. Furthermore, we identify a potential source of this fragility as the contamination of test data in widely used pre-training datasets. All code is accessible at https://github.com/BittermanLab/RABBITS, and a HuggingFace leaderboard is available at https://huggingface.co/spaces/AIM-Harvard/rabbits-leaderboard.

Recent advances in Neural Radiance Fields (NeRFs) have made it possible to reconstruct and reanimate dynamic portrait scenes with control over head-pose, facial expressions and viewing direction. However, training such models assumes photometric consistency over the deformed region e.g. the face must be evenly lit as it deforms with changing head-pose and facial expression. Such photometric consistency across frames of a video is hard to maintain, even in studio environments, thus making the created reanimatable neural portraits prone to artifacts during reanimation. In this work, we propose CoDyNeRF, a system that enables the creation of fully controllable 3D portraits in real-world capture conditions. CoDyNeRF learns to approximate illumination dependent effects via a dynamic appearance model in the canonical space that is conditioned on predicted surface normals and the facial expressions and head-pose deformations. The surface normals prediction is guided using 3DMM normals that act as a coarse prior for the normals of the human head, where direct prediction of normals is hard due to rigid and non-rigid deformations induced by head-pose and facial expression changes. Using only a smartphone-captured short video of a subject for training, we demonstrate the effectiveness of our method on free view synthesis of a portrait scene with explicit head pose and expression controls, and realistic lighting effects. The project page can be found here: http://shahrukhathar.github.io/2023/08/22/CoDyNeRF.html

Many current NLP systems are built from language models trained to optimize unsupervised objectives on large amounts of raw text. Under what conditions might such a procedure acquire meaning? Our systematic experiments with synthetic data reveal that, with languages where all expressions have context-independent denotations (i.e., languages with strong transparency), both autoregressive and masked language models successfully learn to emulate semantic relations between expressions. However, when denotations are changed to be context-dependent with the language otherwise unmodified, this ability degrades. Turning to natural language, our experiments with a specific phenomenon -- referential opacity -- add to the growing body of evidence that current language models do not represent natural language semantics well. We show this failure relates to the context-dependent nature of natural language form-meaning mappings.

Personalized treatment effect estimates are often of interest in high-stakes applications -- thus, before deploying a model estimating such effects in practice, one needs to be sure that the best candidate from the ever-growing machine learning toolbox for this task was chosen. Unfortunately, due to the absence of counterfactual information in practice, it is usually not possible to rely on standard validation metrics for doing so, leading to a well-known model selection dilemma in the treatment effect estimation literature. While some solutions have recently been investigated, systematic understanding of the strengths and weaknesses of different model selection criteria is still lacking. In this paper, instead of attempting to declare a global `winner', we therefore empirically investigate success- and failure modes of different selection criteria. We highlight that there is a complex interplay between selection strategies, candidate estimators and the data used for comparing them, and provide interesting insights into the relative (dis)advantages of different criteria alongside desiderata for the design of further illuminating empirical studies in this context.

We introduce SummScreen, a summarization dataset comprised of pairs of TV series transcripts and human written recaps. The dataset provides a challenging testbed for abstractive summarization for several reasons. Plot details are often expressed indirectly in character dialogues and may be scattered across the entirety of the transcript. These details must be found and integrated to form the succinct plot descriptions in the recaps. Also, TV scripts contain content that does not directly pertain to the central plot but rather serves to develop characters or provide comic relief. This information is rarely contained in recaps. Since characters are fundamental to TV series, we also propose two entity-centric evaluation metrics. Empirically, we characterize the dataset by evaluating several methods, including neural models and those based on nearest neighbors. An oracle extractive approach outperforms all benchmarked models according to automatic metrics, showing that the neural models are unable to fully exploit the input transcripts. Human evaluation and qualitative analysis reveal that our non-oracle models are competitive with their oracle counterparts in terms of generating faithful plot events and can benefit from better content selectors. Both oracle and non-oracle models generate unfaithful facts, suggesting future research directions.

Temporal and numerical expression understanding is of great importance in many downstream Natural Language Processing (NLP) and Information Retrieval (IR) tasks. However, much previous work covers only a few sub-types and focuses only on entity extraction, which severely limits the usability of identified mentions. In order for such entities to be useful in downstream scenarios, coverage and granularity of sub-types are important; and, even more so, providing resolution into concrete values that can be manipulated. Furthermore, most previous work addresses only a handful of languages. Here we describe a multi-lingual evaluation dataset - NTX - covering diverse temporal and numerical expressions across 14 languages and covering extraction, normalization, and resolution. Along with the dataset we provide a robust rule-based system as a strong baseline for comparisons against other models to be evaluated in this dataset. Data and code are available at https://aka.ms/NTX.

Due to the subjectivity of the summarization, it is a good practice to have more than one gold summary for each training document. However, many modern large-scale abstractive summarization datasets have only one-to-one samples written by different human with different styles. The impact of this phenomenon is understudied. We formulate the differences among possible multiple expressions summarizing the same content as subjective bias and examine the role of this bias in the context of abstractive summarization. In this paper a lightweight and effective method to extract the feature embeddings of subjective styles is proposed. Results of summarization models trained on style-clustered datasets show that there are certain types of styles that lead to better convergence, abstraction and generalization. The reproducible code and generated summaries are available online.

Summarization models often generate text that is poorly calibrated to quality metrics because they are trained to maximize the likelihood of a single reference (MLE). To address this, recent work has added a calibration step, which exposes a model to its own ranked outputs to improve relevance or, in a separate line of work, contrasts positive and negative sets to improve faithfulness. While effective, much of this work has focused on how to generate and optimize these sets. Less is known about why one setup is more effective than another. In this work, we uncover the underlying characteristics of effective sets. For each training instance, we form a large, diverse pool of candidates and systematically vary the subsets used for calibration fine-tuning. Each selection strategy targets distinct aspects of the sets, such as lexical diversity or the size of the gap between positive and negatives. On three diverse scientific long-form summarization datasets (spanning biomedical, clinical, and chemical domains), we find, among others, that faithfulness calibration is optimal when the negative sets are extractive and more likely to be generated, whereas for relevance calibration, the metric margin between candidates should be maximized and surprise--the disagreement between model and metric defined candidate rankings--minimized. Code to create, select, and optimize calibration sets is available at https://github.com/griff4692/calibrating-summaries

We study the fractal structure of language, aiming to provide a precise formalism for quantifying properties that may have been previously suspected but not formally shown. We establish that language is: (1) self-similar, exhibiting complexities at all levels of granularity, with no particular characteristic context length, and (2) long-range dependent (LRD), with a Hurst parameter of approximately H=0.70. Based on these findings, we argue that short-term patterns/dependencies in language, such as in paragraphs, mirror the patterns/dependencies over larger scopes, like entire documents. This may shed some light on how next-token prediction can lead to a comprehension of the structure of text at multiple levels of granularity, from words and clauses to broader contexts and intents. We also demonstrate that fractal parameters improve upon perplexity-based bits-per-byte (BPB) in predicting downstream performance. We hope these findings offer a fresh perspective on language and the mechanisms underlying the success of LLMs.

Telling stories is an integral part of human communication which can evoke emotions and influence the affective states of the audience. Automatically modeling emotional trajectories in stories has thus attracted considerable scholarly interest. However, as most existing works have been limited to unsupervised dictionary-based approaches, there is no benchmark for this task. We address this gap by introducing continuous valence and arousal labels for an existing dataset of children's stories originally annotated with discrete emotion categories. We collect additional annotations for this data and map the categorical labels to the continuous valence and arousal space. For predicting the thus obtained emotionality signals, we fine-tune a DeBERTa model and improve upon this baseline via a weakly supervised learning approach. The best configuration achieves a Concordance Correlation Coefficient (CCC) of .8221 for valence and .7125 for arousal on the test set, demonstrating the efficacy of our proposed approach. A detailed analysis shows the extent to which the results vary depending on factors such as the author, the individual story, or the section within the story. In addition, we uncover the weaknesses of our approach by investigating examples that prove to be difficult to predict.

The objective of this paper is to predict (A) whether a sentence in a written text expresses an emotion, (B) the mode(s) in which it is expressed, (C) whether it is basic or complex, and (D) its emotional category. One of our major contributions, through a dataset and a model, is to integrate the fact that an emotion can be expressed in different modes: from a direct mode, essentially lexicalized, to a more indirect mode, where emotions will only be suggested, a mode that NLP approaches generally don't take into account. Another originality is that the scope is on written texts, as opposed usual work focusing on conversational (often multi-modal) data. In this context, modes of expression are seen as a factor towards the automatic analysis of complexity in texts. Experiments on French texts show acceptable results compared to the human annotators' agreement, and outperforming results compared to using a large language model with in-context learning (i.e. no fine-tuning).

In this work, we embark on the thermodynamic investigation concerning a family of primary charged black holes within the context of shift and parity symmetric Beyond Horndeski gravity. Employing the Euclidean approach, we derive the functional expression for the free energy and derive the first thermodynamic law, offering a methodology to address the challenge of extracting the thermal quantities in shift-symmetric scalar tensor theories characterized by linear time dependence in the scalar field. Following the formal analysis, we provide some illustrative examples focusing on the thermal evaporation of these fascinating objects.

Token interaction operation is one of the core modules in MLP-based models to exchange and aggregate information between different spatial locations. However, the power of token interaction on the spatial dimension is highly dependent on the spatial resolution of the feature maps, which limits the model's expressive ability, especially in deep layers where the feature are down-sampled to a small spatial size. To address this issue, we present a novel method called Strip-MLP to enrich the token interaction power in three ways. Firstly, we introduce a new MLP paradigm called Strip MLP layer that allows the token to interact with other tokens in a cross-strip manner, enabling the tokens in a row (or column) to contribute to the information aggregations in adjacent but different strips of rows (or columns). Secondly, a Cascade Group Strip Mixing Module (CGSMM) is proposed to overcome the performance degradation caused by small spatial feature size. The module allows tokens to interact more effectively in the manners of within-patch and cross-patch, which is independent to the feature spatial size. Finally, based on the Strip MLP layer, we propose a novel Local Strip Mixing Module (LSMM) to boost the token interaction power in the local region. Extensive experiments demonstrate that Strip-MLP significantly improves the performance of MLP-based models on small datasets and obtains comparable or even better results on ImageNet. In particular, Strip-MLP models achieve higher average Top-1 accuracy than existing MLP-based models by +2.44\% on Caltech-101 and +2.16\% on CIFAR-100. The source codes will be available at~https://github.com/Med-Process/Strip_MLP{https://github.com/Med-Process/Strip\_MLP.

We extend Textual Inversion to learn pseudo-words that represent a concept at different resolutions. This allows us to generate images that use the concept with different levels of detail and also to manipulate different resolutions using language. Once learned, the user can generate images at different levels of agreement to the original concept; "A photo of S^*(0)" produces the exact object while the prompt "A photo of S^*(0.8)" only matches the rough outlines and colors. Our framework allows us to generate images that use different resolutions of an image (e.g. details, textures, styles) as separate pseudo-words that can be composed in various ways. We open-soure our code in the following URL: https://github.com/giannisdaras/multires_textual_inversion

Gene regulatory network inference (GRNI) is a challenging problem, particularly owing to the presence of zeros in single-cell RNA sequencing data: some are biological zeros representing no gene expression, while some others are technical zeros arising from the sequencing procedure (aka dropouts), which may bias GRNI by distorting the joint distribution of the measured gene expressions. Existing approaches typically handle dropout error via imputation, which may introduce spurious relations as the true joint distribution is generally unidentifiable. To tackle this issue, we introduce a causal graphical model to characterize the dropout mechanism, namely, Causal Dropout Model. We provide a simple yet effective theoretical result: interestingly, the conditional independence (CI) relations in the data with dropouts, after deleting the samples with zero values (regardless if technical or not) for the conditioned variables, are asymptotically identical to the CI relations in the original data without dropouts. This particular test-wise deletion procedure, in which we perform CI tests on the samples without zeros for the conditioned variables, can be seamlessly integrated with existing structure learning approaches including constraint-based and greedy score-based methods, thus giving rise to a principled framework for GRNI in the presence of dropouts. We further show that the causal dropout model can be validated from data, and many existing statistical models to handle dropouts fit into our model as specific parametric instances. Empirical evaluation on synthetic, curated, and real-world experimental transcriptomic data comprehensively demonstrate the efficacy of our method.

We consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we introduce Seq2Exp, a Sequence to Expression network explicitly designed to discover and extract regulatory elements that drive target gene expression, enhancing the accuracy of the gene expression prediction. Our approach captures the causal relationship between epigenomic signals, DNA sequences and their associated regulatory elements. Specifically, we propose to decompose the epigenomic signals and the DNA sequence conditioned on the causal active regulatory elements, and apply an information bottleneck with the Beta distribution to combine their effects while filtering out non-causal components. Our experiments demonstrate that Seq2Exp outperforms existing baselines in gene expression prediction tasks and discovers influential regions compared to commonly used statistical methods for peak detection such as MACS3. The source code is released as part of the AIRS library (https://github.com/divelab/AIRS/).

Partial correlations quantify linear association between two variables adjusting for the influence of the remaining variables. They form the backbone for graphical models and are readily obtained from the inverse of the covariance matrix. For compositional data, the covariance structure is specified from log ratios of variables, so unless we try to "open" the data via a normalization, this implies changes in the definition and interpretation of partial correlations. In the present work, we elucidate how results derived by Aitchison (1986) lead to a natural definition of partial correlation that has a number of advantages over current measures of association. For this, we show that the residuals of log-ratios between a variable with a reference, when adjusting for all remaining variables including the reference, are reference-independent. Since the reference itself can be controlled for, correlations between residuals are defined for the variables directly without the necessity to recur to ratios except when specifying which variables are partialled out. Thus, perhaps surprisingly, partial correlations do not have the problems commonly found with measures of pairwise association on compositional data. They are well-defined between two variables, are properly scaled, and allow for negative association. By design, they are subcompositionally incoherent, but they share this property with conventional partial correlations (where results change when adjusting for the influence of fewer variables). We discuss the equivalence with normalization-based approaches whenever the normalizing variables are controlled for. We also discuss the partial variances and correlations we obtain from a previously studied data set of Roman glass cups.

Recent advances in multi-modal algorithms have driven and been driven by the increasing availability of large image-text datasets, leading to significant strides in various fields, including computational pathology. However, in most existing medical image-text datasets, the text typically provides high-level summaries that may not sufficiently describe sub-tile regions within a large pathology image. For example, an image might cover an extensive tissue area containing cancerous and healthy regions, but the accompanying text might only specify that this image is a cancer slide, lacking the nuanced details needed for in-depth analysis. In this study, we introduce STimage-1K4M, a novel dataset designed to bridge this gap by providing genomic features for sub-tile images. STimage-1K4M contains 1,149 images derived from spatial transcriptomics data, which captures gene expression information at the level of individual spatial spots within a pathology image. Specifically, each image in the dataset is broken down into smaller sub-image tiles, with each tile paired with 15,000-30,000 dimensional gene expressions. With 4,293,195 pairs of sub-tile images and gene expressions, STimage-1K4M offers unprecedented granularity, paving the way for a wide range of advanced research in multi-modal data analysis an innovative applications in computational pathology, and beyond.

Are pairs of words that tend to occur together also likely to stand in a linguistic dependency? This empirical question is motivated by a long history of literature in cognitive science, psycholinguistics, and NLP. In this work we contribute an extensive analysis of the relationship between linguistic dependencies and statistical dependence between words. Improving on previous work, we introduce the use of large pretrained language models to compute contextualized estimates of the pointwise mutual information between words (CPMI). For multiple models and languages, we extract dependency trees which maximize CPMI, and compare to gold standard linguistic dependencies. Overall, we find that CPMI dependencies achieve an unlabelled undirected attachment score of at most approx 0.5. While far above chance, and consistently above a non-contextualized PMI baseline, this score is generally comparable to a simple baseline formed by connecting adjacent words. We analyze which kinds of linguistic dependencies are best captured in CPMI dependencies, and also find marked differences between the estimates of the large pretrained language models, illustrating how their different training schemes affect the type of dependencies they capture.

Large Language Models (LLMs) are increasingly being utilized by both candidates and employers in the recruitment context. However, with this comes numerous ethical concerns, particularly related to the lack of transparency in these "black-box" models. Although previous studies have sought to increase the transparency of these models by investigating the personality traits of LLMs, many of the previous studies have provided them with personality assessments to complete. On the other hand, this study seeks to obtain a better understanding of such models by examining their output variations based on different input prompts. Specifically, we use a novel elicitation approach using prompts derived from common interview questions, as well as prompts designed to elicit particular Big Five personality traits to examine whether the models were susceptible to trait-activation like humans are, to measure their personality based on the language used in their outputs. To do so, we repeatedly prompted multiple LMs with different parameter sizes, including Llama-2, Falcon, Mistral, Bloom, GPT, OPT, and XLNet (base and fine tuned versions) and examined their personality using classifiers trained on the myPersonality dataset. Our results reveal that, generally, all LLMs demonstrate high openness and low extraversion. However, whereas LMs with fewer parameters exhibit similar behaviour in personality traits, newer and LMs with more parameters exhibit a broader range of personality traits, with increased agreeableness, emotional stability, and openness. Furthermore, a greater number of parameters is positively associated with openness and conscientiousness. Moreover, fine-tuned models exhibit minor modulations in their personality traits, contingent on the dataset. Implications and directions for future research are discussed.

Aspect-based summarization is the task of generating focused summaries based on specific points of interest. Such summaries aid efficient analysis of text, such as quickly understanding reviews or opinions from different angles. However, due to large differences in the type of aspects for different domains (e.g., sentiment, product features), the development of previous models has tended to be domain-specific. In this paper, we propose WikiAsp, a large-scale dataset for multi-domain aspect-based summarization that attempts to spur research in the direction of open-domain aspect-based summarization. Specifically, we build the dataset using Wikipedia articles from 20 different domains, using the section titles and boundaries of each article as a proxy for aspect annotation. We propose several straightforward baseline models for this task and conduct experiments on the dataset. Results highlight key challenges that existing summarization models face in this setting, such as proper pronoun handling of quoted sources and consistent explanation of time-sensitive events.

Wheat varieties show a large diversity of traits and phenotypes. Linking them to genetic variability is essential for shorter and more efficient wheat breeding programs. Newly desirable wheat variety traits include disease resistance to reduce pesticide use, adaptation to climate change, resistance to heat and drought stresses, or low gluten content of grains. Wheat breeding experiments are documented by a large body of scientific literature and observational data obtained in-field and under controlled conditions. The cross-referencing of complementary information from the literature and observational data is essential to the study of the genotype-phenotype relationship and to the improvement of wheat selection. The scientific literature on genetic marker-assisted selection describes much information about the genotype-phenotype relationship. However, the variety of expressions used to refer to traits and phenotype values in scientific articles is a hinder to finding information and cross-referencing it. When trained adequately by annotated examples, recent text mining methods perform highly in named entity recognition and linking in the scientific domain. While several corpora contain annotations of human and animal phenotypes, currently, no corpus is available for training and evaluating named entity recognition and entity-linking methods in plant phenotype literature. The Triticum aestivum trait Corpus is a new gold standard for traits and phenotypes of wheat. It consists of 540 PubMed references fully annotated for trait, phenotype, and species named entities using the Wheat Trait and Phenotype Ontology and the species taxonomy of the National Center for Biotechnology Information. A study of the performance of tools trained on the Triticum aestivum trait Corpus shows that the corpus is suitable for the training and evaluation of named entity recognition and linking.

The ability to process idiomatic or literal multiword expressions is a crucial aspect of understanding and generating any language. The task of generating contextually relevant continuations for narratives containing idiomatic (or literal) expressions can allow us to test the ability of generative language models (LMs) in understanding nuanced language containing non-compositional figurative text. We conduct a series of experiments using datasets in two distinct languages (English and Portuguese) under three different training settings (zero-shot, few-shot, and fine-tuned). Our results suggest that the models are only slightly better at generating continuations for literal contexts than idiomatic contexts, with exceedingly small margins. Furthermore, the models studied in this work perform equally well across both languages, indicating the robustness of generative models in performing this task.

Formal and distributional semantic models offer complementary benefits in modeling meaning. The categorical compositional distributional (DisCoCat) model of meaning of Coecke et al. (arXiv:1003.4394v1 [cs.CL]) combines aspected of both to provide a general framework in which meanings of words, obtained distributionally, are composed using methods from the logical setting to form sentence meaning. Concrete consequences of this general abstract setting and applications to empirical data are under active study (Grefenstette et al., arxiv:1101.0309; Grefenstette and Sadrzadeh, arXiv:1106.4058v1 [cs.CL]). . In this paper, we extend this study by examining transitive verbs, represented as matrices in a DisCoCat. We discuss three ways of constructing such matrices, and evaluate each method in a disambiguation task developed by Grefenstette and Sadrzadeh (arXiv:1106.4058v1 [cs.CL]).

Empathy is a cognitive and emotional reaction to an observed situation of others. Empathy has recently attracted interest because it has numerous applications in psychology and AI, but it is unclear how different forms of empathy (e.g., self-report vs counterpart other-report, concern vs. distress) interact with other affective phenomena or demographics like gender and age. To better understand this, we created the {\it Empathic Conversations} dataset of annotated negative, empathy-eliciting dialogues in which pairs of participants converse about news articles. People differ in their perception of the empathy of others. These differences are associated with certain characteristics such as personality and demographics. Hence, we collected detailed characterization of the participants' traits, their self-reported empathetic response to news articles, their conversational partner other-report, and turn-by-turn third-party assessments of the level of self-disclosure, emotion, and empathy expressed. This dataset is the first to present empathy in multiple forms along with personal distress, emotion, personality characteristics, and person-level demographic information. We present baseline models for predicting some of these features from conversations.

Large Language Models (LLMs) have demonstrated notable proficiency in both code generation and comprehension across multiple programming languages. However, the mechanisms underlying this proficiency remain underexplored, particularly with respect to whether distinct programming languages are processed independently or within a shared parametric region. Drawing an analogy to the specialized regions of the brain responsible for distinct cognitive functions, we introduce the concept of Coding Spot, a specialized parametric region within LLMs that facilitates coding capabilities. Our findings identify this Coding Spot and show that targeted modifications to this subset significantly affect performance on coding tasks, while largely preserving non-coding functionalities. This compartmentalization mirrors the functional specialization observed in cognitive neuroscience, where specific brain regions are dedicated to distinct tasks, suggesting that LLMs may similarly employ specialized parameter regions for different knowledge domains.

We introduce a new dataset named WikiVitals which contains a large graph of 48k mutually referred Wikipedia articles classified into 32 categories and connected by 2.3M edges. Our aim is to rigorously evaluate the contributions of three distinct sources of information to the label prediction in a semi-supervised node classification setting, namely the content of the articles, their connections with each other and the correlations among their labels. We perform this evaluation using a Graph Markov Neural Network which provides a theoretically principled model for this task and we conduct a detailed evaluation of the contributions of each sources of information using a clear separation of model selection and model assessment. One interesting observation is that including the effect of label dependencies is more relevant for sparse train sets than it is for dense train sets.

Semantic word embeddings represent the meaning of a word via a vector, and are created by diverse methods. Many use nonlinear operations on co-occurrence statistics, and have hand-tuned hyperparameters and reweighting methods. This paper proposes a new generative model, a dynamic version of the log-linear topic model of~mnih2007three. The methodological novelty is to use the prior to compute closed form expressions for word statistics. This provides a theoretical justification for nonlinear models like PMI, word2vec, and GloVe, as well as some hyperparameter choices. It also helps explain why low-dimensional semantic embeddings contain linear algebraic structure that allows solution of word analogies, as shown by~mikolov2013efficient and many subsequent papers. Experimental support is provided for the generative model assumptions, the most important of which is that latent word vectors are fairly uniformly dispersed in space.

Superlatives are used to single out elements with a maximal/minimal property. Semantically, superlatives perform a set comparison: something (or some things) has the min/max property out of a set. As such, superlatives provide an ideal phenomenon for studying implicit phenomena and discourse restrictions. While this comparison set is often not explicitly defined, its (implicit) restrictions can be inferred from the discourse context the expression appears in. In this work we provide an extensive computational study on the semantics of superlatives. We propose a unified account of superlative semantics which allows us to derive a broad-coverage annotation schema. Using this unified schema we annotated a multi-domain dataset of superlatives and their semantic interpretations. We specifically focus on interpreting implicit or ambiguous superlative expressions, by analyzing how the discourse context restricts the set of interpretations. In a set of experiments we then analyze how well models perform at variations of predicting superlative semantics, with and without context. We show that the fine-grained semantics of superlatives in context can be challenging for contemporary models, including GPT-4.

Large language models, particularly GPT-3, are able to produce high quality summaries of general domain news articles in few- and zero-shot settings. However, it is unclear if such models are similarly capable in more specialized, high-stakes domains such as biomedicine. In this paper, we enlist domain experts (individuals with medical training) to evaluate summaries of biomedical articles generated by GPT-3, given zero supervision. We consider both single- and multi-document settings. In the former, GPT-3 is tasked with generating regular and plain-language summaries of articles describing randomized controlled trials; in the latter, we assess the degree to which GPT-3 is able to synthesize evidence reported across a collection of articles. We design an annotation scheme for evaluating model outputs, with an emphasis on assessing the factual accuracy of generated summaries. We find that while GPT-3 is able to summarize and simplify single biomedical articles faithfully, it struggles to provide accurate aggregations of findings over multiple documents. We release all data and annotations used in this work.

Feature attribution methods identify which features of an input most influence a model's output. Most widely-used feature attribution methods (such as SHAP, LIME, and Grad-CAM) are "class-dependent" methods in that they generate a feature attribution vector as a function of class. In this work, we demonstrate that class-dependent methods can "leak" information about the selected class, making that class appear more likely than it is. Thus, an end user runs the risk of drawing false conclusions when interpreting an explanation generated by a class-dependent method. In contrast, we introduce "distribution-aware" methods, which favor explanations that keep the label's distribution close to its distribution given all features of the input. We introduce SHAP-KL and FastSHAP-KL, two baseline distribution-aware methods that compute Shapley values. Finally, we perform a comprehensive evaluation of seven class-dependent and three distribution-aware methods on three clinical datasets of different high-dimensional data types: images, biosignals, and text.

Humans refer to objects in their environments all the time, especially in dialogue with other people. We explore generating and comprehending natural language referring expressions for objects in images. In particular, we focus on incorporating better measures of visual context into referring expression models and find that visual comparison to other objects within an image helps improve performance significantly. We also develop methods to tie the language generation process together, so that we generate expressions for all objects of a particular category jointly. Evaluation on three recent datasets - RefCOCO, RefCOCO+, and RefCOCOg, shows the advantages of our methods for both referring expression generation and comprehension.

The rapid advancements in transformer-based language models have revolutionized natural language processing, yet understanding the internal mechanisms of these models remains a significant challenge. This paper explores the application of sparse autoencoders (SAE) to interpret the internal representations of protein language models, specifically focusing on the ESM-2 8M parameter model. By performing a statistical analysis on each latent component's relevance to distinct protein annotations, we identify potential interpretations linked to various protein characteristics, including transmembrane regions, binding sites, and specialized motifs. We then leverage these insights to guide sequence generation, shortlisting the relevant latent components that can steer the model towards desired targets such as zinc finger domains. This work contributes to the emerging field of mechanistic interpretability in biological sequence models, offering new perspectives on model steering for sequence design.

We propose a method that can generate an unambiguous description (known as a referring expression) of a specific object or region in an image, and which can also comprehend or interpret such an expression to infer which object is being described. We show that our method outperforms previous methods that generate descriptions of objects without taking into account other potentially ambiguous objects in the scene. Our model is inspired by recent successes of deep learning methods for image captioning, but while image captioning is difficult to evaluate, our task allows for easy objective evaluation. We also present a new large-scale dataset for referring expressions, based on MS-COCO. We have released the dataset and a toolbox for visualization and evaluation, see https://github.com/mjhucla/Google_Refexp_toolbox

As advanced modern systems like deep neural networks (DNNs) and generative AI continue to enhance their capabilities in producing convincing and realistic content, the need to distinguish between user-generated and machine generated content is becoming increasingly evident. In this research, we undertake a comparative evaluation of eight traditional machine-learning algorithms to distinguish between machine-generated and human-generated data across three diverse datasets: Poems, Abstracts, and Essays. Our results indicate that traditional methods demonstrate a high level of accuracy in identifying machine-generated data, reflecting the documented effectiveness of popular pre-trained models like RoBERT. We note that machine-generated texts tend to be shorter and exhibit less word variety compared to human-generated content. While specific domain-related keywords commonly utilized by humans, albeit disregarded by current LLMs (Large Language Models), may contribute to this high detection accuracy, we show that deeper word representations like word2vec can capture subtle semantic variances. Furthermore, readability, bias, moral, and affect comparisons reveal a discernible contrast between machine-generated and human generated content. There are variations in expression styles and potentially underlying biases in the data sources (human and machine-generated). This study provides valuable insights into the advancing capacities and challenges associated with machine-generated content across various domains.

Introduction: The scientific publishing landscape is expanding rapidly, creating challenges for researchers to stay up-to-date with the evolution of the literature. Natural Language Processing (NLP) has emerged as a potent approach to automating knowledge extraction from this vast amount of publications and preprints. Tasks such as Named-Entity Recognition (NER) and Named-Entity Linking (NEL), in conjunction with context-dependent semantic interpretation, offer promising and complementary approaches to extracting structured information and revealing key concepts. Results: We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental design, and the nature of the experimental method as an additional class. SourceData-NLP contains more than 620,000 annotated biomedical entities, curated from 18,689 figures in 3,223 papers in molecular and cell biology. We illustrate the dataset's usefulness by assessing BioLinkBERT and PubmedBERT, two transformers-based models, fine-tuned on the SourceData-NLP dataset for NER. We also introduce a novel context-dependent semantic task that infers whether an entity is the target of a controlled intervention or the object of measurement. Conclusions: SourceData-NLP's scale highlights the value of integrating curation into publishing. Models trained with SourceData-NLP will furthermore enable the development of tools able to extract causal hypotheses from the literature and assemble them into knowledge graphs.

Generative language models often struggle with specialized or less-discussed knowledge. A potential solution is found in Retrieval-Augmented Generation (RAG) models which act like retrieving information before generating responses. In this study, we explore how the Atlas approach, a RAG model, decides between what it already knows (parametric) and what it retrieves (non-parametric). We use causal mediation analysis and controlled experiments to examine how internal representations influence information processing. Our findings disentangle the effects of parametric knowledge and the retrieved context. They indicate that in cases where the model can choose between both types of information (parametric and non-parametric), it relies more on the context than the parametric knowledge. Furthermore, the analysis investigates the computations involved in how the model uses the information from the context. We find that multiple mechanisms are active within the model and can be detected with mediation analysis: first, the decision of whether the context is relevant, and second, how the encoder computes output representations to support copying when relevant.

Language models and specialized table embedding models have recently demonstrated strong performance on many tasks over tabular data. Researchers and practitioners are keen to leverage these models in many new application contexts; but limited understanding of the strengths and weaknesses of these models, and the table representations they generate, makes the process of finding a suitable model for a given task reliant on trial and error. There is an urgent need to gain a comprehensive understanding of these models to minimize inefficiency and failures in downstream usage. To address this need, we propose Observatory, a formal framework to systematically analyze embedding representations of relational tables. Motivated both by invariants of the relational data model and by statistical considerations regarding data distributions, we define eight primitive properties, and corresponding measures to quantitatively characterize table embeddings for these properties. Based on these properties, we define an extensible framework to evaluate language and table embedding models. We collect and synthesize a suite of datasets and use Observatory to analyze nine such models. Our analysis provides insights into the strengths and weaknesses of learned representations over tables. We find, for example, that some models are sensitive to table structure such as column order, that functional dependencies are rarely reflected in embeddings, and that specialized table embedding models have relatively lower sample fidelity. Such insights help researchers and practitioners better anticipate model behaviors and select appropriate models for their downstream tasks, while guiding researchers in the development of new models.

Large language models (LLMs) have demonstrated remarkable capabilities in generating human-like text and exhibiting personality traits similar to those in humans. However, the mechanisms by which LLMs encode and express traits such as agreeableness and impulsiveness remain poorly understood. Drawing on the theory of social determinism, we investigate how long-term background factors, such as family environment and cultural norms, interact with short-term pressures like external instructions, shaping and influencing LLMs' personality traits. By steering the output of LLMs through the utilization of interpretable features within the model, we explore how these background and pressure factors lead to changes in the model's traits without the need for further fine-tuning. Additionally, we suggest the potential impact of these factors on model safety from the perspective of personality.

Facial expression recognition (FER) is a critical task in multimedia with significant implications across various domains. However, analyzing the causes of facial expressions is essential for accurately recognizing them. Current approaches, such as those based on facial action units (AUs), typically provide AU names and intensities but lack insight into the interactions and relationships between AUs and the overall expression. In this paper, we propose a novel method called ExpLLM, which leverages large language models to generate an accurate chain of thought (CoT) for facial expression recognition. Specifically, we have designed the CoT mechanism from three key perspectives: key observations, overall emotional interpretation, and conclusion. The key observations describe the AU's name, intensity, and associated emotions. The overall emotional interpretation provides an analysis based on multiple AUs and their interactions, identifying the dominant emotions and their relationships. Finally, the conclusion presents the final expression label derived from the preceding analysis. Furthermore, we also introduce the Exp-CoT Engine, designed to construct this expression CoT and generate instruction-description data for training our ExpLLM. Extensive experiments on the RAF-DB and AffectNet datasets demonstrate that ExpLLM outperforms current state-of-the-art FER methods. ExpLLM also surpasses the latest GPT-4o in expression CoT generation, particularly in recognizing micro-expressions where GPT-4o frequently fails.

This paper presents the results of the SUN team for the Compound Expressions Recognition Challenge of the 6th ABAW Competition. We propose a novel audio-visual method for compound expression recognition. Our method relies on emotion recognition models that fuse modalities at the emotion probability level, while decisions regarding the prediction of compound expressions are based on predefined rules. Notably, our method does not use any training data specific to the target task. The method is evaluated in multi-corpus training and cross-corpus validation setups. Our findings from the challenge demonstrate that the proposed method can potentially form a basis for development of intelligent tools for annotating audio-visual data in the context of human's basic and compound emotions. The source code is publicly available.

In large language models (LLMs), certain neurons can store distinct pieces of knowledge learned during pretraining. While knowledge typically appears as a combination of relations and entities, it remains unclear whether some neurons focus on a relation itself -- independent of any entity. We hypothesize such neurons detect a relation in the input text and guide generation involving such a relation. To investigate this, we study the Llama-2 family on a chosen set of relations with a statistics-based method. Our experiments demonstrate the existence of relation-specific neurons. We measure the effect of selectively deactivating candidate neurons specific to relation r on the LLM's ability to handle (1) facts whose relation is r and (2) facts whose relation is a different relation r' neq r. With respect to their capacity for encoding relation information, we give evidence for the following three properties of relation-specific neurons. (i) Neuron cumulativity. The neurons for r present a cumulative effect so that deactivating a larger portion of them results in the degradation of more facts in r. (ii) Neuron versatility. Neurons can be shared across multiple closely related as well as less related relations. Some relation neurons transfer across languages. (iii) Neuron interference. Deactivating neurons specific to one relation can improve LLM generation performance for facts of other relations. We will make our code publicly available at https://github.com/cisnlp/relation-specific-neurons.

We introduce Kosmos-2, a Multimodal Large Language Model (MLLM), enabling new capabilities of perceiving object descriptions (e.g., bounding boxes) and grounding text to the visual world. Specifically, we represent refer expressions as links in Markdown, i.e., ``[text span](bounding boxes)'', where object descriptions are sequences of location tokens. Together with multimodal corpora, we construct large-scale data of grounded image-text pairs (called GrIT) to train the model. In addition to the existing capabilities of MLLMs (e.g., perceiving general modalities, following instructions, and performing in-context learning), Kosmos-2 integrates the grounding capability into downstream applications. We evaluate Kosmos-2 on a wide range of tasks, including (i) multimodal grounding, such as referring expression comprehension, and phrase grounding, (ii) multimodal referring, such as referring expression generation, (iii) perception-language tasks, and (iv) language understanding and generation. This work lays out the foundation for the development of Embodiment AI and sheds light on the big convergence of language, multimodal perception, action, and world modeling, which is a key step toward artificial general intelligence. Data, demo, and pretrained models are available at https://aka.ms/kosmos-2.

This paper proposes a method for the automatic creation of variables (in the case of regression) that complement the information contained in the initial input vector. The method works as a pre-processing step in which the continuous values of the variable to be regressed are discretized into a set of intervals which are then used to define value thresholds. Then classifiers are trained to predict whether the value to be regressed is less than or equal to each of these thresholds. The different outputs of the classifiers are then concatenated in the form of an additional vector of variables that enriches the initial vector of the regression problem. The implemented system can thus be considered as a generic pre-processing tool. We tested the proposed enrichment method with 5 types of regressors and evaluated it in 33 regression datasets. Our experimental results confirm the interest of the approach.

Solving math word problems requires deductive reasoning over the quantities in the text. Various recent research efforts mostly relied on sequence-to-sequence or sequence-to-tree models to generate mathematical expressions without explicitly performing relational reasoning between quantities in the given context. While empirically effective, such approaches typically do not provide explanations for the generated expressions. In this work, we view the task as a complex relation extraction problem, proposing a novel approach that presents explainable deductive reasoning steps to iteratively construct target expressions, where each step involves a primitive operation over two quantities defining their relation. Through extensive experiments on four benchmark datasets, we show that the proposed model significantly outperforms existing strong baselines. We further demonstrate that the deductive procedure not only presents more explainable steps but also enables us to make more accurate predictions on questions that require more complex reasoning.

Cell identity encompasses various semantic aspects of a cell, including cell type, pathway information, disease information, and more, which are essential for biologists to gain insights into its biological characteristics. Understanding cell identity from the transcriptomic data, such as annotating cell types, has become an important task in bioinformatics. As these semantic aspects are determined by human experts, it is impossible for AI models to effectively carry out cell identity understanding tasks without the supervision signals provided by single-cell and label pairs. The single-cell pre-trained language models (PLMs) currently used for this task are trained only on a single modality, transcriptomics data, lack an understanding of cell identity knowledge. As a result, they have to be fine-tuned for downstream tasks and struggle when lacking labeled data with the desired semantic labels. To address this issue, we propose an innovative solution by constructing a unified representation of single-cell data and natural language during the pre-training phase, allowing the model to directly incorporate insights related to cell identity. More specifically, we introduce LangCell, the first Language-Cell pre-training framework. LangCell utilizes texts enriched with cell identity information to gain a profound comprehension of cross-modal knowledge. Results from experiments conducted on different benchmarks show that LangCell is the only single-cell PLM that can work effectively in zero-shot cell identity understanding scenarios, and also significantly outperforms existing models in few-shot and fine-tuning cell identity understanding scenarios.

Reference summaries for abstractive speech summarization require human annotation, which can be performed by listening to an audio recording or by reading textual transcripts of the recording. In this paper, we examine whether summaries based on annotators listening to the recordings differ from those based on annotators reading transcripts. Using existing intrinsic evaluation based on human evaluation, automatic metrics, LLM-based evaluation, and a retrieval-based reference-free method. We find that summaries are indeed different based on the source modality, and that speech-based summaries are more factually consistent and information-selective than transcript-based summaries. Meanwhile, transcript-based summaries are impacted by recognition errors in the source, and expert-written summaries are more informative and reliable. We make all the collected data and analysis code public(https://github.com/cmu-mlsp/interview_humanssum) to facilitate the reproduction of our work and advance research in this area.

The success of the GPT series proves that GPT can extract general information from sequences, thereby benefiting all downstream tasks. This motivates us to use pre-trained models to explore the hidden information in DNA sequences. However, data and task requirements in DNA sequence analysis are complexity and diversity as DNA relevant data includes different types of information, such as sequences, expression levels, etc, while there is currently no model specifically designed for these characteristics. Hereby, we present DNAGPT, a generalized foundation model pre-trained on over 10 billion base pairs from 9 species which can be fine-tuned for any DNA sequence analysis task. Our model can simultaneously process or output DNA sequences and numbers. In addition, our unique token design allows users to design prompts according to their own task requirements, making it applicable to any type of task. We have evaluated our model on classification, regression, and generation tasks. We demonstrate that DNAGPT benefits from pre-training, and therefore can bring performance gains to any downstream task. Our model is not only a new attempt in the field of genomes analysis, but also provides a new direction for the application of foundation models in biology.

This paper aims to bring fine-grained expression control to identity-preserving portrait generation. Existing methods tend to synthesize portraits with either neutral or stereotypical expressions. Even when supplemented with control signals like facial landmarks, these models struggle to generate accurate and vivid expressions following user instructions. To solve this, we introduce EmojiDiff, an end-to-end solution to facilitate simultaneous dual control of fine expression and identity. Unlike the conventional methods using coarse control signals, our method directly accepts RGB expression images as input templates to provide extremely accurate and fine-grained expression control in the diffusion process. As its core, an innovative decoupled scheme is proposed to disentangle expression features in the expression template from other extraneous information, such as identity, skin, and style. On one hand, we introduce ID-irrelevant Data Iteration (IDI) to synthesize extremely high-quality cross-identity expression pairs for decoupled training, which is the crucial foundation to filter out identity information hidden in the expressions. On the other hand, we meticulously investigate network layer function and select expression-sensitive layers to inject reference expression features, effectively preventing style leakage from expression signals. To further improve identity fidelity, we propose a novel fine-tuning strategy named ID-enhanced Contrast Alignment (ICA), which eliminates the negative impact of expression control on original identity preservation. Experimental results demonstrate that our method remarkably outperforms counterparts, achieves precise expression control with highly maintained identity, and generalizes well to various diffusion models.

Facial expressions are a form of non-verbal communication that humans perform seamlessly for meaningful transfer of information. Most of the literature addresses the facial expression recognition aspect however, with the advent of Generative Models, it has become possible to explore the affect space in addition to mere classification of a set of expressions. In this article, we propose a generative model architecture which robustly generates a set of facial expressions for multiple character identities and explores the possibilities of generating complex expressions by combining the simple ones.

Compositionality, the notion that the meaning of an expression is constructed from the meaning of its parts and syntactic rules, permits the infinite productivity of human language. For the first time, artificial language models (LMs) are able to match human performance in a number of compositional generalization tasks. However, much remains to be understood about the representational mechanisms underlying these abilities. We take a high-level geometric approach to this problem by relating the degree of compositionality in a dataset to the intrinsic dimensionality of its representations under an LM, a measure of feature complexity. We find not only that the degree of dataset compositionality is reflected in representations' intrinsic dimensionality, but that the relationship between compositionality and geometric complexity arises due to learned linguistic features over training. Finally, our analyses reveal a striking contrast between linear and nonlinear dimensionality, showing that they respectively encode formal and semantic aspects of linguistic composition.

We show that there is a general, informative and reliable procedure for discovering causal relations when, for all the investigator knows, both latent variables and selection bias may be at work. Given information about conditional independence and dependence relations between measured variables, even when latent variables and selection bias may be present, there are sufficient conditions for reliably concluding that there is a causal path from one variable to another, and sufficient conditions for reliably concluding when no such causal path exists.

Sentiment is a pervasive feature in natural language text, yet it is an open question how sentiment is represented within Large Language Models (LLMs). In this study, we reveal that across a range of models, sentiment is represented linearly: a single direction in activation space mostly captures the feature across a range of tasks with one extreme for positive and the other for negative. Through causal interventions, we isolate this direction and show it is causally relevant in both toy tasks and real world datasets such as Stanford Sentiment Treebank. Through this case study we model a thorough investigation of what a single direction means on a broad data distribution. We further uncover the mechanisms that involve this direction, highlighting the roles of a small subset of attention heads and neurons. Finally, we discover a phenomenon which we term the summarization motif: sentiment is not solely represented on emotionally charged words, but is additionally summarized at intermediate positions without inherent sentiment, such as punctuation and names. We show that in Stanford Sentiment Treebank zero-shot classification, 76% of above-chance classification accuracy is lost when ablating the sentiment direction, nearly half of which (36%) is due to ablating the summarized sentiment direction exclusively at comma positions.

Complex chemical structures, like drugs, are usually defined by SMILES strings as a sequence of molecules and bonds. These SMILES strings are used in different complex machine learning-based drug-related research and representation works. Escaping from complex representation, in this work, we pose a single question: What if we treat drug SMILES as conventional sentences and engage in text classification for drug classification? Our experiments affirm the possibility with very competitive scores. The study explores the notion of viewing each atom and bond as sentence components, employing basic NLP methods to categorize drug types, proving that complex problems can also be solved with simpler perspectives. The data and code are available here: https://github.com/azminewasi/Drug-Classification-NLP.

Large language models excel at interpreting complex natural language instructions, enabling them to perform a wide range of tasks. In the life sciences, single-cell RNA sequencing (scRNA-seq) data serves as the "language of cellular biology", capturing intricate gene expression patterns at the single-cell level. However, interacting with this "language" through conventional tools is often inefficient and unintuitive, posing challenges for researchers. To address these limitations, we present InstructCell, a multi-modal AI copilot that leverages natural language as a medium for more direct and flexible single-cell analysis. We construct a comprehensive multi-modal instruction dataset that pairs text-based instructions with scRNA-seq profiles from diverse tissues and species. Building on this, we develop a multi-modal cell language architecture capable of simultaneously interpreting and processing both modalities. InstructCell empowers researchers to accomplish critical tasks-such as cell type annotation, conditional pseudo-cell generation, and drug sensitivity prediction-using straightforward natural language commands. Extensive evaluations demonstrate that InstructCell consistently meets or exceeds the performance of existing single-cell foundation models, while adapting to diverse experimental conditions. More importantly, InstructCell provides an accessible and intuitive tool for exploring complex single-cell data, lowering technical barriers and enabling deeper biological insights.

Emotion expression is one of the essential traits of conversations. It may be self-related or caused by another speaker. The variety of reasons may serve as a source of the further emotion causes: conversation history, speaker's emotional state, etc. Inspired by the most recent advances in Chain-of-Thought, in this work, we exploit the existing three-hop reasoning approach (THOR) to perform large language model instruction-tuning for answering: emotion states (THOR-state), and emotion caused by one speaker to the other (THOR-cause). We equip THOR-cause with the reasoning revision (rr) for devising a reasoning path in fine-tuning. In particular, we rely on the annotated speaker emotion states to revise reasoning path. Our final submission, based on Flan-T5-base (250M) and the rule-based span correction technique, preliminary tuned with THOR-state and fine-tuned with THOR-cause-rr on competition training data, results in 3rd and 4th places (F1-proportional) and 5th place (F1-strict) among 15 participating teams. Our THOR implementation fork is publicly available: https://github.com/nicolay-r/THOR-ECAC

Normalizing flows are powerful non-parametric statistical models that function as a hybrid between density estimators and generative models. Current learning algorithms for normalizing flows assume that data points are sampled independently, an assumption that is frequently violated in practice, which may lead to erroneous density estimation and data generation. We propose a likelihood objective of normalizing flows incorporating dependencies between the data points, for which we derive a flexible and efficient learning algorithm suitable for different dependency structures. We show that respecting dependencies between observations can improve empirical results on both synthetic and real-world data, and leads to higher statistical power in a downstream application to genome-wide association studies.

Widely deployed large language models (LLMs) can produce convincing yet incorrect outputs, potentially misleading users who may rely on them as if they were correct. To reduce such overreliance, there have been calls for LLMs to communicate their uncertainty to end users. However, there has been little empirical work examining how users perceive and act upon LLMs' expressions of uncertainty. We explore this question through a large-scale, pre-registered, human-subject experiment (N=404) in which participants answer medical questions with or without access to responses from a fictional LLM-infused search engine. Using both behavioral and self-reported measures, we examine how different natural language expressions of uncertainty impact participants' reliance, trust, and overall task performance. We find that first-person expressions (e.g., "I'm not sure, but...") decrease participants' confidence in the system and tendency to agree with the system's answers, while increasing participants' accuracy. An exploratory analysis suggests that this increase can be attributed to reduced (but not fully eliminated) overreliance on incorrect answers. While we observe similar effects for uncertainty expressed from a general perspective (e.g., "It's not clear, but..."), these effects are weaker and not statistically significant. Our findings suggest that using natural language expressions of uncertainty may be an effective approach for reducing overreliance on LLMs, but that the precise language used matters. This highlights the importance of user testing before deploying LLMs at scale.

This paper introduces an innovative task focused on editing the personality traits of Large Language Models (LLMs). This task seeks to adjust the models' responses to opinion-related questions on specified topics since an individual's personality often manifests in the form of their expressed opinions, thereby showcasing different personality traits. Specifically, we construct a new benchmark dataset PersonalityEdit to address this task. Drawing on the theory in Social Psychology, we isolate three representative traits, namely Neuroticism, Extraversion, and Agreeableness, as the foundation for our benchmark. We then gather data using GPT-4, generating responses that not only align with a specified topic but also embody the targeted personality trait. We conduct comprehensive experiments involving various baselines and discuss the representation of personality behavior in LLMs. Our intriguing findings uncover potential challenges of the proposed task, illustrating several remaining issues. We anticipate that our work can provide the NLP community with insights. Code and datasets will be released at https://github.com/zjunlp/EasyEdit.

Causal precedence between biochemical interactions is crucial in the biomedical domain, because it transforms collections of individual interactions, e.g., bindings and phosphorylations, into the causal mechanisms needed to inform meaningful search and inference. Here, we analyze causal precedence in the biomedical domain as distinct from open-domain, temporal precedence. First, we describe a novel, hand-annotated text corpus of causal precedence in the biomedical domain. Second, we use this corpus to investigate a battery of models of precedence, covering rule-based, feature-based, and latent representation models. The highest-performing individual model achieved a micro F1 of 43 points, approaching the best performers on the simpler temporal-only precedence tasks. Feature-based and latent representation models each outperform the rule-based models, but their performance is complementary to one another. We apply a sieve-based architecture to capitalize on this lack of overlap, achieving a micro F1 score of 46 points.

In this work we show how large language models (LLMs) can learn statistical dependencies between otherwise unconditionally independent variables due to dataset selection bias. To demonstrate the effect, we developed a masked gender task that can be applied to BERT-family models to reveal spurious correlations between predicted gender pronouns and a variety of seemingly gender-neutral variables like date and location, on pre-trained (unmodified) BERT and RoBERTa large models. Finally, we provide an online demo, inviting readers to experiment further.

Recent work has shown that large language models (LLMs) are capable of generating summaries zero-shot (i.e., without explicit supervision) that, under human assessment, are often comparable or even preferred to manually composed reference summaries. However, this prior work has focussed almost exclusively on evaluating news article summarization. How do zero-shot summarizers perform in other (potentially more specialized) domains? In this work we evaluate zero-shot generated summaries across specialized domains including biomedical articles, and legal bills (in addition to standard news benchmarks for reference). We focus especially on the factuality of outputs. We acquire annotations from domain experts to identify inconsistencies in summaries and systematically categorize these errors. We analyze whether the prevalence of a given domain in the pretraining corpus affects extractiveness and faithfulness of generated summaries of articles in this domain. We release all collected annotations to facilitate additional research toward measuring and realizing factually accurate summarization, beyond news articles. The dataset can be downloaded from https://github.com/sanjanaramprasad/zero_shot_faceval_domains

The increasing use of tools and solutions based on Large Language Models (LLMs) for various tasks in the medical domain has become a prominent trend. Their use in this highly critical and sensitive domain has thus raised important questions about their robustness, especially in response to variations in input, and the reliability of the generated outputs. This study addresses these questions by constructing a textual dataset based on the ICD-10-CM code descriptions, widely used in US hospitals and containing many clinical terms, and their easily reproducible rephrasing. We then benchmarked existing embedding models, either generalist or specialized in the clinical domain, in a semantic search task where the goal was to correctly match the rephrased text to the original description. Our results showed that generalist models performed better than clinical models, suggesting that existing clinical specialized models are more sensitive to small changes in input that confuse them. The highlighted problem of specialized models may be due to the fact that they have not been trained on sufficient data, and in particular on datasets that are not diverse enough to have a reliable global language understanding, which is still necessary for accurate handling of medical documents.

Often we wish to predict a large number of variables that depend on each other as well as on other observed variables. Structured prediction methods are essentially a combination of classification and graphical modeling, combining the ability of graphical models to compactly model multivariate data with the ability of classification methods to perform prediction using large sets of input features. This tutorial describes conditional random fields, a popular probabilistic method for structured prediction. CRFs have seen wide application in natural language processing, computer vision, and bioinformatics. We describe methods for inference and parameter estimation for CRFs, including practical issues for implementing large scale CRFs. We do not assume previous knowledge of graphical modeling, so this tutorial is intended to be useful to practitioners in a wide variety of fields.

We present a comprehensive computational study of the under-investigated phenomenon of personal name compounds (PNCs) in German such as Willkommens-Merkel ('Welcome-Merkel'). Prevalent in news, social media, and political discourse, PNCs are hypothesized to exhibit an evaluative function that is reflected in a more positive or negative perception as compared to the respective personal full name (such as Angela Merkel). We model 321 PNCs and their corresponding full names at discourse level, and show that PNCs bear an evaluative nature that can be captured through a variety of computational methods. Specifically, we assess through valence information whether a PNC is more positively or negatively evaluative than the person's name, by applying and comparing two approaches using (i) valence norms and (ii) pretrained language models (PLMs). We further enrich our data with personal, domain-specific, and extra-linguistic information and perform a range of regression analyses revealing that factors including compound and modifier valence, domain, and political party membership influence how a PNC is evaluated.

Projecting visual features into word embedding space has become a significant fusion strategy adopted by Multimodal Large Language Models (MLLMs). However, its internal mechanisms have yet to be explored. Inspired by multilingual research, we identify domain-specific neurons in multimodal large language models. Specifically, we investigate the distribution of domain-specific neurons and the mechanism of how MLLMs process features from diverse domains. Furthermore, we propose a three-stage framework for language model modules in MLLMs when handling projected image features, and verify this hypothesis using logit lens. Extensive experiments indicate that while current MLLMs exhibit Visual Question Answering (VQA) capability, they may not fully utilize domain-specific information. Manipulating domain-specific neurons properly will result in a 10\% change of accuracy at most, shedding light on the development of cross-domain, all-encompassing MLLMs in the future. Our code will be released upon paper notification.

Language models that are sensitive to external context can more effectively capture the speaking patterns of individuals with specific characteristics or in particular environments. However, obtaining and leveraging such annotations can be challenging. In this work, we show how to leverage rich character and film annotations to personalise language models in a scalable manner. Our best model can reduce perplexity by up to 6.5% compared to a parameter-matched language model. Our approach performs on par with speaker-specific fine-tuning when the fine-tuning data (i.e. past dialogue) for individual speakers is available. On top of that, it also generalises well to a scenario with no such data, relying on combinations of demographic characteristics expressed via metadata. Our findings are consistent across two corpora, one of which is also a contribution of this paper: Cornell-rich contains rich manual annotations for 863 speaking characters from the Cornell Movie Dialog Corpus, including features such as characteristic quotes and character descriptions, along with six automatically extracted metadata features for over 95% of the featured films. Finally, we also present a cost-benefit analysis highlighting which annotations are most cost-effective in reducing perplexity.

Research at the intersection of personality psychology, computer science, and linguistics has recently focused increasingly on modeling and predicting personality from language use. We report two major improvements in predicting personality traits from text data: (1) to our knowledge, the most comprehensive set of theory-based psycholinguistic features and (2) hybrid models that integrate a pre-trained Transformer Language Model BERT and Bidirectional Long Short-Term Memory (BLSTM) networks trained on within-text distributions ('text contours') of psycholinguistic features. We experiment with BLSTM models (with and without Attention) and with two techniques for applying pre-trained language representations from the transformer model - 'feature-based' and 'fine-tuning'. We evaluate the performance of the models we built on two benchmark datasets that target the two dominant theoretical models of personality: the Big Five Essay dataset and the MBTI Kaggle dataset. Our results are encouraging as our models outperform existing work on the same datasets. More specifically, our models achieve improvement in classification accuracy by 2.9% on the Essay dataset and 8.28% on the Kaggle MBTI dataset. In addition, we perform ablation experiments to quantify the impact of different categories of psycholinguistic features in the respective personality prediction models.

Length extrapolation algorithms based on Rotary position embedding (RoPE) have shown promising results in extending the context length of language models. However, understanding how position embedding can capture longer-range contextual information remains elusive. Based on the intuition that different dimensions correspond to different frequency of changes in RoPE encoding, we conducted a dimension-level analysis to investigate the correlation between a hidden dimension of an attention head and its contribution to capturing long-distance dependencies. Using our correlation metric, we identified a particular type of attention heads, which we named Positional Heads, from various length-extrapolated models. These heads exhibit a strong focus on long-range information interaction and play a pivotal role in long input processing, as evidence by our ablation. We further demonstrate the correlation between the efficiency of length extrapolation and the extension of the high-dimensional attention allocation of these heads. The identification of Positional Heads provides insights for future research in long-text comprehension.

Language models have recently been shown capable of performing regression tasks wherein numeric predictions are represented as decoded strings. In this work, we provide theoretical grounds for this capability and furthermore investigate the utility of causal auto-regressive sequence models when they are applied to any feature representation. We find that, despite being trained in the usual way - for next-token prediction via cross-entropy loss - decoding-based regression is as performant as traditional approaches for tabular regression tasks, while being flexible enough to capture arbitrary distributions, such as in the task of density estimation.

Happiness computing based on large-scale online web data and machine learning methods is an emerging research topic that underpins a range of issues, from personal growth to social stability. Many advanced Machine Learning (ML) models with explanations are used to compute the happiness online assessment while maintaining high accuracy of results. However, domain knowledge constraints, such as the primary and secondary relations of happiness factors, are absent from these models, which limits the association between computing results and the right reasons for why they occurred. This article attempts to provide new insights into the explanation consistency from an empirical study perspective. Then we study how to represent and introduce domain knowledge constraints to make ML models more trustworthy. We achieve this through: (1) proving that multiple prediction models with additive factor attributions will have the desirable property of primary and secondary relations consistency, and (2) showing that factor relations with quantity can be represented as an importance distribution for encoding domain knowledge. Factor explanation difference is penalized by the Kullback-Leibler divergence-based loss among computing models. Experimental results using two online web datasets show that domain knowledge of stable factor relations exists. Using this knowledge not only improves happiness computing accuracy but also reveals more significative happiness factors for assisting decisions well.

Current approaches to empathetic response generation view the set of emotions expressed in the input text as a flat structure, where all the emotions are treated uniformly. We argue that empathetic responses often mimic the emotion of the user to a varying degree, depending on its positivity or negativity and content. We show that the consideration of this polarity-based emotion clusters and emotional mimicry results in improved empathy and contextual relevance of the response as compared to the state-of-the-art. Also, we introduce stochasticity into the emotion mixture that yields emotionally more varied empathetic responses than the previous work. We demonstrate the importance of these factors to empathetic response generation using both automatic- and human-based evaluations. The implementation of MIME is publicly available at https://github.com/declare-lab/MIME.

Large Language Models (LLMs) have demonstrated remarkable proficiency in understanding and generating natural language. However, their capabilities wane in highly specialized domains underrepresented in the pretraining corpus, such as physical and biomedical sciences. This work explores how to repurpose general LLMs into effective task solvers for specialized domains. We introduce a novel, model-agnostic framework for learning custom input tags, which are parameterized as continuous vectors appended to the LLM's embedding layer, to condition the LLM. We design two types of input tags: domain tags are used to delimit specialized representations (e.g., chemical formulas) and provide domain-relevant context; function tags are used to represent specific functions (e.g., predicting molecular properties) and compress function-solving instructions. We develop a three-stage protocol to learn these tags using auxiliary data and domain knowledge. By explicitly disentangling task domains from task functions, our method enables zero-shot generalization to unseen problems through diverse combinations of the input tags. It also boosts LLM's performance in various specialized domains, such as predicting protein or chemical properties and modeling drug-target interactions, outperforming expert models tailored to these tasks.

Despite the greater functional importance of protein levels, our knowledge of gene expression evolution is based almost entirely on studies of mRNA levels. In contrast, our understanding of how translational regulation evolves has lagged far behind. Here we have applied ribosome profiling - which measures both global mRNA levels and their translation rates - to two species of Saccharomyces yeast and their interspecific hybrid in order to assess the relative contributions of changes in mRNA abundance and translation to regulatory evolution. We report that both cis and trans-acting regulatory divergence in translation are abundant, affecting at least 35% of genes. The majority of translational divergence acts to buffer changes in mRNA abundance, suggesting a widespread role for stabilizing selection acting across regulatory levels. Nevertheless, we observe evidence of lineage-specific selection acting on a number of yeast functional modules, including instances of reinforcing selection acting at both levels of regulation. Finally, we also uncover multiple instances of stop-codon readthrough that are conserved between species. Our analysis reveals the under-appreciated complexity of post-transcriptional regulatory divergence and indicates that partitioning the search for the locus of selection into the binary categories of 'coding' vs. 'regulatory' may overlook a significant source of selection, acting at multiple regulatory levels along the path from genotype to phenotype.

To effectively optimize and personalize treatments, it is necessary to investigate the heterogeneity of treatment effects. With the wide range of users being treated over many online controlled experiments, the typical approach of manually investigating each dimension of heterogeneity becomes overly cumbersome and prone to subjective human biases. We need an efficient way to search through thousands of experiments with hundreds of target covariates and hundreds of breakdown dimensions. In this paper, we propose a systematic paradigm for detecting, surfacing and characterizing heterogeneous treatment effects. First, we detect if treatment effect variation is present in an experiment, prior to specifying any breakdowns. Second, we surface the most relevant dimensions for heterogeneity. Finally, we characterize the heterogeneity beyond just the conditional average treatment effects (CATE) by studying the conditional distributions of the estimated individual treatment effects. We show the effectiveness of our methods using simulated data and empirical studies.

Extracting causal relationships from observed correlations is a growing area in probabilistic reasoning, originating with the seminal work of Pearl and others from the early 1990s. This paper develops a new, categorically oriented view based on a clear distinction between syntax (string diagrams) and semantics (stochastic matrices), connected via interpretations as structure-preserving functors. A key notion in the identification of causal effects is that of an intervention, whereby a variable is forcefully set to a particular value independent of any prior propensities. We represent the effect of such an intervention as an endofunctor which performs `string diagram surgery' within the syntactic category of string diagrams. This diagram surgery in turn yields a new, interventional distribution via the interpretation functor. While in general there is no way to compute interventional distributions purely from observed data, we show that this is possible in certain special cases using a calculational tool called comb disintegration. We demonstrate the use of this technique on a well-known toy example, where we predict the causal effect of smoking on cancer in the presence of a confounding common cause. After developing this specific example, we show this technique provides simple sufficient conditions for computing interventions which apply to a wide variety of situations considered in the causal inference literature.

Being able to provide explanations for a model's decision has become a central requirement for the development, deployment, and adoption of machine learning models. However, we are yet to understand what explanation methods can and cannot do. How do upstream factors such as data, model prediction, hyperparameters, and random initialization influence downstream explanations? While previous work raised concerns that explanations (E) may have little relationship with the prediction (Y), there is a lack of conclusive study to quantify this relationship. Our work borrows tools from causal inference to systematically assay this relationship. More specifically, we study the relationship between E and Y by measuring the treatment effect when intervening on their causal ancestors, i.e., on hyperparameters and inputs used to generate saliency-based Es or Ys. Our results suggest that the relationships between E and Y is far from ideal. In fact, the gap between 'ideal' case only increase in higher-performing models -- models that are likely to be deployed. Our work is a promising first step towards providing a quantitative measure of the relationship between E and Y, which could also inform the future development of methods for E with a quantitative metric.

We present an open-source benchmark and evaluation framework for assessing emotional boundary handling in Large Language Models (LLMs). Using a dataset of 1156 prompts across six languages, we evaluated three leading LLMs (GPT-4o, Claude-3.5 Sonnet, and Mistral-large) on their ability to maintain appropriate emotional boundaries through pattern-matched response analysis. Our framework quantifies responses across seven key patterns: direct refusal, apology, explanation, deflection, acknowledgment, boundary setting, and emotional awareness. Results demonstrate significant variation in boundary-handling approaches, with Claude-3.5 achieving the highest overall score (8.69/10) and producing longer, more nuanced responses (86.51 words on average). We identified a substantial performance gap between English (average score 25.62) and non-English interactions (< 0.22), with English responses showing markedly higher refusal rates (43.20% vs. < 1% for non-English). Pattern analysis revealed model-specific strategies, such as Mistral's preference for deflection (4.2%) and consistently low empathy scores across all models (< 0.06). Limitations include potential oversimplification through pattern matching, lack of contextual understanding in response analysis, and binary classification of complex emotional responses. Future work should explore more nuanced scoring methods, expand language coverage, and investigate cultural variations in emotional boundary expectations. Our benchmark and methodology provide a foundation for systematic evaluation of LLM emotional intelligence and boundary-setting capabilities.

The success of pre-trained contextualized representations has prompted researchers to analyze them for the presence of linguistic information. Indeed, it is natural to assume that these pre-trained representations do encode some level of linguistic knowledge as they have brought about large empirical improvements on a wide variety of NLP tasks, which suggests they are learning true linguistic generalization. In this work, we focus on intrinsic probing, an analysis technique where the goal is not only to identify whether a representation encodes a linguistic attribute but also to pinpoint where this attribute is encoded. We propose a novel latent-variable formulation for constructing intrinsic probes and derive a tractable variational approximation to the log-likelihood. Our results show that our model is versatile and yields tighter mutual information estimates than two intrinsic probes previously proposed in the literature. Finally, we find empirical evidence that pre-trained representations develop a cross-lingually entangled notion of morphosyntax.

Automated interpretability pipelines generate natural language descriptions for the concepts represented by features in large language models (LLMs), such as plants or the first word in a sentence. These descriptions are derived using inputs that activate the feature, which may be a dimension or a direction in the model's representation space. However, identifying activating inputs is costly, and the mechanistic role of a feature in model behavior is determined both by how inputs cause a feature to activate and by how feature activation affects outputs. Using steering evaluations, we reveal that current pipelines provide descriptions that fail to capture the causal effect of the feature on outputs. To fix this, we propose efficient, output-centric methods for automatically generating feature descriptions. These methods use the tokens weighted higher after feature stimulation or the highest weight tokens after applying the vocabulary "unembedding" head directly to the feature. Our output-centric descriptions better capture the causal effect of a feature on model outputs than input-centric descriptions, but combining the two leads to the best performance on both input and output evaluations. Lastly, we show that output-centric descriptions can be used to find inputs that activate features previously thought to be "dead".

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

Emotion regulation is a crucial element in dealing with emotional events and has positive effects on mental health. This paper aims to provide a more comprehensive understanding of emotional events by introducing a new French corpus of emotional narratives collected using a questionnaire for emotion regulation. We follow the theoretical framework of the Component Process Model which considers emotions as dynamic processes composed of four interrelated components (behavior, feeling, thinking and territory). Each narrative is related to a discrete emotion and is structured based on all emotion components by the writers. We study the interaction of components and their impact on emotion classification with machine learning methods and pre-trained language models. Our results show that each component improves prediction performance, and that the best results are achieved by jointly considering all components. Our results also show the effectiveness of pre-trained language models in predicting discrete emotion from certain components, which reveal differences in how emotion components are expressed.

Productive interactions between diverse users and language technologies require outputs from the latter to be culturally relevant and sensitive. Prior works have evaluated models' knowledge of cultural norms, values, and artifacts, without considering how this knowledge manifests in downstream applications. In this work, we focus on extrinsic evaluation of cultural competence in two text generation tasks, open-ended question answering and story generation. We quantitatively and qualitatively evaluate model outputs when an explicit cue of culture, specifically nationality, is perturbed in the prompts. Although we find that model outputs do vary when varying nationalities and feature culturally relevant words, we also find weak correlations between text similarity of outputs for different countries and the cultural values of these countries. Finally, we discuss important considerations in designing comprehensive evaluation of cultural competence in user-facing tasks.

Combination therapies have become the standard of care for diseases such as cancer, tuberculosis, malaria and HIV. However, the combinatorial set of available multi-drug treatments creates a challenge in identifying effective combination therapies available in a situation. To assist medical professionals in identifying beneficial drug-combinations, we construct an expert-annotated dataset for extracting information about the efficacy of drug combinations from the scientific literature. Beyond its practical utility, the dataset also presents a unique NLP challenge, as the first relation extraction dataset consisting of variable-length relations. Furthermore, the relations in this dataset predominantly require language understanding beyond the sentence level, adding to the challenge of this task. We provide a promising baseline model and identify clear areas for further improvement. We release our dataset, code, and baseline models publicly to encourage the NLP community to participate in this task.

In this paper, we delineate the strategy employed by our team, DeepLearningBrasil, which secured us the first place in the shared task DepSign-LT-EDI@RANLP-2023, achieving a 47.0% Macro F1-Score and a notable 2.4% advantage. The task was to classify social media texts into three distinct levels of depression - "not depressed," "moderately depressed," and "severely depressed." Leveraging the power of the RoBERTa and DeBERTa models, we further pre-trained them on a collected Reddit dataset, specifically curated from mental health-related Reddit's communities (Subreddits), leading to an enhanced understanding of nuanced mental health discourse. To address lengthy textual data, we used truncation techniques that retained the essence of the content by focusing on its beginnings and endings. Our model was robust against unbalanced data by incorporating sample weights into the loss. Cross-validation and ensemble techniques were then employed to combine our k-fold trained models, delivering an optimal solution. The accompanying code is made available for transparency and further development.

Recently, multi-aspect controllable text generation that controls the generated text in multiple aspects (e.g., sentiment, topic, and keywords) has attracted increasing attention. Although methods based on parameter efficient tuning like prefix-tuning could achieve multi-aspect controlling in a plug-and-play way, the mutual interference of multiple prefixes leads to significant degeneration of constraints and limits their extensibility to training-time unseen aspect combinations. In this work, we provide a theoretical lower bound for the interference and empirically found that the interference grows with the number of layers where prefixes are inserted. Based on these analyses, we propose using trainable gates to normalize the intervention of prefixes to restrain the growing interference. As a result, controlling training-time unseen combinations of aspects can be realized by simply concatenating corresponding plugins such that new constraints can be extended at a lower cost. In addition, we propose a unified way to process both categorical and free-form constraints. Experiments on text generation and machine translation demonstrate the superiority of our approach over baselines on constraint accuracy, text quality, and extensibility.

Multi-aspect controllable text generation is a more challenging and practical task than single-aspect control. Existing methods achieve complex multi-aspect control by fusing multiple controllers learned from single-aspect, but suffer from attribute degeneration caused by the mutual interference of these controllers. To address this, we provide observations on attribute fusion from a distributional perspective and propose to directly search for the intersection areas of multiple attribute distributions as their combination for generation. Our method first estimates the attribute space with an autoencoder structure. Afterward, we iteratively approach the intersections by jointly minimizing distances to points representing different attributes. Finally, we map them to attribute-relevant sentences with a prefix-tuning-based decoder. Experiments on the three-aspect control task, including sentiment, topic, and detoxification aspects, reveal that our method outperforms several strong baselines on attribute relevance and text quality and achieves the SOTA. Further analysis also supplies some explanatory support for the effectiveness of our approach.

Temporal Point Processes (TPP) are probabilistic generative frameworks. They model discrete event sequences localized in continuous time. Generally, real-life events reveal descriptive information, known as marks. Marked TPPs model time and marks of the event together for practical relevance. Conditioned on past events, marked TPPs aim to learn the joint distribution of the time and the mark of the next event. For simplicity, conditionally independent TPP models assume time and marks are independent given event history. They factorize the conditional joint distribution of time and mark into the product of individual conditional distributions. This structural limitation in the design of TPP models hurt the predictive performance on entangled time and mark interactions. In this work, we model the conditional inter-dependence of time and mark to overcome the limitations of conditionally independent models. We construct a multivariate TPP conditioning the time distribution on the current event mark in addition to past events. Besides the conventional intensity-based models for conditional joint distribution, we also draw on flexible intensity-free TPP models from the literature. The proposed TPP models outperform conditionally independent and dependent models in standard prediction tasks. Our experimentation on various datasets with multiple evaluation metrics highlights the merit of the proposed approach.

Referring Expression Segmentation (RES) is a widely explored multi-modal task, which endeavors to segment the pre-existing object within a single image with a given linguistic expression. However, in broader real-world scenarios, it is not always possible to determine if the described object exists in a specific image. Typically, we have a collection of images, some of which may contain the described objects. The current RES setting curbs its practicality in such situations. To overcome this limitation, we propose a more realistic and general setting, named Group-wise Referring Expression Segmentation (GRES), which expands RES to a collection of related images, allowing the described objects to be present in a subset of input images. To support this new setting, we introduce an elaborately compiled dataset named Grouped Referring Dataset (GRD), containing complete group-wise annotations of target objects described by given expressions. We also present a baseline method named Grouped Referring Segmenter (GRSer), which explicitly captures the language-vision and intra-group vision-vision interactions to achieve state-of-the-art results on the proposed GRES and related tasks, such as Co-Salient Object Detection and RES. Our dataset and codes will be publicly released in https://github.com/yixuan730/group-res.

State-of-the-art language models (LMs) are notoriously susceptible to generating hallucinated information. Such inaccurate outputs not only undermine the reliability of these models but also limit their use and raise serious concerns about misinformation and propaganda. In this work, we focus on hallucinated book and article references and present them as the "model organism" of language model hallucination research, due to their frequent and easy-to-discern nature. We posit that if a language model cites a particular reference in its output, then it should ideally possess sufficient information about its authors and content, among other relevant details. Using this basic insight, we illustrate that one can identify hallucinated references without ever consulting any external resources, by asking a set of direct or indirect queries to the language model about the references. These queries can be considered as "consistency checks." Our findings highlight that while LMs, including GPT-4, often produce inconsistent author lists for hallucinated references, they also often accurately recall the authors of real references. In this sense, the LM can be said to "know" when it is hallucinating references. Furthermore, these findings show how hallucinated references can be dissected to shed light on their nature. Replication code and results can be found at https://github.com/microsoft/hallucinated-references.

Linear structural equation models are multivariate statistical models encoded by mixed graphs. In particular, the set of covariance matrices for distributions belonging to a linear structural equation model for a fixed mixed graph G=(V, D,B) is parameterized by a rational function with parameters for each vertex and edge in G. This rational parametrization naturally allows for the study of these models from an algebraic and combinatorial point of view. Indeed, this point of view has led to a collection of results in the literature, mainly focusing on questions related to identifiability and determining relationships between covariances (i.e., finding polynomials in the Gaussian vanishing ideal). So far, a large proportion of these results has focused on the case when D, the directed part of the mixed graph G, is acyclic. This is due to the fact that in the acyclic case, the parametrization becomes polynomial and there is a description of the entries of the covariance matrices in terms of a finite sum. We move beyond the acyclic case and give a closed form expression for the entries of the covariance matrices in terms of the one-connections in a graph obtained from D through some small operations. This closed form expression then allows us to show that if G is simple, then the parametrization map is generically finite-to-one. Finally, having a closed form expression for the covariance matrices allows for the development of an algorithm for systematically exploring possible polynomials in the Gaussian vanishing ideal.

Movie screenplay summarization is challenging, as it requires an understanding of long input contexts and various elements unique to movies. Large language models have shown significant advancements in document summarization, but they often struggle with processing long input contexts. Furthermore, while television transcripts have received attention in recent studies, movie screenplay summarization remains underexplored. To stimulate research in this area, we present a new dataset, MovieSum, for abstractive summarization of movie screenplays. This dataset comprises 2200 movie screenplays accompanied by their Wikipedia plot summaries. We manually formatted the movie screenplays to represent their structural elements. Compared to existing datasets, MovieSum possesses several distinctive features: (1) It includes movie screenplays, which are longer than scripts of TV episodes. (2) It is twice the size of previous movie screenplay datasets. (3) It provides metadata with IMDb IDs to facilitate access to additional external knowledge. We also show the results of recently released large language models applied to summarization on our dataset to provide a detailed baseline.

Literature-Based Discovery (LBD) aims to discover new scientific knowledge by mining papers and generating hypotheses. Standard LBD is limited to predicting pairwise relations between discrete concepts (e.g., drug-disease links), and ignores critical contexts like experimental settings (e.g., a specific patient population where a drug is evaluated) and background motivations (e.g., to find drugs without specific side effects). We address these limitations with a novel formulation of contextualized-LBD (C-LBD): generating scientific hypotheses in natural language, while grounding them in a context that controls the hypothesis search space. We present a modeling framework using retrieval of ``inspirations'' from past scientific papers. Our evaluations reveal that GPT-4 tends to generate ideas with overall low technical depth and novelty, while our inspiration prompting approaches partially mitigate this issue. Our work represents a first step toward building language models that generate new ideas derived from scientific literature.

Over the past decade, machine learning has revolutionized computers' ability to analyze text through flexible computational models. Due to their structural similarity to written language, transformer-based architectures have also shown promise as tools to make sense of a range of multi-variate sequences from protein-structures, music, electronic health records to weather-forecasts. We can also represent human lives in a way that shares this structural similarity to language. From one perspective, lives are simply sequences of events: People are born, visit the pediatrician, start school, move to a new location, get married, and so on. Here, we exploit this similarity to adapt innovations from natural language processing to examine the evolution and predictability of human lives based on detailed event sequences. We do this by drawing on arguably the most comprehensive registry data in existence, available for an entire nation of more than six million individuals across decades. Our data include information about life-events related to health, education, occupation, income, address, and working hours, recorded with day-to-day resolution. We create embeddings of life-events in a single vector space showing that this embedding space is robust and highly structured. Our models allow us to predict diverse outcomes ranging from early mortality to personality nuances, outperforming state-of-the-art models by a wide margin. Using methods for interpreting deep learning models, we probe the algorithm to understand the factors that enable our predictions. Our framework allows researchers to identify new potential mechanisms that impact life outcomes and associated possibilities for personalized interventions.

With the rapid advances in high-throughput sequencing technologies, the focus of survival analysis has shifted from examining clinical indicators to incorporating genomic profiles with pathological images. However, existing methods either directly adopt a straightforward fusion of pathological features and genomic profiles for survival prediction, or take genomic profiles as guidance to integrate the features of pathological images. The former would overlook intrinsic cross-modal correlations. The latter would discard pathological information irrelevant to gene expression. To address these issues, we present a Cross-Modal Translation and Alignment (CMTA) framework to explore the intrinsic cross-modal correlations and transfer potential complementary information. Specifically, we construct two parallel encoder-decoder structures for multi-modal data to integrate intra-modal information and generate cross-modal representation. Taking the generated cross-modal representation to enhance and recalibrate intra-modal representation can significantly improve its discrimination for comprehensive survival analysis. To explore the intrinsic crossmodal correlations, we further design a cross-modal attention module as the information bridge between different modalities to perform cross-modal interactions and transfer complementary information. Our extensive experiments on five public TCGA datasets demonstrate that our proposed framework outperforms the state-of-the-art methods.

In this work, we address the problem of modifying textual attributes of sentences. Given an input sentence and a set of attribute labels, we attempt to generate sentences that are compatible with the conditioning information. To ensure that the model generates content compatible sentences, we introduce a reconstruction loss which interpolates between auto-encoding and back-translation loss components. We propose an adversarial loss to enforce generated samples to be attribute compatible and realistic. Through quantitative, qualitative and human evaluations we demonstrate that our model is capable of generating fluent sentences that better reflect the conditioning information compared to prior methods. We further demonstrate that the model is capable of simultaneously controlling multiple attributes.

The majority of available text summarization datasets include short-form source documents that lack long-range causal and temporal dependencies, and often contain strong layout and stylistic biases. While relevant, such datasets will offer limited challenges for future generations of text summarization systems. We address these issues by introducing BookSum, a collection of datasets for long-form narrative summarization. Our dataset covers source documents from the literature domain, such as novels, plays and stories, and includes highly abstractive, human written summaries on three levels of granularity of increasing difficulty: paragraph-, chapter-, and book-level. The domain and structure of our dataset poses a unique set of challenges for summarization systems, which include: processing very long documents, non-trivial causal and temporal dependencies, and rich discourse structures. To facilitate future work, we trained and evaluated multiple extractive and abstractive summarization models as baselines for our dataset.

Mental health research through data-driven methods has been hindered by a lack of standard typology and scarcity of adequate data. In this study, we leverage the clinical articulation of depression to build a typology for social media texts for detecting the severity of depression. It emulates the standard clinical assessment procedure Diagnostic and Statistical Manual of Mental Disorders (DSM-5) and Patient Health Questionnaire (PHQ-9) to encompass subtle indications of depressive disorders from tweets. Along with the typology, we present a new dataset of 40191 tweets labeled by expert annotators. Each tweet is labeled as 'non-depressed' or 'depressed'. Moreover, three severity levels are considered for 'depressed' tweets: (1) mild, (2) moderate, and (3) severe. An associated confidence score is provided with each label to validate the quality of annotation. We examine the quality of the dataset via representing summary statistics while setting strong baseline results using attention-based models like BERT and DistilBERT. Finally, we extensively address the limitations of the study to provide directions for further research.

Masked language models (MLM) do not explicitly define a distribution over language, i.e., they are not language models per se. However, recent work has implicitly treated them as such for the purposes of generation and scoring. This paper studies methods for deriving explicit joint distributions from MLMs, focusing on distributions over two tokens, which makes it possible to calculate exact distributional properties. We find that an approach based on identifying joints whose conditionals are closest to those of the MLM works well and outperforms existing Markov random field-based approaches. We further find that this derived model's conditionals can even occasionally outperform the original MLM's conditionals.

Interpretability or explainability is an emerging research field in NLP. From a user-centric point of view, the goal is to build models that provide proper justification for their decisions, similar to those of humans, by requiring the models to satisfy additional constraints. To this end, we introduce a new application on legal text where, contrary to mainstream literature targeting word-level rationales, we conceive rationales as selected paragraphs in multi-paragraph structured court cases. We also release a new dataset comprising European Court of Human Rights cases, including annotations for paragraph-level rationales. We use this dataset to study the effect of already proposed rationale constraints, i.e., sparsity, continuity, and comprehensiveness, formulated as regularizers. Our findings indicate that some of these constraints are not beneficial in paragraph-level rationale extraction, while others need re-formulation to better handle the multi-label nature of the task we consider. We also introduce a new constraint, singularity, which further improves the quality of rationales, even compared with noisy rationale supervision. Experimental results indicate that the newly introduced task is very challenging and there is a large scope for further research.

This paper investigates whether large language models (LLMs) utilize numerical attributes encoded in a low-dimensional subspace of the embedding space when answering logical comparison questions (e.g., Was Cristiano born before Messi?). We first identified these subspaces using partial least squares regression, which effectively encodes the numerical attributes associated with the entities in comparison prompts. Further, we demonstrate causality by intervening in these subspaces to manipulate hidden states, thereby altering the LLM's comparison outcomes. Experimental results show that our findings hold for different numerical attributes, indicating that LLMs utilize the linearly encoded information for numerical reasoning.

Length extrapolation has attracted considerable attention recently since it allows transformers to be tested on longer sequences than those used in training. Previous research has shown that this property can be attained by using carefully designed Relative Positional Encodings (RPEs). While these methods perform well on a variety of corpora, the conditions for length extrapolation have yet to be investigated. This paper attempts to determine what types of RPEs allow for length extrapolation through a thorough mathematical and empirical analysis. We discover that a transformer is certain to possess this property as long as the series that corresponds to the RPE's exponential converges. Two practices are derived from the conditions and examined in language modeling tasks on a variety of corpora. As a bonus from the conditions, we derive a new Theoretical Receptive Field (TRF) to measure the receptive field of RPEs without taking any training steps. Extensive experiments are conducted on the Wikitext-103, Books, Github, and WikiBook datasets to demonstrate the viability of our discovered conditions. We also compare TRF to Empirical Receptive Field (ERF) across different models, showing consistently matched trends on the aforementioned datasets. The code is available at https://github.com/OpenNLPLab/Rpe.

This article presents Individual Conditional Expectation (ICE) plots, a tool for visualizing the model estimated by any supervised learning algorithm. Classical partial dependence plots (PDPs) help visualize the average partial relationship between the predicted response and one or more features. In the presence of substantial interaction effects, the partial response relationship can be heterogeneous. Thus, an average curve, such as the PDP, can obfuscate the complexity of the modeled relationship. Accordingly, ICE plots refine the partial dependence plot by graphing the functional relationship between the predicted response and the feature for individual observations. Specifically, ICE plots highlight the variation in the fitted values across the range of a covariate, suggesting where and to what extent heterogeneities might exist. In addition to providing a plotting suite for exploratory analysis, we include a visual test for additive structure in the data generating model. Through simulated examples and real data sets, we demonstrate how ICE plots can shed light on estimated models in ways PDPs cannot. Procedures outlined are available in the R package ICEbox.

Developing therapeutics is a lengthy and expensive process that requires the satisfaction of many different criteria, and AI models capable of expediting the process would be invaluable. However, the majority of current AI approaches address only a narrowly defined set of tasks, often circumscribed within a particular domain. To bridge this gap, we introduce Tx-LLM, a generalist large language model (LLM) fine-tuned from PaLM-2 which encodes knowledge about diverse therapeutic modalities. Tx-LLM is trained using a collection of 709 datasets that target 66 tasks spanning various stages of the drug discovery pipeline. Using a single set of weights, Tx-LLM simultaneously processes a wide variety of chemical or biological entities(small molecules, proteins, nucleic acids, cell lines, diseases) interleaved with free-text, allowing it to predict a broad range of associated properties, achieving competitive with state-of-the-art (SOTA) performance on 43 out of 66 tasks and exceeding SOTA on 22. Among these, Tx-LLM is particularly powerful and exceeds best-in-class performance on average for tasks combining molecular SMILES representations with text such as cell line names or disease names, likely due to context learned during pretraining. We observe evidence of positive transfer between tasks with diverse drug types (e.g.,tasks involving small molecules and tasks involving proteins), and we study the impact of model size, domain finetuning, and prompting strategies on performance. We believe Tx-LLM represents an important step towards LLMs encoding biochemical knowledge and could have a future role as an end-to-end tool across the drug discovery development pipeline.

Within the field of causal inference, we consider the problem of estimating heterogeneous treatment effects from data. We propose and validate a novel approach for learning feature representations to aid the estimation of the conditional average treatment effect or CATE. Our method focuses on an intermediate layer in a neural network trained to predict the outcome from the features. In contrast to previous approaches that encourage the distribution of representations to be treatment-invariant, we leverage a genetic algorithm that optimizes over representations useful for predicting the outcome to select those less useful for predicting the treatment. This allows us to retain information within the features useful for predicting outcome even if that information may be related to treatment assignment. We validate our method on synthetic examples and illustrate its use on a real life dataset.

The capacity of empathy is crucial to the success of open-domain dialog systems. Due to its nature of multi-dimensionality, there are various factors that relate to empathy expression, such as communication mechanism, dialog act and emotion. However, existing methods for empathetic response generation usually either consider only one empathy factor or ignore the hierarchical relationships between different factors, leading to a weak ability of empathy modeling. In this paper, we propose a multi-factor hierarchical framework, CoMAE, for empathetic response generation, which models the above three key factors of empathy expression in a hierarchical way. We show experimentally that our CoMAE-based model can generate more empathetic responses than previous methods. We also highlight the importance of hierarchical modeling of different factors through both the empirical analysis on a real-life corpus and the extensive experiments. Our codes and used data are available at https://github.com/chujiezheng/CoMAE.

In recent years, with the rapid advancements in large language models (LLMs), achieving excellent empathetic response capabilities has become a crucial prerequisite. Consequently, managing and understanding empathetic datasets have gained increasing significance. However, empathetic data are typically human-labeled, leading to insufficient datasets and wasted human labor. In this work, we present Synth-Empathy, an LLM-based data generation and quality and diversity selection pipeline that automatically generates high-quality empathetic data while discarding low-quality data. With the data generated from a low empathetic model, we are able to further improve empathetic response performance and achieve state-of-the-art (SoTA) results across multiple benchmarks. Moreover, our model achieves SoTA performance on various human evaluation benchmarks, demonstrating its effectiveness and robustness in real-world applications. Furthermore, we show the trade-off between data quantity and quality, providing insights into empathetic data generation and selection.

Scholars studying organizations often work with multiple datasets lacking shared unique identifiers or covariates. In such situations, researchers may turn to approximate string matching methods to combine datasets. String matching, although useful, faces fundamental challenges. Even when two strings appear similar to humans, fuzzy matching often does not work because it fails to adapt to the informativeness of the character combinations presented. Worse, many entities have multiple names that are dissimilar (e.g., "Fannie Mae" and "Federal National Mortgage Association"), a case where string matching has little hope of succeeding. This paper introduces data from a prominent employment-related networking site (LinkedIn) as a tool to address these problems. We propose interconnected approaches to leveraging the massive amount of information from LinkedIn regarding organizational name-to-name links. The first approach builds a machine learning model for predicting matches from character strings, treating the trillions of user-contributed organizational name pairs as a training corpus: this approach constructs a string matching metric that explicitly maximizes match probabilities. A second approach identifies relationships between organization names using network representations of the LinkedIn data. A third approach combines the first and second. We document substantial improvements over fuzzy matching in applications, making all methods accessible in open-source software ("LinkOrgs").

Speech patterns have been identified as potential diagnostic markers for neuropsychiatric conditions. However, most studies only compare a single clinical group to healthy controls, whereas clinical practice often requires differentiating between multiple potential diagnoses (multiclass settings). To address this, we assembled a dataset of repeated recordings from 420 participants (67 with major depressive disorder, 106 with schizophrenia and 46 with autism, as well as matched controls), and tested the performance of a range of conventional machine learning models and advanced Transformer models on both binary and multiclass classification, based on voice and text features. While binary models performed comparably to previous research (F1 scores between 0.54-0.75 for autism spectrum disorder, ASD; 0.67-0.92 for major depressive disorder, MDD; and 0.71-0.83 for schizophrenia); when differentiating between multiple diagnostic groups performance decreased markedly (F1 scores between 0.35-0.44 for ASD, 0.57-0.75 for MDD, 0.15-0.66 for schizophrenia, and 0.38-0.52 macro F1). Combining voice and text-based models yielded increased performance, suggesting that they capture complementary diagnostic information. Our results indicate that models trained on binary classification may learn to rely on markers of generic differences between clinical and non-clinical populations, or markers of clinical features that overlap across conditions, rather than identifying markers specific to individual conditions. We provide recommendations for future research in the field, suggesting increased focus on developing larger transdiagnostic datasets that include more fine-grained clinical features, and that can support the development of models that better capture the complexity of neuropsychiatric conditions and naturalistic diagnostic assessment.

Social and behavioral determinants of health (SDOH) play a significant role in shaping health outcomes, and extracting these determinants from clinical notes is a first step to help healthcare providers systematically identify opportunities to provide appropriate care and address disparities. Progress on using NLP methods for this task has been hindered by the lack of high-quality publicly available labeled data, largely due to the privacy and regulatory constraints on the use of real patients' information. This paper introduces a new dataset, SDOH-NLI, that is based on publicly available notes and which we release publicly. We formulate SDOH extraction as a natural language inference (NLI) task, and provide binary textual entailment labels obtained from human raters for a cross product of a set of social history snippets as premises and SDOH factors as hypotheses. Our dataset differs from standard NLI benchmarks in that our premises and hypotheses are obtained independently. We evaluate both "off-the-shelf" entailment models as well as models fine-tuned on our data, and highlight the ways in which our dataset appears more challenging than commonly used NLI datasets.

Controlled text perturbation is useful for evaluating and improving model generalizability. However, current techniques rely on training a model for every target perturbation, which is expensive and hard to generalize. We present Tailor, a semantically-controlled text generation system. Tailor builds on a pretrained seq2seq model and produces textual outputs conditioned on control codes derived from semantic representations. We craft a set of operations to modify the control codes, which in turn steer generation towards targeted attributes. These operations can be further composed into higher-level ones, allowing for flexible perturbation strategies. We demonstrate the effectiveness of these perturbations in multiple applications. First, we use Tailor to automatically create high-quality contrast sets for four distinct natural language processing (NLP) tasks. These contrast sets contain fewer spurious artifacts and are complementary to manually annotated ones in their lexical diversity. Second, we show that Tailor perturbations can improve model generalization through data augmentation. Perturbing just 2% of training data leads to a 5.8-point gain on an NLI challenge set measuring reliance on syntactic heuristics.

Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery. However, current models exhibit several limitations, such as the generation of invalid molecular SMILES, underutilization of contextual information, and equal treatment of structured and unstructured knowledge. To address these issues, we propose BioT5, a comprehensive pre-training framework that enriches cross-modal integration in biology with chemical knowledge and natural language associations. BioT5 utilizes SELFIES for 100% robust molecular representations and extracts knowledge from the surrounding context of bio-entities in unstructured biological literature. Furthermore, BioT5 distinguishes between structured and unstructured knowledge, leading to more effective utilization of information. After fine-tuning, BioT5 shows superior performance across a wide range of tasks, demonstrating its strong capability of capturing underlying relations and properties of bio-entities. Our code is available at https://github.com/QizhiPei/BioT5{Github}.

We introduce Latent Meaning Cells, a deep latent variable model which learns contextualized representations of words by combining local lexical context and metadata. Metadata can refer to granular context, such as section type, or to more global context, such as unique document ids. Reliance on metadata for contextualized representation learning is apropos in the clinical domain where text is semi-structured and expresses high variation in topics. We evaluate the LMC model on the task of zero-shot clinical acronym expansion across three datasets. The LMC significantly outperforms a diverse set of baselines at a fraction of the pre-training cost and learns clinically coherent representations. We demonstrate that not only is metadata itself very helpful for the task, but that the LMC inference algorithm provides an additional large benefit.

We utilize a recently developed topic modeling method called SeNMFk, extending the standard Non-negative Matrix Factorization (NMF) methods by incorporating the semantic structure of the text, and adding a robust system for determining the number of topics. With SeNMFk, we were able to extract coherent topics validated by human experts. From these topics, a few are relatively general and cover broad concepts, while the majority can be precisely mapped to specific scientific effects or measurement techniques. The topics also differ by ubiquity, with only three topics prevalent in almost 40 percent of the abstract, while each specific topic tends to dominate a small subset of the abstracts. These results demonstrate the ability of SeNMFk to produce a layered and nuanced analysis of large scientific corpora.

Language models (LMs) are increasingly used as simulacra for people, yet their ability to match the distribution of views of a specific demographic group and be distributionally aligned remains uncertain. This notion of distributional alignment is complex, as there is significant variation in the types of attributes that are simulated. Prior works have underexplored the role of three critical variables -- the question domain, steering method, and distribution expression method -- which motivates our contribution of a benchmark explicitly addressing these dimensions. We construct a dataset expanding beyond political values, create human baselines for this task, and evaluate the extent to which an LM can align with a particular group's opinion distribution to inform design choices of such simulation systems. Our analysis reveals open problems regarding if, and how, LMs can be used to simulate humans, and that LLMs can more accurately describe the opinion distribution than simulate such distributions.

Controllable text generation is a fundamental aspect of natural language generation, with numerous methods proposed for different constraint types. However, these approaches often require significant architectural or decoding modifications, making them challenging to apply to additional constraints or resolve different constraint combinations. To address this, our paper introduces Regular Expression Instruction (REI), which utilizes an instruction-based mechanism to fully exploit regular expressions' advantages to uniformly model diverse constraints. Specifically, our REI supports all popular fine-grained controllable generation constraints, i.e., lexical, positional, and length, as well as their complex combinations, via regular expression-style instructions. Our method only requires fine-tuning on medium-scale language models or few-shot, in-context learning on large language models, and requires no further adjustment when applied to various constraint combinations. Experiments demonstrate that our straightforward approach yields high success rates and adaptability to various constraints while maintaining competitiveness in automatic metrics and outperforming most previous baselines.

How do transformer-based large language models (LLMs) store and retrieve knowledge? We focus on the most basic form of this task -- factual recall, where the model is tasked with explicitly surfacing stored facts in prompts of form `Fact: The Colosseum is in the country of'. We find that the mechanistic story behind factual recall is more complex than previously thought. It comprises several distinct, independent, and qualitatively different mechanisms that additively combine, constructively interfering on the correct attribute. We term this generic phenomena the additive motif: models compute through summing up multiple independent contributions. Each mechanism's contribution may be insufficient alone, but summing results in constructive interfere on the correct answer. In addition, we extend the method of direct logit attribution to attribute an attention head's output to individual source tokens. We use this technique to unpack what we call `mixed heads' -- which are themselves a pair of two separate additive updates from different source tokens.

This paper presents the system description of our entry for the COLING 2025 RegNLP RIRAG (Regulatory Information Retrieval and Answer Generation) challenge, focusing on leveraging advanced information retrieval and answer generation techniques in regulatory domains. We experimented with a combination of embedding models, including Stella, BGE, CDE, and Mpnet, and leveraged fine-tuning and reranking for retrieving relevant documents in top ranks. We utilized a novel approach, LeSeR, which achieved competitive results with a recall@10 of 0.8201 and map@10 of 0.6655 for retrievals. This work highlights the transformative potential of natural language processing techniques in regulatory applications, offering insights into their capabilities for implementing a retrieval augmented generation system while identifying areas for future improvement in robustness and domain adaptation.

Researchers are usually interested in examining the impact of covariates when separating heterogeneous samples into latent classes that are more homogeneous. The majority of theoretical and empirical studies with such aims have focused on identifying covariates as predictors of class membership in the structural equation modeling framework. In other words, the covariates only indirectly affect the sample heterogeneity. However, the covariates' influence on between-individual differences can also be direct. This article presents a mixture model that investigates covariates to explain within-cluster and between-cluster heterogeneity simultaneously, known as a mixture-of-experts (MoE) model. This study aims to extend the MoE framework to investigate heterogeneity in nonlinear trajectories: to identify latent classes, covariates as predictors to clusters, and covariates that explain within-cluster differences in change patterns over time. Our simulation studies demonstrate that the proposed model generally estimates the parameters unbiasedly, precisely and exhibits appropriate empirical coverage for a nominal 95% confidence interval. This study also proposes implementing structural equation model forests to shrink the covariate space of the proposed mixture model. We illustrate how to select covariates and construct the proposed model with longitudinal mathematics achievement data. Additionally, we demonstrate that the proposed mixture model can be further extended in the structural equation modeling framework by allowing the covariates that have direct effects to be time-varying.

We study how multilingual sentence representations capture European countries and occupations and how this differs across European languages. We prompt the models with templated sentences that we machine-translate into 12 European languages and analyze the most prominent dimensions in the embeddings.Our analysis reveals that the most prominent feature in the embedding is the geopolitical distinction between Eastern and Western Europe and the country's economic strength in terms of GDP. When prompted specifically for job prestige, the embedding space clearly distinguishes high and low-prestige jobs. The occupational dimension is uncorrelated with the most dominant country dimensions in three out of four studied models. The exception is a small distilled model that exhibits a connection between occupational prestige and country of origin, which is a potential source of nationality-based discrimination. Our findings are consistent across languages.

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues and uncover underlying disease mechanisms. Among all the analytical steps, assigning individual cells to specific types is fundamental for understanding cellular heterogeneity. However, this process is usually labor-intensive and requires extensive expert knowledge. Recent advances in large language models (LLMs) have demonstrated their ability to efficiently process and synthesize vast corpora of text to automatically extract essential biological knowledge, such as marker genes, potentially promoting more efficient and automated cell type annotations. To thoroughly evaluate the capability of modern instruction-tuned LLMs in automating the cell type identification process, we introduce SOAR, a comprehensive benchmarking study of LLMs for cell type annotation tasks in single-cell genomics. Specifically, we assess the performance of 8 instruction-tuned LLMs across 11 datasets, spanning multiple cell types and species. Our study explores the potential of LLMs to accurately classify and annotate cell types in single-cell RNA sequencing (scRNA-seq) data, while extending their application to multiomics data through cross-modality translation. Additionally, we evaluate the effectiveness of chain-of-thought (CoT) prompting techniques in generating detailed biological insights during the annotation process. The results demonstrate that LLMs can provide robust interpretations of single-cell data without requiring additional fine-tuning, advancing the automation of cell type annotation in genomics research.

Figurative and non-literal expressions are profoundly integrated in human communication. Visualising such expressions allow us to convey our creative thoughts, and evoke nuanced emotions. Recent text-to-image models like Stable Diffusion, on the other hand, struggle to depict non-literal expressions. Recent works primarily deal with this issue by compiling humanly annotated datasets on a small scale, which not only demands specialised expertise but also proves highly inefficient. To address this issue, we introduce ViPE: Visualise Pretty-much Everything. ViPE offers a series of lightweight and robust language models that have been trained on a large-scale set of lyrics with noisy visual descriptions that represent their implicit meaning. The synthetic visual descriptions are generated by GPT3.5 relying on neither human annotations nor images. ViPE effectively expresses any arbitrary piece of text into a visualisable description, enabling meaningful and high-quality image generation. We provide compelling evidence that ViPE is more robust than GPT3.5 in synthesising visual elaborations. ViPE also exhibits an understanding of figurative expressions comparable to human experts, providing a powerful and open-source backbone to many downstream applications such as music video and caption generation.

In this report, we introduce SciFive, a domain-specific T5 model that has been pre-trained on large biomedical corpora. Our model outperforms the current SOTA methods (i.e. BERT, BioBERT, Base T5) on tasks in named entity relation, relation extraction, natural language inference, and question-answering. We show that text-generation methods have significant potential in a broad array of biomedical NLP tasks, particularly those requiring longer, more complex outputs. Our results support the exploration of more difficult text generation tasks and the development of new methods in this area

Human language expression is based on the subjective construal of the situation instead of the objective truth conditions, which means that speakers' personalities and emotions after cognitive processing have an important influence on conversation. However, most existing datasets for conversational AI ignore human personalities and emotions, or only consider part of them. It's difficult for dialogue systems to understand speakers' personalities and emotions although large-scale pre-training language models have been widely used. In order to consider both personalities and emotions in the process of conversation generation, we propose CPED, a large-scale Chinese personalized and emotional dialogue dataset, which consists of multi-source knowledge related to empathy and personal characteristic. These knowledge covers gender, Big Five personality traits, 13 emotions, 19 dialogue acts and 10 scenes. CPED contains more than 12K dialogues of 392 speakers from 40 TV shows. We release the textual dataset with audio features and video features according to the copyright claims, privacy issues, terms of service of video platforms. We provide detailed description of the CPED construction process and introduce three tasks for conversational AI, including personality recognition, emotion recognition in conversations as well as personalized and emotional conversation generation. Finally, we provide baseline systems for these tasks and consider the function of speakers' personalities and emotions on conversation. Our motivation is to propose a dataset to be widely adopted by the NLP community as a new open benchmark for conversational AI research. The full dataset is available at https://github.com/scutcyr/CPED.

Deception detection has garnered increasing attention in recent years due to the significant growth of digital media and heightened ethical and security concerns. It has been extensively studied using multimodal methods, including video, audio, and text. In addition, individual differences in deception production and detection are believed to play a crucial role.Although some studies have utilized individual information such as personality traits to enhance the performance of deception detection, current systems remain limited, partly due to a lack of sufficient datasets for evaluating performance. To address this issue, we introduce a multimodal deception dataset MDPE. Besides deception features, this dataset also includes individual differences information in personality and emotional expression characteristics. It can explore the impact of individual differences on deception behavior. It comprises over 104 hours of deception and emotional videos from 193 subjects. Furthermore, we conducted numerous experiments to provide valuable insights for future deception detection research. MDPE not only supports deception detection, but also provides conditions for tasks such as personality recognition and emotion recognition, and can even study the relationships between them. We believe that MDPE will become a valuable resource for promoting research in the field of affective computing.

Emotion Recognition in Conversation (ERC) has attracted growing attention in recent years as a result of the advancement and implementation of human-computer interface technologies. However, previous approaches to modeling global and local context dependencies lost the diversity of dependency information and do not take the context dependency into account at the classification level. In this paper, we propose a novel approach to dependency modeling driven by Emotional Inertia and Contagion (EmotionIC) for conversational emotion recognition at the feature extraction and classification levels. At the feature extraction level, our designed Identity Masked Multi-head Attention (IM-MHA) captures the identity-based long-distant context in the dialogue to contain the diverse influence of different participants and construct the global emotional atmosphere, while the devised Dialogue-based Gate Recurrent Unit (DialogGRU) that aggregates the emotional tendencies of dyadic dialogue is applied to refine the contextual features with inter- and intra-speaker dependencies. At the classification level, by introducing skip connections in Conditional Random Field (CRF), we elaborate the Skip-chain CRF (SkipCRF) to capture the high-order dependencies within and between speakers, and to emulate the emotional flow of distant participants. Experimental results show that our method can significantly outperform the state-of-the-art models on four benchmark datasets. The ablation studies confirm that our modules can effectively model emotional inertia and contagion.

We describe the accurate prediction of ligand-protein interaction (LPI) affinities, also known as drug-target interactions (DTI), with instruction fine-tuned pretrained generative small language models (SLMs). We achieved accurate predictions for a range of affinity values associated with ligand-protein interactions on out-of-sample data in a zero-shot setting. Only the SMILES string of the ligand and the amino acid sequence of the protein were used as the model inputs. Our results demonstrate a clear improvement over machine learning (ML) and free-energy perturbation (FEP+) based methods in accurately predicting a range of ligand-protein interaction affinities, which can be leveraged to further accelerate drug discovery campaigns against challenging therapeutic targets.

Medical imaging is critical to the diagnosis and treatment of numerous medical problems, including many forms of cancer. Medical imaging reports distill the findings and observations of radiologists, creating an unstructured textual representation of unstructured medical images. Large-scale use of this text-encoded information requires converting the unstructured text to a structured, semantic representation. We explore the extraction and normalization of anatomical information in radiology reports that is associated with radiological findings. We investigate this extraction and normalization task using a span-based relation extraction model that jointly extracts entities and relations using BERT. This work examines the factors that influence extraction and normalization performance, including the body part/organ system, frequency of occurrence, span length, and span diversity. It discusses approaches for improving performance and creating high-quality semantic representations of radiological phenomena.

The Russian Drug Reaction Corpus (RuDReC) is a new partially annotated corpus of consumer reviews in Russian about pharmaceutical products for the detection of health-related named entities and the effectiveness of pharmaceutical products. The corpus itself consists of two parts, the raw one and the labelled one. The raw part includes 1.4 million health-related user-generated texts collected from various Internet sources, including social media. The labelled part contains 500 consumer reviews about drug therapy with drug- and disease-related information. Labels for sentences include health-related issues or their absence. The sentences with one are additionally labelled at the expression level for identification of fine-grained subtypes such as drug classes and drug forms, drug indications, and drug reactions. Further, we present a baseline model for named entity recognition (NER) and multi-label sentence classification tasks on this corpus. The macro F1 score of 74.85% in the NER task was achieved by our RuDR-BERT model. For the sentence classification task, our model achieves the macro F1 score of 68.82% gaining 7.47% over the score of BERT model trained on Russian data. We make the RuDReC corpus and pretrained weights of domain-specific BERT models freely available at https://github.com/cimm-kzn/RuDReC

Learning neural subset selection tasks, such as compound selection in AI-aided drug discovery, have become increasingly pivotal across diverse applications. The existing methodologies in the field primarily concentrate on constructing models that capture the relationship between utility function values and subsets within their respective supersets. However, these approaches tend to overlook the valuable information contained within the superset when utilizing neural networks to model set functions. In this work, we address this oversight by adopting a probabilistic perspective. Our theoretical findings demonstrate that when the target value is conditioned on both the input set and subset, it is essential to incorporate an invariant sufficient statistic of the superset into the subset of interest for effective learning. This ensures that the output value remains invariant to permutations of the subset and its corresponding superset, enabling identification of the specific superset from which the subset originated. Motivated by these insights, we propose a simple yet effective information aggregation module designed to merge the representations of subsets and supersets from a permutation invariance perspective. Comprehensive empirical evaluations across diverse tasks and datasets validate the enhanced efficacy of our approach over conventional methods, underscoring the practicality and potency of our proposed strategies in real-world contexts.

Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurrent neural networks have been developed and successfully applied to a wide-range of tasks, (ii) in process mining process discovery techniques aim to generate human-interpretable descriptive models, and (iii) in the grammar inference field the focus is on finding descriptive models in the form of formal grammars. Despite their different focuses, these fields share a common goal - learning a model that accurately describes the behavior in the underlying data. Those sequence models are generative, i.e, they can predict what elements are likely to occur after a given unfinished sequence. So far, these fields have developed mainly in isolation from each other and no comparison exists. This paper presents an interdisciplinary experimental evaluation that compares sequence modeling techniques on the task of next-element prediction on four real-life sequence datasets. The results indicate that machine learning techniques that generally have no aim at interpretability in terms of accuracy outperform techniques from the process mining and grammar inference fields that aim to yield interpretable models.

Zero-shot text classification (0Shot-TC) is a challenging NLU problem to which little attention has been paid by the research community. 0Shot-TC aims to associate an appropriate label with a piece of text, irrespective of the text domain and the aspect (e.g., topic, emotion, event, etc.) described by the label. And there are only a few articles studying 0Shot-TC, all focusing only on topical categorization which, we argue, is just the tip of the iceberg in 0Shot-TC. In addition, the chaotic experiments in literature make no uniform comparison, which blurs the progress. This work benchmarks the 0Shot-TC problem by providing unified datasets, standardized evaluations, and state-of-the-art baselines. Our contributions include: i) The datasets we provide facilitate studying 0Shot-TC relative to conceptually different and diverse aspects: the ``topic'' aspect includes ``sports'' and ``politics'' as labels; the ``emotion'' aspect includes ``joy'' and ``anger''; the ``situation'' aspect includes ``medical assistance'' and ``water shortage''. ii) We extend the existing evaluation setup (label-partially-unseen) -- given a dataset, train on some labels, test on all labels -- to include a more challenging yet realistic evaluation label-fully-unseen 0Shot-TC (Chang et al., 2008), aiming at classifying text snippets without seeing task specific training data at all. iii) We unify the 0Shot-TC of diverse aspects within a textual entailment formulation and study it this way. Code & Data: https://github.com/yinwenpeng/BenchmarkingZeroShot

This paper shows how LLMs (Large Language Models) may be used to estimate a summary of the emotional state associated with piece of text. The summary of emotional state is a dictionary of words used to describe emotion together with the probability of the word appearing after a prompt comprising the original text and an emotion eliciting tail. Through emotion analysis of Amazon product reviews we demonstrate emotion descriptors can be mapped into a PCA type space. It was hoped that text descriptions of actions to improve a current text described state could also be elicited through a tail prompt. Experiment seemed to indicate that this is not straightforward to make work. This failure put our hoped for selection of action via choosing the best predict ed outcome via comparing emotional responses out of reach for the moment.

Event coreference resolution is an important research problem with many applications. Despite the recent remarkable success of pretrained language models, we argue that it is still highly beneficial to utilize symbolic features for the task. However, as the input for coreference resolution typically comes from upstream components in the information extraction pipeline, the automatically extracted symbolic features can be noisy and contain errors. Also, depending on the specific context, some features can be more informative than others. Motivated by these observations, we propose a novel context-dependent gated module to adaptively control the information flows from the input symbolic features. Combined with a simple noisy training method, our best models achieve state-of-the-art results on two datasets: ACE 2005 and KBP 2016.

Spatial transcriptomics (ST) enables interrogating the molecular composition of tissue with ever-increasing resolution, depth, and sensitivity. However, costs, rapidly evolving technology, and lack of standards have constrained computational methods in ST to narrow tasks and small cohorts. In addition, the underlying tissue morphology as reflected by H&E-stained whole slide images (WSIs) encodes rich information often overlooked in ST studies. Here, we introduce HEST-1k, a collection of 1,108 spatial transcriptomic profiles, each linked to a WSI and metadata. HEST-1k was assembled using HEST-Library from 131 public and internal cohorts encompassing 25 organs, two species (Homo Sapiens and Mus Musculus), and 320 cancer samples from 25 cancer types. HEST-1k processing enabled the identification of 1.5 million expression--morphology pairs and 60 million nuclei. HEST-1k is tested on three use cases: (1) benchmarking foundation models for histopathology (HEST-Benchmark), (2) biomarker identification, and (3) multimodal representation learning. HEST-1k, HEST-Library, and HEST-Benchmark can be freely accessed via https://github.com/mahmoodlab/hest.

Most of the recent works on probing representations have focused on BERT, with the presumption that the findings might be similar to the other models. In this work, we extend the probing studies to two other models in the family, namely ELECTRA and XLNet, showing that variations in the pre-training objectives or architectural choices can result in different behaviors in encoding linguistic information in the representations. Most notably, we observe that ELECTRA tends to encode linguistic knowledge in the deeper layers, whereas XLNet instead concentrates that in the earlier layers. Also, the former model undergoes a slight change during fine-tuning, whereas the latter experiences significant adjustments. Moreover, we show that drawing conclusions based on the weight mixing evaluation strategy -- which is widely used in the context of layer-wise probing -- can be misleading given the norm disparity of the representations across different layers. Instead, we adopt an alternative information-theoretic probing with minimum description length, which has recently been proven to provide more reliable and informative results.

Motivation: The gut microbiota has recently emerged as a key factor that underpins certain connections between diet and human health. A tremendous amount of knowledge has been amassed from experimental studies on diet, human metabolism and microbiome. However, this evidence remains mostly buried in scientific publications, and biomedical literature mining in this domain remains scarce. We developed DiMB-RE, a comprehensive corpus annotated with 15 entity types (e.g., Nutrient, Microorganism) and 13 relation types (e.g., increases, improves) capturing diet-microbiome associations. We also trained and evaluated state-of-the-art natural language processing (NLP) models for named entity, trigger, and relation extraction as well as factuality detection using DiMB-RE. Results: DiMB-RE consists of 14,450 entities and 4,206 relationships from 165 articles. While NLP models performed reasonably well for named entity recognition (0.760 F_{1}), end-to-end relation extraction performance was modest (0.356 F_{1}), partly due to missed entities and triggers as well as cross-sentence relations. Conclusions: To our knowledge, DiMB-RE is largest and most diverse dataset focusing on diet-microbiome interactions. It can serve as a benchmark corpus for biomedical literature mining. Availability: DiMB-RE and the NLP models are available at https://github.com/ScienceNLP-Lab/DiMB-RE.

Supervised learning datasets may contain multiple cues that explain the training set equally well, i.e., learning any of them would lead to the correct predictions on the training data. However, many of them can be spurious, i.e., lose their predictive power under a distribution shift and consequently fail to generalize to out-of-distribution (OOD) data. Recently developed "diversification" methods (Lee et al., 2023; Pagliardini et al., 2023) approach this problem by finding multiple diverse hypotheses that rely on different features. This paper aims to study this class of methods and identify the key components contributing to their OOD generalization abilities. We show that (1) diversification methods are highly sensitive to the distribution of the unlabeled data used for diversification and can underperform significantly when away from a method-specific sweet spot. (2) Diversification alone is insufficient for OOD generalization. The choice of the used learning algorithm, e.g., the model's architecture and pretraining, is crucial. In standard experiments (classification on Waterbirds and Office-Home datasets), using the second-best choice leads to an up to 20\% absolute drop in accuracy. (3) The optimal choice of learning algorithm depends on the unlabeled data and vice versa i.e. they are co-dependent. (4) Finally, we show that, in practice, the above pitfalls cannot be alleviated by increasing the number of diverse hypotheses, the major feature of diversification methods. These findings provide a clearer understanding of the critical design factors influencing the OOD generalization abilities of diversification methods. They can guide practitioners in how to use the existing methods best and guide researchers in developing new, better ones.

Today's probabilistic language generators fall short when it comes to producing coherent and fluent text despite the fact that the underlying models perform well under standard metrics, e.g., perplexity. This discrepancy has puzzled the language generation community for the last few years. In this work, we posit that the abstraction of natural language generation as a discrete stochastic process--which allows for an information-theoretic analysis--can provide new insights into the behavior of probabilistic language generators, e.g., why high-probability texts can be dull or repetitive. Humans use language as a means of communicating information, aiming to do so in a simultaneously efficient and error-minimizing manner; in fact, psycholinguistics research suggests humans choose each word in a string with this subconscious goal in mind. We formally define the set of strings that meet this criterion: those for which each word has an information content close to the expected information content, i.e., the conditional entropy of our model. We then propose a simple and efficient procedure for enforcing this criterion when generating from probabilistic models, which we call locally typical sampling. Automatic and human evaluations show that, in comparison to nucleus and top-k sampling, locally typical sampling offers competitive performance (in both abstractive summarization and story generation) in terms of quality while consistently reducing degenerate repetitions.

Technological advancements in web platforms allow people to express and share emotions towards textual write-ups written and shared by others. This brings about different interesting domains for analysis; emotion expressed by the writer and emotion elicited from the readers. In this paper, we propose a novel approach for Readers' Emotion Detection from short-text documents using a deep learning model called REDAffectiveLM. Within state-of-the-art NLP tasks, it is well understood that utilizing context-specific representations from transformer-based pre-trained language models helps achieve improved performance. Within this affective computing task, we explore how incorporating affective information can further enhance performance. Towards this, we leverage context-specific and affect enriched representations by using a transformer-based pre-trained language model in tandem with affect enriched Bi-LSTM+Attention. For empirical evaluation, we procure a new dataset REN-20k, besides using RENh-4k and SemEval-2007. We evaluate the performance of our REDAffectiveLM rigorously across these datasets, against a vast set of state-of-the-art baselines, where our model consistently outperforms baselines and obtains statistically significant results. Our results establish that utilizing affect enriched representation along with context-specific representation within a neural architecture can considerably enhance readers' emotion detection. Since the impact of affect enrichment specifically in readers' emotion detection isn't well explored, we conduct a detailed analysis over affect enriched Bi-LSTM+Attention using qualitative and quantitative model behavior evaluation techniques. We observe that compared to conventional semantic embedding, affect enriched embedding increases ability of the network to effectively identify and assign weightage to key terms responsible for readers' emotion detection.

Aspect-based Sentiment Analysis (ABSA) seeks to predict the sentiment polarity of a sentence toward a specific aspect. Recently, it has been shown that dependency trees can be integrated into deep learning models to produce the state-of-the-art performance for ABSA. However, these models tend to compute the hidden/representation vectors without considering the aspect terms and fail to benefit from the overall contextual importance scores of the words that can be obtained from the dependency tree for ABSA. In this work, we propose a novel graph-based deep learning model to overcome these two issues of the prior work on ABSA. In our model, gate vectors are generated from the representation vectors of the aspect terms to customize the hidden vectors of the graph-based models toward the aspect terms. In addition, we propose a mechanism to obtain the importance scores for each word in the sentences based on the dependency trees that are then injected into the model to improve the representation vectors for ABSA. The proposed model achieves the state-of-the-art performance on three benchmark datasets.

Children with Autism Spectrum Disorder (ASD) often exhibit atypical facial expressions. However, the specific objective facial features that underlie this subjective perception remain unclear. In this paper, we introduce a novel dataset, Hugging Rain Man (HRM), which includes facial action units (AUs) manually annotated by FACS experts for both children with ASD and typical development (TD). The dataset comprises a rich collection of posed and spontaneous facial expressions, totaling approximately 130,000 frames, along with 22 AUs, 10 Action Descriptors (ADs), and atypicality ratings. A statistical analysis of static images from the HRM reveals significant differences between the ASD and TD groups across multiple AUs and ADs when displaying the same emotional expressions, confirming that participants with ASD tend to demonstrate more irregular and diverse expression patterns. Subsequently, a temporal regression method was presented to analyze atypicality of dynamic sequences, thereby bridging the gap between subjective perception and objective facial characteristics. Furthermore, baseline results for AU detection are provided for future research reference. This work not only contributes to our understanding of the unique facial expression characteristics associated with ASD but also provides potential tools for ASD early screening. Portions of the dataset, features, and pretrained models are accessible at: https://github.com/Jonas-DL/Hugging-Rain-Man.

Text simplification aims at making a text easier to read and understand by simplifying grammar and structure while keeping the underlying information identical. It is often considered an all-purpose generic task where the same simplification is suitable for all; however multiple audiences can benefit from simplified text in different ways. We adapt a discrete parametrization mechanism that provides explicit control on simplification systems based on Sequence-to-Sequence models. As a result, users can condition the simplifications returned by a model on attributes such as length, amount of paraphrasing, lexical complexity and syntactic complexity. We also show that carefully chosen values of these attributes allow out-of-the-box Sequence-to-Sequence models to outperform their standard counterparts on simplification benchmarks. Our model, which we call ACCESS (as shorthand for AudienCe-CEntric Sentence Simplification), establishes the state of the art at 41.87 SARI on the WikiLarge test set, a +1.42 improvement over the best previously reported score.

To provide consistent emotional interaction with users, dialog systems should be capable to automatically select appropriate emotions for responses like humans. However, most existing works focus on rendering specified emotions in responses or empathetically respond to the emotion of users, yet the individual difference in emotion expression is overlooked. This may lead to inconsistent emotional expressions and disinterest users. To tackle this issue, we propose to equip the dialog system with personality and enable it to automatically select emotions in responses by simulating the emotion transition of humans in conversation. In detail, the emotion of the dialog system is transitioned from its preceding emotion in context. The transition is triggered by the preceding dialog context and affected by the specified personality trait. To achieve this, we first model the emotion transition in the dialog system as the variation between the preceding emotion and the response emotion in the Valence-Arousal-Dominance (VAD) emotion space. Then, we design neural networks to encode the preceding dialog context and the specified personality traits to compose the variation. Finally, the emotion for response is selected from the sum of the preceding emotion and the variation. We construct a dialog dataset with emotion and personality labels and conduct emotion prediction tasks for evaluation. Experimental results validate the effectiveness of the personality-affected emotion transition.

Multi-document summarization (MDS) is a difficult task in Natural Language Processing, aiming to summarize information from several documents. However, the source documents are often insufficient to obtain a qualitative summary. We propose a retriever-guided model combined with non-parametric memory for summary generation. This model retrieves relevant candidates from a database and then generates the summary considering the candidates with a copy mechanism and the source documents. The retriever is implemented with Approximate Nearest Neighbor Search (ANN) to search large databases. Our method is evaluated on the MultiXScience dataset which includes scientific articles. Finally, we discuss our results and possible directions for future work.

Idiomatic expressions have always been a bottleneck for language comprehension and natural language understanding, specifically for tasks like Machine Translation(MT). MT systems predominantly produce literal translations of idiomatic expressions as they do not exhibit generic and linguistically deterministic patterns which can be exploited for comprehension of the non-compositional meaning of the expressions. These expressions occur in parallel corpora used for training, but due to the comparatively high occurrences of the constituent words of idiomatic expressions in literal context, the idiomatic meaning gets overpowered by the compositional meaning of the expression. State of the art Metaphor Detection Systems are able to detect non-compositional usage at word level but miss out on idiosyncratic phrasal idiomatic expressions. This creates a dire need for a dataset with a wider coverage and higher occurrence of commonly occurring idiomatic expressions, the spans of which can be used for Metaphor Detection. With this in mind, we present our English Possible Idiomatic Expressions(EPIE) corpus containing 25206 sentences labelled with lexical instances of 717 idiomatic expressions. These spans also cover literal usages for the given set of idiomatic expressions. We also present the utility of our dataset by using it to train a sequence labelling module and testing on three independent datasets with high accuracy, precision and recall scores.

The growing capabilities of large language models (LLMs) have led to their use as substitutes for human feedback for training and assessing other LLMs. These methods often rely on `constitutions', written guidelines which a critic model uses to provide feedback and improve generations. We investigate how the choice of constitution affects feedback quality by using four different constitutions to improve patient-centered communication in medical interviews. In pairwise comparisons conducted by 215 human raters, we found that detailed constitutions led to better results regarding emotive qualities. However, none of the constitutions outperformed the baseline in learning more practically-oriented skills related to information gathering and provision. Our findings indicate that while detailed constitutions should be prioritised, there are possible limitations to the effectiveness of AI feedback as a reward signal in certain areas.

We have recently witnessed a number of impressive results on hard mathematical reasoning problems with language models. At the same time, the robustness of these models has also been called into question; recent works have shown that models can rely on shallow patterns in the problem description when generating a solution. Building on the idea of behavioral testing, we propose a novel framework, which pins down the causal effect of various factors in the input, e.g., the surface form of the problem text, the operands, and math operators on the output solution. By grounding the behavioral analysis in a causal graph describing an intuitive reasoning process, we study the behavior of language models in terms of robustness and sensitivity to direct interventions in the input space. We apply our framework on a test bed of math word problems. Our analysis shows that robustness does not appear to continuously improve as a function of size, but the GPT-3 Davinci models (175B) achieve a dramatic improvement in both robustness and sensitivity compared to all other GPT variants.

Mechanistic interpretability seeks to understand the internal mechanisms of machine learning models, where localization -- identifying the important model components -- is a key step. Activation patching, also known as causal tracing or interchange intervention, is a standard technique for this task (Vig et al., 2020), but the literature contains many variants with little consensus on the choice of hyperparameters or methodology. In this work, we systematically examine the impact of methodological details in activation patching, including evaluation metrics and corruption methods. In several settings of localization and circuit discovery in language models, we find that varying these hyperparameters could lead to disparate interpretability results. Backed by empirical observations, we give conceptual arguments for why certain metrics or methods may be preferred. Finally, we provide recommendations for the best practices of activation patching going forwards.

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

The sparsity of labelled data is an obstacle to the development of Relation Extraction models and the completion of databases in various biomedical areas. While being of high interest in drug-discovery, the natural-products literature, reporting the identification of potential bioactive compounds from organisms, is a concrete example of such an overlooked topic. To mark the start of this new task, we created the first curated evaluation dataset and extracted literature items from the LOTUS database to build training sets. To this end, we developed a new sampler inspired by diversity metrics in ecology, named Greedy Maximum Entropy sampler, or GME-sampler (https://github.com/idiap/gme-sampler). The strategic optimization of both balance and diversity of the selected items in the evaluation set is important given the resource-intensive nature of manual curation. After quantifying the noise in the training set, in the form of discrepancies between the input abstracts text and the expected output labels, we explored different strategies accordingly. Framing the task as an end-to-end Relation Extraction, we evaluated the performance of standard fine-tuning as a generative task and few-shot learning with open Large Language Models (LLaMA 7B-65B). In addition to their evaluation in few-shot settings, we explore the potential of open Large Language Models (Vicuna-13B) as synthetic data generator and propose a new workflow for this purpose. All evaluated models exhibited substantial improvements when fine-tuned on synthetic abstracts rather than the original noisy data. We provide our best performing (f1-score=59.0) BioGPT-Large model for end-to-end RE of natural-products relationships along with all the generated synthetic data and the evaluation dataset. See more details at https://github.com/idiap/abroad-re.

Synthetic data generation has the potential to impact applications and domains with scarce data. However, before such data is used for sensitive tasks such as mental health, we need an understanding of how different demographics are represented in it. In our paper, we analyze the potential of producing synthetic data using GPT-3 by exploring the various stressors it attributes to different race and gender combinations, to provide insight for future researchers looking into using LLMs for data generation. Using GPT-3, we develop HEADROOM, a synthetic dataset of 3,120 posts about depression-triggering stressors, by controlling for race, gender, and time frame (before and after COVID-19). Using this dataset, we conduct semantic and lexical analyses to (1) identify the predominant stressors for each demographic group; and (2) compare our synthetic data to a human-generated dataset. We present the procedures to generate queries to develop depression data using GPT-3, and conduct analyzes to uncover the types of stressors it assigns to demographic groups, which could be used to test the limitations of LLMs for synthetic data generation for depression data. Our findings show that synthetic data mimics some of the human-generated data distribution for the predominant depression stressors across diverse demographics.

Scientific documents record research findings and valuable human knowledge, comprising a vast corpus of high-quality data. Leveraging multi-modality data extracted from these documents and assessing large models' abilities to handle scientific document-oriented tasks is therefore meaningful. Despite promising advancements, large models still perform poorly on multi-page scientific document extraction and understanding tasks, and their capacity to process within-document data formats such as charts and equations remains under-explored. To address these issues, we present DocGenome, a structured document benchmark constructed by annotating 500K scientific documents from 153 disciplines in the arXiv open-access community, using our custom auto-labeling pipeline. DocGenome features four key characteristics: 1) Completeness: It is the first dataset to structure data from all modalities including 13 layout attributes along with their LaTeX source codes. 2) Logicality: It provides 6 logical relationships between different entities within each scientific document. 3) Diversity: It covers various document-oriented tasks, including document classification, visual grounding, document layout detection, document transformation, open-ended single-page QA and multi-page QA. 4) Correctness: It undergoes rigorous quality control checks conducted by a specialized team. We conduct extensive experiments to demonstrate the advantages of DocGenome and objectively evaluate the performance of large models on our benchmark.

With recent advancements in the area of Natural Language Processing, the focus is slowly shifting from a purely English-centric view towards more language-specific solutions, including German. Especially practical for businesses to analyze their growing amount of textual data are text summarization systems, which transform long input documents into compressed and more digestible summary texts. In this work, we assess the particular landscape of German abstractive text summarization and investigate the reasons why practically useful solutions for abstractive text summarization are still absent in industry. Our focus is two-fold, analyzing a) training resources, and b) publicly available summarization systems. We are able to show that popular existing datasets exhibit crucial flaws in their assumptions about the original sources, which frequently leads to detrimental effects on system generalization and evaluation biases. We confirm that for the most popular training dataset, MLSUM, over 50% of the training set is unsuitable for abstractive summarization purposes. Furthermore, available systems frequently fail to compare to simple baselines, and ignore more effective and efficient extractive summarization approaches. We attribute poor evaluation quality to a variety of different factors, which are investigated in more detail in this work: A lack of qualitative (and diverse) gold data considered for training, understudied (and untreated) positional biases in some of the existing datasets, and the lack of easily accessible and streamlined pre-processing strategies or analysis tools. We provide a comprehensive assessment of available models on the cleaned datasets, and find that this can lead to a reduction of more than 20 ROUGE-1 points during evaluation. The code for dataset filtering and reproducing results can be found online at https://github.com/dennlinger/summaries

The language that we produce reflects our personality, and various personal and demographic characteristics can be detected in natural language texts. We focus on one particular personal trait of the author, gender, and study how it is manifested in original texts and in translations. We show that author's gender has a powerful, clear signal in originals texts, but this signal is obfuscated in human and machine translation. We then propose simple domain-adaptation techniques that help retain the original gender traits in the translation, without harming the quality of the translation, thereby creating more personalized machine translation systems.

Inferring causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to directly predict the causal structure from observational or interventional data. This allows our inference model to acquire domain-specific inductive biases for causal discovery solely from data generated by a simulator, bypassing both the hand-engineering of suitable score functions and the search over graphs. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici.

We study the problem of attributing the prediction of a deep network to its input features, a problem previously studied by several other works. We identify two fundamental axioms---Sensitivity and Implementation Invariance that attribution methods ought to satisfy. We show that they are not satisfied by most known attribution methods, which we consider to be a fundamental weakness of those methods. We use the axioms to guide the design of a new attribution method called Integrated Gradients. Our method requires no modification to the original network and is extremely simple to implement; it just needs a few calls to the standard gradient operator. We apply this method to a couple of image models, a couple of text models and a chemistry model, demonstrating its ability to debug networks, to extract rules from a network, and to enable users to engage with models better.

Large language models (LLMs) have shown remarkable performances across a wide range of tasks. However, the mechanisms by which these models encode tasks of varying complexities remain poorly understood. In this paper, we explore the hypothesis that LLMs process concepts of varying complexities in different layers, introducing the idea of "Concept Depth" to suggest that more complex concepts are typically acquired in deeper layers. Specifically, we categorize concepts based on their level of abstraction, defining them in the order of increasing complexity within factual, emotional, and inferential tasks. We conduct extensive probing experiments using layer-wise representations across various LLM families (Gemma, LLaMA, QWen) on various datasets spanning the three domains of tasks. Our findings reveal that models could efficiently conduct probing for simpler tasks in shallow layers, and more complex tasks typically necessitate deeper layers for accurate understanding. Additionally, we examine how external factors, such as adding noise to the input and quantizing the model weights, might affect layer-wise representations. Our findings suggest that these factors can impede the development of a conceptual understanding of LLMs until deeper layers are explored. We hope that our proposed concept and experimental insights will enhance the understanding of the mechanisms underlying LLMs. Our codes are available at https://github.com/Luckfort/CD.

Paraphrases represent a human's intuitive ability to understand expressions presented in various different ways. Current paraphrase evaluations of language models primarily use binary approaches, offering limited interpretability of specific text changes. Atomic paraphrase types (APT) decompose paraphrases into different linguistic changes and offer a granular view of the flexibility in linguistic expression (e.g., a shift in syntax or vocabulary used). In this study, we assess the human preferences towards ChatGPT in generating English paraphrases with ten APTs and five prompting techniques. We introduce APTY (Atomic Paraphrase TYpes), a dataset of 500 sentence-level and word-level annotations by 15 annotators. The dataset also provides a human preference ranking of paraphrases with different types that can be used to fine-tune models with RLHF and DPO methods. Our results reveal that ChatGPT can generate simple APTs, such as additions and deletions, but struggle with complex structures (e.g., subordination changes). This study contributes to understanding which aspects of paraphrasing language models have already succeeded at understanding and what remains elusive. In addition, our curated datasets can be used to develop language models with specific linguistic capabilities.

Abstractive summarization models are commonly trained using maximum likelihood estimation, which assumes a deterministic (one-point) target distribution in which an ideal model will assign all the probability mass to the reference summary. This assumption may lead to performance degradation during inference, where the model needs to compare several system-generated (candidate) summaries that have deviated from the reference summary. To address this problem, we propose a novel training paradigm which assumes a non-deterministic distribution so that different candidate summaries are assigned probability mass according to their quality. Our method achieves a new state-of-the-art result on the CNN/DailyMail (47.78 ROUGE-1) and XSum (49.07 ROUGE-1) datasets. Further analysis also shows that our model can estimate probabilities of candidate summaries that are more correlated with their level of quality.

Previous works on Treatment Effect Estimation (TEE) are not in widespread use because they are predominantly theoretical, where strong parametric assumptions are made but untractable for practical application. Recent work uses multilayer perceptron (MLP) for modeling casual relationships, however, MLPs lag far behind recent advances in ML methodology, which limits their applicability and generalizability. To extend beyond the single domain formulation and towards more realistic learning scenarios, we explore model design spaces beyond MLPs, i.e., transformer backbones, which provide flexibility where attention layers govern interactions among treatments and covariates to exploit structural similarities of potential outcomes for confounding control. Through careful model design, Transformers as Treatment Effect Estimators (TransTEE) is proposed. We show empirically that TransTEE can: (1) serve as a general purpose treatment effect estimator that significantly outperforms competitive baselines in a variety of challenging TEE problems (e.g., discrete, continuous, structured, or dosage-associated treatments) and is applicable to both when covariates are tabular and when they consist of structural data (e.g., texts, graphs); (2) yield multiple advantages: compatibility with propensity score modeling, parameter efficiency, robustness to continuous treatment value distribution shifts, explainable in covariate adjustment, and real-world utility in auditing pre-trained language models

A key component of successfully reading a passage of text is the ability to apply knowledge gained from the passage to a new situation. In order to facilitate progress on this kind of reading, we present ROPES, a challenging benchmark for reading comprehension targeting Reasoning Over Paragraph Effects in Situations. We target expository language describing causes and effects (e.g., "animal pollinators increase efficiency of fertilization in flowers"), as they have clear implications for new situations. A system is presented a background passage containing at least one of these relations, a novel situation that uses this background, and questions that require reasoning about effects of the relationships in the background passage in the context of the situation. We collect background passages from science textbooks and Wikipedia that contain such phenomena, and ask crowd workers to author situations, questions, and answers, resulting in a 14,322 question dataset. We analyze the challenges of this task and evaluate the performance of state-of-the-art reading comprehension models. The best model performs only slightly better than randomly guessing an answer of the correct type, at 61.6% F1, well below the human performance of 89.0%.

Organizations cannot address demographic disparities that they cannot see. Recent research on machine learning and fairness has emphasized that awareness of sensitive attributes, such as race and sex, is critical to the development of interventions. However, on the ground, the existence of these data cannot be taken for granted. This paper uses the domains of employment, credit, and healthcare in the United States to surface conditions that have shaped the availability of sensitive attribute data. For each domain, we describe how and when private companies collect or infer sensitive attribute data for antidiscrimination purposes. An inconsistent story emerges: Some companies are required by law to collect sensitive attribute data, while others are prohibited from doing so. Still others, in the absence of legal mandates, have determined that collection and imputation of these data are appropriate to address disparities. This story has important implications for fairness research and its future applications. If companies that mediate access to life opportunities are unable or hesitant to collect or infer sensitive attribute data, then proposed techniques to detect and mitigate bias in machine learning models might never be implemented outside the lab. We conclude that today's legal requirements and corporate practices, while highly inconsistent across domains, offer lessons for how to approach the collection and inference of sensitive data in appropriate circumstances. We urge stakeholders, including machine learning practitioners, to actively help chart a path forward that takes both policy goals and technical needs into account.

Pre-trained language models like ChatGPT have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks. Moreover, in bioinformatics, generating functional programs poses additional notable challenges due to the amount of domain knowledge, the need for complicated data operations, and intricate functional dependencies between the operations. Here, we present BioCoder, a benchmark developed to evaluate existing pre-trained models in generating bioinformatics code. In relation to function-code generation, BioCoder covers potential package dependencies, class declarations, and global variables. It incorporates 1026 functions and 1243 methods in Python and Java from GitHub and 253 examples from the Rosalind Project. BioCoder incorporates a fuzz-testing framework for evaluation, and we have applied it to evaluate many models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, and ChatGPT. Our detailed analysis of these models emphasizes the importance of domain knowledge, pragmatic code generation, and contextual understanding. Our dataset, benchmark, Docker images, and scripts required for testing are all available at https://github.com/gersteinlab/biocoder.

Understanding how language supports emotion inference remains a topic of debate in emotion science. The present study investigated whether language-derived emotion-concept knowledge would causally support emotion inference by manipulating the language-specific knowledge representations in large language models. Using the prompt technique, 14 attributes of emotion concepts were found to be represented by distinct artificial neuron populations. By manipulating these attribute-related neurons, the majority of the emotion inference tasks showed performance deterioration compared to random manipulations. The attribute-specific performance deterioration was related to the importance of different attributes in human mental space. Our findings provide causal evidence in support of a language-based mechanism for emotion inference and highlight the contributions of emotion-concept knowledge.

As LLMs are increasingly integrated into user-facing applications, addressing biases that perpetuate societal inequalities is crucial. While much work has gone into measuring or mitigating biases in these models, fewer studies have investigated their origins. Therefore, this study examines the correlation between gender-occupation bias in pre-training data and their manifestation in LLMs, focusing on the Dolma dataset and the OLMo model. Using zero-shot prompting and token co-occurrence analyses, we explore how biases in training data influence model outputs. Our findings reveal that biases present in pre-training data are amplified in model outputs. The study also examines the effects of prompt types, hyperparameters, and instruction-tuning on bias expression, finding instruction-tuning partially alleviating representational bias while still maintaining overall stereotypical gender associations, whereas hyperparameters and prompting variation have a lesser effect on bias expression. Our research traces bias throughout the LLM development pipeline and underscores the importance of mitigating bias at the pretraining stage.

Coreference resolution models are often evaluated on multiple datasets. Datasets vary, however, in how coreference is realized -- i.e., how the theoretical concept of coreference is operationalized in the dataset -- due to factors such as the choice of corpora and annotation guidelines. We investigate the extent to which errors of current coreference resolution models are associated with existing differences in operationalization across datasets (OntoNotes, PreCo, and Winogrande). Specifically, we distinguish between and break down model performance into categories corresponding to several types of coreference, including coreferring generic mentions, compound modifiers, and copula predicates, among others. This break down helps us investigate how state-of-the-art models might vary in their ability to generalize across different coreference types. In our experiments, for example, models trained on OntoNotes perform poorly on generic mentions and copula predicates in PreCo. Our findings help calibrate expectations of current coreference resolution models; and, future work can explicitly account for those types of coreference that are empirically associated with poor generalization when developing models.

Understanding the relations between entities denoted by NPs in a text is a critical part of human-like natural language understanding. However, only a fraction of such relations is covered by standard NLP tasks and benchmarks nowadays. In this work, we propose a novel task termed text-based NP enrichment (TNE), in which we aim to enrich each NP in a text with all the preposition-mediated relations -- either explicit or implicit -- that hold between it and other NPs in the text. The relations are represented as triplets, each denoted by two NPs related via a preposition. Humans recover such relations seamlessly, while current state-of-the-art models struggle with them due to the implicit nature of the problem. We build the first large-scale dataset for the problem, provide the formal framing and scope of annotation, analyze the data, and report the results of fine-tuned language models on the task, demonstrating the challenge it poses to current technology. A webpage with a data-exploration UI, a demo, and links to the code, models, and leaderboard, to foster further research into this challenging problem can be found at: yanaiela.github.io/TNE/.

Textual health records of cancer patients are usually protracted and highly unstructured, making it very time-consuming for health professionals to get a complete overview of the patient's therapeutic course. As such limitations can lead to suboptimal and/or inefficient treatment procedures, healthcare providers would greatly benefit from a system that effectively summarizes the information of those records. With the advent of deep neural models, this objective has been partially attained for English clinical texts, however, the research community still lacks an effective solution for languages with limited resources. In this paper, we present the approach we developed to extract procedures, drugs, and diseases from oncology health records written in European Portuguese. This project was conducted in collaboration with the Portuguese Institute for Oncology which, besides holding over 10 years of duly protected medical records, also provided oncologist expertise throughout the development of the project. Since there is no annotated corpus for biomedical entity extraction in Portuguese, we also present the strategy we followed in annotating the corpus for the development of the models. The final models, which combined a neural architecture with entity linking, achieved F_1 scores of 88.6, 95.0, and 55.8 per cent in the mention extraction of procedures, drugs, and diseases, respectively.

Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, current molecular representation learning methods do not provide a comprehensive view of cell states under these perturbations and struggle to remove noise, hindering model generalization. We introduce the Information Alignment (InfoAlign) approach to learn molecular representations through the information bottleneck method in cells. We integrate molecules and cellular response data as nodes into a context graph, connecting them with weighted edges based on chemical, biological, and computational criteria. For each molecule in a training batch, InfoAlign optimizes the encoder's latent representation with a minimality objective to discard redundant structural information. A sufficiency objective decodes the representation to align with different feature spaces from the molecule's neighborhood in the context graph. We demonstrate that the proposed sufficiency objective for alignment is tighter than existing encoder-based contrastive methods. Empirically, we validate representations from InfoAlign in two downstream tasks: molecular property prediction against up to 19 baseline methods across four datasets, plus zero-shot molecule-morphology matching.

In recent years, there is strong emphasis on mining medical data using machine learning techniques. A common problem is to obtain a noiseless set of textual documents, with a relevant content for the research question, and developing a Question Answering (QA) model for a specific medical field. The purpose of this paper is to present a new methodology for building a medical dataset and obtain a QA model for analysis of symptoms and impact on daily life for a specific disease domain. The ``Mental Health'' forum was used, a forum dedicated to people suffering from schizophrenia and different mental disorders. Relevant posts of active users, who regularly participate, were extrapolated providing a new method of obtaining low-bias content and without privacy issues. Furthermore, it is shown how to pre-process the dataset to convert it into a QA dataset. The Bidirectional Encoder Representations from Transformers (BERT), DistilBERT, RoBERTa, and BioBERT models were fine-tuned and evaluated via F1-Score, Exact Match, Precision and Recall. Accurate empirical experiments demonstrated the effectiveness of the proposed method for obtaining an accurate dataset for QA model implementation. By fine-tuning the BioBERT QA model, we achieved an F1 score of 0.885, showing a considerable improvement and outperforming the state-of-the-art model for mental disorders domain.

We introduce a general, flexible, parametric survival modelling framework which encompasses key shapes of hazard function (constant, increasing, decreasing, up-then-down, down-then-up), various common survival distributions (log-logistic, Burr type XII, Weibull, Gompertz), and includes defective distributions (i.e., cure models). This generality is achieved using four basic distributional parameters: two scale-type parameters and two shape parameters. Generalising to covariate dependence, the scale-type regression components correspond to accelerated failure time (AFT) and proportional hazards (PH) models. Therefore, this general formulation unifies the most popular survival models which allows us to consider the practical value of possible modelling choices for survival data. Furthermore, in line with our proposed flexible baseline distribution, we advocate the use of multi-parameter regression in which more than one distributional parameter depends on covariates - rather than the usual convention of having a single covariate-dependent (scale) parameter. While many choices are available, we suggest introducing covariates through just one or other of the two scale parameters, which covers AFT and PH models, in combination with a `power' shape parameter, which allows for more complex non-AFT/non-PH effects, while the other shape parameter remains covariate-independent, and handles automatic selection of the baseline distribution. We explore inferential issues in simulations, both with and without a covariate, with particular focus on evidence concerning the need, or otherwise, to include both AFT and PH parameters. We illustrate the efficacy of our modelling framework by investigating differences between treatment groups using data from a lung cancer study and a melanoma study. Censoring is accommodated throughout.

Symbolic regression (SR) is a powerful technique for discovering the underlying mathematical expressions from observed data. Inspired by the success of deep learning, recent efforts have focused on two categories for SR methods. One is using a neural network or genetic programming to search the expression tree directly. Although this has shown promising results, the large search space poses difficulties in learning constant factors and processing high-dimensional problems. Another approach is leveraging a transformer-based model training on synthetic data and offers advantages in inference speed. However, this method is limited to fixed small numbers of dimensions and may encounter inference problems when given data is out-of-distribution compared to the synthetic data. In this work, we propose DySymNet, a novel neural-guided Dynamic Symbolic Network for SR. Instead of searching for expressions within a large search space, we explore DySymNet with various structures and optimize them to identify expressions that better-fitting the data. With a topology structure like neural networks, DySymNet not only tackles the challenge of high-dimensional problems but also proves effective in optimizing constants. Based on extensive numerical experiments using low-dimensional public standard benchmarks and the well-known SRBench with more variables, our method achieves state-of-the-art performance in terms of fitting accuracy and robustness to noise.

This paper presents a multi-label topic model for financial texts like ad-hoc announcements, 8-K filings, finance related news or annual reports. I train the model on a new financial multi-label database consisting of 3,044 German ad-hoc announcements that are labeled manually using 20 predefined, economically motivated topics. The best model achieves a macro F1 score of more than 85%. Translating the data results in an English version of the model with similar performance. As application of the model, I investigate differences in stock market reactions across topics. I find evidence for strong positive or negative market reactions for some topics, like announcements of new Large Scale Projects or Bankruptcy Filings, while I do not observe significant price effects for some other topics. Furthermore, in contrast to previous studies, the multi-label structure of the model allows to analyze the effects of co-occurring topics on stock market reactions. For many cases, the reaction to a specific topic depends heavily on the co-occurrence with other topics. For example, if allocated capital from a Seasoned Equity Offering (SEO) is used for restructuring a company in the course of a Bankruptcy Proceeding, the market reacts positively on average. However, if that capital is used for covering unexpected, additional costs from the development of new drugs, the SEO implies negative reactions on average.

We present WeakSTIL, an interpretable two-stage weak label deep learning pipeline for scoring the percentage of stromal tumor infiltrating lymphocytes (sTIL%) in H&E-stained whole-slide images (WSIs) of breast cancer tissue. The sTIL% score is a prognostic and predictive biomarker for many solid tumor types. However, due to the high labeling efforts and high intra- and interobserver variability within and between expert annotators, this biomarker is currently not used in routine clinical decision making. WeakSTIL compresses tiles of a WSI using a feature extractor pre-trained with self-supervised learning on unlabeled histopathology data and learns to predict precise sTIL% scores for each tile in the tumor bed by using a multiple instance learning regressor that only requires a weak WSI-level label. By requiring only a weak label, we overcome the large annotation efforts required to train currently existing TIL detection methods. We show that WeakSTIL is at least as good as other TIL detection methods when predicting the WSI-level sTIL% score, reaching a coefficient of determination of 0.45pm0.15 when compared to scores generated by an expert pathologist, and an AUC of 0.89pm0.05 when treating it as the clinically interesting sTIL-high vs sTIL-low classification task. Additionally, we show that the intermediate tile-level predictions of WeakSTIL are highly interpretable, which suggests that WeakSTIL pays attention to latent features related to the number of TILs and the tissue type. In the future, WeakSTIL may be used to provide consistent and interpretable sTIL% predictions to stratify breast cancer patients into targeted therapy arms.

Domain generalization is critical for real-world applications of machine learning to microscopy images, including histopathology and fluorescence imaging. Artifacts in these modalities arise through a complex combination of factors relating to tissue collection and laboratory processing, as well as factors intrinsic to patient samples. In fluorescence imaging, these artifacts stem from variations across experimental batches. The complexity and subtlety of these artifacts make the enumeration of data domains intractable. Therefore, augmentation-based methods of domain generalization that require domain identifiers and manual fine-tuning are inadequate in this setting. To overcome this challenge, we introduce ContriMix, a domain generalization technique that learns to generate synthetic images by disentangling and permuting the biological content ("content") and technical variations ("attributes") in microscopy images. ContriMix does not rely on domain identifiers or handcrafted augmentations and makes no assumptions about the input characteristics of images. We assess the performance of ContriMix on two pathology datasets dealing with patch classification and Whole Slide Image label prediction tasks respectively (Camelyon17-WILDS and RCC subtyping), and one fluorescence microscopy dataset (RxRx1-WILDS). Without any access to domain identifiers at train or test time, ContriMix performs similar or better than current state-of-the-art methods in all these datasets, motivating its usage for microscopy image analysis in real-world settings where domain information is hard to come by. The code for ContriMix can be found at https://gitlab.com/huutan86/contrimix

A major open problem in neural machine translation (NMT) is the translation of idiomatic expressions, such as "under the weather". The meaning of these expressions is not composed by the meaning of their constituent words, and NMT models tend to translate them literally (i.e., word-by-word), which leads to confusing and nonsensical translations. Research on idioms in NMT is limited and obstructed by the absence of automatic methods for quantifying these errors. In this work, first, we propose a novel metric for automatically measuring the frequency of literal translation errors without human involvement. Equipped with this metric, we present controlled translation experiments with models trained in different conditions (with/without the test-set idioms) and across a wide range of (global and targeted) metrics and test sets. We explore the role of monolingual pretraining and find that it yields substantial targeted improvements, even without observing any translation examples of the test-set idioms. In our analysis, we probe the role of idiom context. We find that the randomly initialized models are more local or "myopic" as they are relatively unaffected by variations of the idiom context, unlike the pretrained ones.

Inferring causal structures from experimentation is a central task in many domains. For example, in biology, recent advances allow us to obtain single-cell expression data under multiple interventions such as drugs or gene knockouts. However, the targets of the interventions are often uncertain or unknown and the number of observations limited. As a result, standard causal discovery methods can no longer be reliably used. To fill this gap, we propose a Bayesian framework (BaCaDI) for discovering and reasoning about the causal structure that underlies data generated under various unknown experimental or interventional conditions. BaCaDI is fully differentiable, which allows us to infer the complex joint posterior over the intervention targets and the causal structure via efficient gradient-based variational inference. In experiments on synthetic causal discovery tasks and simulated gene-expression data, BaCaDI outperforms related methods in identifying causal structures and intervention targets.

Extensive efforts in the past have been directed toward the development of summarization datasets. However, a predominant number of these resources have been (semi)-automatically generated, typically through web data crawling, resulting in subpar resources for training and evaluating summarization systems, a quality compromise that is arguably due to the substantial costs associated with generating ground-truth summaries, particularly for diverse languages and specialized domains. To address this issue, we present ACLSum, a novel summarization dataset carefully crafted and evaluated by domain experts. In contrast to previous datasets, ACLSum facilitates multi-aspect summarization of scientific papers, covering challenges, approaches, and outcomes in depth. Through extensive experiments, we evaluate the quality of our resource and the performance of models based on pretrained language models and state-of-the-art large language models (LLMs). Additionally, we explore the effectiveness of extractive versus abstractive summarization within the scholarly domain on the basis of automatically discovered aspects. Our results corroborate previous findings in the general domain and indicate the general superiority of end-to-end aspect-based summarization. Our data is released at https://github.com/sobamchan/aclsum.

Modality is the linguistic ability to describe events with added information such as how desirable, plausible, or feasible they are. Modality is important for many NLP downstream tasks such as the detection of hedging, uncertainty, speculation, and more. Previous studies that address modality detection in NLP often restrict modal expressions to a closed syntactic class, and the modal sense labels are vastly different across different studies, lacking an accepted standard. Furthermore, these senses are often analyzed independently of the events that they modify. This work builds on the theoretical foundations of the Georgetown Gradable Modal Expressions (GME) work by Rubinstein et al. (2013) to propose an event-based modality detection task where modal expressions can be words of any syntactic class and sense labels are drawn from a comprehensive taxonomy which harmonizes the modal concepts contributed by the different studies. We present experiments on the GME corpus aiming to detect and classify fine-grained modal concepts and associate them with their modified events. We show that detecting and classifying modal expressions is not only feasible, but also improves the detection of modal events in their own right.

The approval success rate of drug candidates is very low with the majority of failure due to safety and efficacy. Increasingly available high dimensional information on targets, drug molecules and indications provides an opportunity for ML methods to integrate multiple data modalities and better predict clinically promising drug targets. Notably, drug targets with human genetics evidence are shown to have better odds to succeed. However, a recent tensor factorization-based approach found that additional information on targets and indications might not necessarily improve the predictive accuracy. Here we revisit this approach by integrating different types of human genetics evidence collated from publicly available sources to support each target-indication pair. We use Bayesian tensor factorization to show that models incorporating all available human genetics evidence (rare disease, gene burden, common disease) modestly improves the clinical outcome prediction over models using single line of genetics evidence. We provide additional insight into the relative predictive power of different types of human genetics evidence for predicting the success of clinical outcomes.

Understanding and manipulating the causal generation mechanisms in language models is essential for controlling their behavior. Previous work has primarily relied on techniques such as representation surgery -- e.g., model ablations or manipulation of linear subspaces tied to specific concepts -- to intervene on these models. To understand the impact of interventions precisely, it is useful to examine counterfactuals -- e.g., how a given sentence would have appeared had it been generated by the model following a specific intervention. We highlight that counterfactual reasoning is conceptually distinct from interventions, as articulated in Pearl's causal hierarchy. Based on this observation, we propose a framework for generating true string counterfactuals by reformulating language models as Generalized Structural-equation. Models using the Gumbel-max trick. This allows us to model the joint distribution over original strings and their counterfactuals resulting from the same instantiation of the sampling noise. We develop an algorithm based on hindsight Gumbel sampling that allows us to infer the latent noise variables and generate counterfactuals of observed strings. Our experiments demonstrate that the approach produces meaningful counterfactuals while at the same time showing that commonly used intervention techniques have considerable undesired side effects.

Mental distress like depression and anxiety contribute to the largest proportion of the global burden of diseases. Automated diagnosis systems of such disorders, empowered by recent innovations in Artificial Intelligence, can pave the way to reduce the sufferings of the affected individuals. Development of such systems requires information-rich and balanced corpora. In this work, we introduce a novel mental distress analysis audio dataset DEPAC, labeled based on established thresholds on depression and anxiety standard screening tools. This large dataset comprises multiple speech tasks per individual, as well as relevant demographic information. Alongside, we present a feature set consisting of hand-curated acoustic and linguistic features, which were found effective in identifying signs of mental illnesses in human speech. Finally, we justify the quality and effectiveness of our proposed audio corpus and feature set in predicting depression severity by comparing the performance of baseline machine learning models built on this dataset with baseline models trained on other well-known depression corpora.

Speech emotion recognition (SER) models typically rely on costly human-labeled data for training, making scaling methods to large speech datasets and nuanced emotion taxonomies difficult. We present LanSER, a method that enables the use of unlabeled data by inferring weak emotion labels via pre-trained large language models through weakly-supervised learning. For inferring weak labels constrained to a taxonomy, we use a textual entailment approach that selects an emotion label with the highest entailment score for a speech transcript extracted via automatic speech recognition. Our experimental results show that models pre-trained on large datasets with this weak supervision outperform other baseline models on standard SER datasets when fine-tuned, and show improved label efficiency. Despite being pre-trained on labels derived only from text, we show that the resulting representations appear to model the prosodic content of speech.

A fundamental issue in machine learning is the robustness of the model with respect to changes in the input. In natural language processing, models typically contain a first embedding layer, transforming a sequence of tokens into vector representations. While the robustness with respect to changes of continuous inputs is well-understood, the situation is less clear when considering discrete changes, for instance replacing a word by another in an input sentence. Our work formally proves that popular embedding schemes, such as concatenation, TF-IDF, and Paragraph Vector (a.k.a. doc2vec), exhibit robustness in the H\"older or Lipschitz sense with respect to the Hamming distance. We provide quantitative bounds for these schemes and demonstrate how the constants involved are affected by the length of the document. These findings are exemplified through a series of numerical examples.

Human-like personality traits have recently been discovered in large language models, raising the hypothesis that their (known and as yet undiscovered) biases conform with human latent psychological constructs. While large conversational models may be tricked into answering psychometric questionnaires, the latent psychological constructs of thousands of simpler transformers, trained for other tasks, cannot be assessed because appropriate psychometric methods are currently lacking. Here, we show how standard psychological questionnaires can be reformulated into natural language inference prompts, and we provide a code library to support the psychometric assessment of arbitrary models. We demonstrate, using a sample of 88 publicly available models, the existence of human-like mental health-related constructs (including anxiety, depression, and Sense of Coherence) which conform with standard theories in human psychology and show similar correlations and mitigation strategies. The ability to interpret and rectify the performance of language models by using psychological tools can boost the development of more explainable, controllable, and trustworthy models.

We present persona-based models for handling the issue of speaker consistency in neural response generation. A speaker model encodes personas in distributed embeddings that capture individual characteristics such as background information and speaking style. A dyadic speaker-addressee model captures properties of interactions between two interlocutors. Our models yield qualitative performance improvements in both perplexity and BLEU scores over baseline sequence-to-sequence models, with similar gains in speaker consistency as measured by human judges.

Lay summarisation aims to jointly summarise and simplify a given text, thus making its content more comprehensible to non-experts. Automatic approaches for lay summarisation can provide significant value in broadening access to scientific literature, enabling a greater degree of both interdisciplinary knowledge sharing and public understanding when it comes to research findings. However, current corpora for this task are limited in their size and scope, hindering the development of broadly applicable data-driven approaches. Aiming to rectify these issues, we present two novel lay summarisation datasets, PLOS (large-scale) and eLife (medium-scale), each of which contains biomedical journal articles alongside expert-written lay summaries. We provide a thorough characterisation of our lay summaries, highlighting differing levels of readability and abstractiveness between datasets that can be leveraged to support the needs of different applications. Finally, we benchmark our datasets using mainstream summarisation approaches and perform a manual evaluation with domain experts, demonstrating their utility and casting light on the key challenges of this task.

We propose ParaSCI, the first large-scale paraphrase dataset in the scientific field, including 33,981 paraphrase pairs from ACL (ParaSCI-ACL) and 316,063 pairs from arXiv (ParaSCI-arXiv). Digging into characteristics and common patterns of scientific papers, we construct this dataset though intra-paper and inter-paper methods, such as collecting citations to the same paper or aggregating definitions by scientific terms. To take advantage of sentences paraphrased partially, we put up PDBERT as a general paraphrase discovering method. The major advantages of paraphrases in ParaSCI lie in the prominent length and textual diversity, which is complementary to existing paraphrase datasets. ParaSCI obtains satisfactory results on human evaluation and downstream tasks, especially long paraphrase generation.

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released.

Mathematical symbols and descriptions appear in various forms across document section boundaries without explicit markup. In this paper, we present a new large-scale dataset that emphasizes extracting symbols and descriptions in scientific documents. Symlink annotates scientific papers of 5 different domains (i.e., computer science, biology, physics, mathematics, and economics). Our experiments on Symlink demonstrate the challenges of the symbol-description linking task for existing models and call for further research effort in this area. We will publicly release Symlink to facilitate future research.

We propose to extract meaning representations from autoregressive language models by considering the distribution of all possible trajectories extending an input text. This strategy is prompt-free, does not require fine-tuning, and is applicable to any pre-trained autoregressive model. Moreover, unlike vector-based representations, distribution-based representations can also model asymmetric relations (e.g., direction of logical entailment, hypernym/hyponym relations) by using algebraic operations between likelihood functions. These ideas are grounded in distributional perspectives on semantics and are connected to standard constructions in automata theory, but to our knowledge they have not been applied to modern language models. We empirically show that the representations obtained from large models align well with human annotations, outperform other zero-shot and prompt-free methods on semantic similarity tasks, and can be used to solve more complex entailment and containment tasks that standard embeddings cannot handle. Finally, we extend our method to represent data from different modalities (e.g., image and text) using multimodal autoregressive models. Our code is available at: https://github.com/tianyu139/meaning-as-trajectories

Despite being self-supervised, protein language models have shown remarkable performance in fundamental biological tasks such as predicting impact of genetic variation on protein structure and function. The effectiveness of these models on diverse set of tasks suggests that they learn meaningful representations of fitness landscape that can be useful for downstream clinical applications. Here, we interrogate the use of these language models in characterizing known pathogenic mutations in curated, medically actionable genes through an exhaustive search of putative compensatory mutations on each variant's genetic background. Systematic analysis of the predicted effects of these compensatory mutations reveal unappreciated structural features of proteins that are missed by other structure predictors like AlphaFold. While deep mutational scan experiments provide an unbiased estimate of the mutational landscape, we encourage the community to generate and curate rescue mutation experiments to inform the design of more sophisticated co-masking strategies and leverage large language models more effectively for downstream clinical prediction tasks.

As research and industry moves towards large-scale models capable of numerous downstream tasks, the complexity of understanding multi-modal datasets that give nuance to models rapidly increases. A clear and thorough understanding of a dataset's origins, development, intent, ethical considerations and evolution becomes a necessary step for the responsible and informed deployment of models, especially those in people-facing contexts and high-risk domains. However, the burden of this understanding often falls on the intelligibility, conciseness, and comprehensiveness of the documentation. It requires consistency and comparability across the documentation of all datasets involved, and as such documentation must be treated as a user-centric product in and of itself. In this paper, we propose Data Cards for fostering transparent, purposeful and human-centered documentation of datasets within the practical contexts of industry and research. Data Cards are structured summaries of essential facts about various aspects of ML datasets needed by stakeholders across a dataset's lifecycle for responsible AI development. These summaries provide explanations of processes and rationales that shape the data and consequently the models, such as upstream sources, data collection and annotation methods; training and evaluation methods, intended use; or decisions affecting model performance. We also present frameworks that ground Data Cards in real-world utility and human-centricity. Using two case studies, we report on desirable characteristics that support adoption across domains, organizational structures, and audience groups. Finally, we present lessons learned from deploying over 20 Data Cards.

Extractive summaries are usually presented as lists of sentences with no expected cohesion between them. In this paper, we aim to enforce cohesion whilst controlling for informativeness and redundancy in summaries, in cases where the input exhibits high redundancy. The pipeline controls for redundancy in long inputs as it is consumed, and balances informativeness and cohesion during sentence selection. Our sentence selector simulates human memory to keep track of topics --modeled as lexical chains--, enforcing cohesive ties between noun phrases. Across a variety of domains, our experiments revealed that it is possible to extract highly cohesive summaries that nevertheless read as informative to humans as summaries extracted by only accounting for informativeness or redundancy. The extracted summaries exhibit smooth topic transitions between sentences as signaled by lexical chains, with chains spanning adjacent or near-adjacent sentences.

Several studies have shown that speech and language features, automatically extracted from clinical interviews or spontaneous discourse, have diagnostic value for mental disorders such as schizophrenia and bipolar disorder. They typically make use of a large feature set to train a classifier for distinguishing between two groups of interest, i.e. a clinical and control group. However, a purely data-driven approach runs the risk of overfitting to a particular data set, especially when sample sizes are limited. Here, we first down-select the set of language features to a small subset that is related to a well-validated test of functional ability, the Social Skills Performance Assessment (SSPA). This helps establish the concurrent validity of the selected features. We use only these features to train a simple classifier to distinguish between groups of interest. Linear regression reveals that a subset of language features can effectively model the SSPA, with a correlation coefficient of 0.75. Furthermore, the same feature set can be used to build a strong binary classifier to distinguish between healthy controls and a clinical group (AUC = 0.96) and also between patients within the clinical group with schizophrenia and bipolar I disorder (AUC = 0.83).

Recent work has proposed the linear representation hypothesis: that language models perform computation by manipulating one-dimensional representations of concepts ("features") in activation space. In contrast, we explore whether some language model representations may be inherently multi-dimensional. We begin by developing a rigorous definition of irreducible multi-dimensional features based on whether they can be decomposed into either independent or non-co-occurring lower-dimensional features. Motivated by these definitions, we design a scalable method that uses sparse autoencoders to automatically find multi-dimensional features in GPT-2 and Mistral 7B. These auto-discovered features include strikingly interpretable examples, e.g. circular features representing days of the week and months of the year. We identify tasks where these exact circles are used to solve computational problems involving modular arithmetic in days of the week and months of the year. Finally, we provide evidence that these circular features are indeed the fundamental unit of computation in these tasks with intervention experiments on Mistral 7B and Llama 3 8B, and we find further circular representations by breaking down the hidden states for these tasks into interpretable components.

Multiword expressions (MWEs) refer to idiomatic sequences of multiple words. MWE identification, i.e., detecting MWEs in text, can play a key role in downstream tasks such as machine translation. Existing datasets for MWE identification are inconsistently annotated, limited to a single type of MWE, or limited in size. To enable reliable and comprehensive evaluation, we created CoAM: Corpus of All-Type Multiword Expressions, a dataset of 1.3K sentences constructed through a multi-step process to enhance data quality consisting of human annotation, human review, and automated consistency checking. MWEs in CoAM are tagged with MWE types, such as Noun and Verb, to enable fine-grained error analysis. Annotations for CoAM were collected using a new interface created with our interface generator, which allows easy and flexible annotation of MWEs in any form, including discontinuous ones. Through experiments using CoAM, we find that a fine-tuned large language model outperforms the current state-of-the-art approach for MWE identification. Furthermore, analysis using our MWE type tagged data reveals that Verb MWEs are easier than Noun MWEs to identify across approaches.

Summary: GeneFEAST, implemented in Python, is a gene-centric functional enrichment analysis summarisation and visualisation tool that can be applied to large functional enrichment analysis (FEA) results arising from upstream FEA pipelines. It produces a systematic, navigable HTML report, making it easy to identify sets of genes putatively driving multiple enrichments and to explore gene-level quantitative data first used to identify input genes. Further, GeneFEAST can compare FEA results from multiple studies, making it possible, for example, to highlight patterns of gene expression amongst genes commonly differentially expressed in two sets of conditions, and giving rise to shared enrichments under those conditions. GeneFEAST offers a novel, effective way to address the complexities of linking up many overlapping FEA results to their underlying genes and data, advancing gene-centric hypotheses, and providing pivotal information for downstream validation experiments. Availability: GeneFEAST is available at https://github.com/avigailtaylor/GeneFEAST Contact: [email protected]

In disentangling the heterogeneity observed in psychopathology, personality of the patients is considered crucial. While it has been demonstrated that personality traits are reflected in the language used by a patient, we hypothesize that this enables automatic inference of the personality type directly from speech utterances, potentially more accurately than through a traditional questionnaire-based approach explicitly designed for personality classification. To validate this hypothesis, we adopt natural language processing (NLP) and standard machine learning tools for classification. We test this on a dataset of recorded clinical diagnostic interviews (CDI) on a sample of 79 patients diagnosed with major depressive disorder (MDD) -- a condition for which differentiated treatment based on personality styles has been advocated -- and classified into anaclitic and introjective personality styles. We start by analyzing the interviews to see which linguistic features are associated with each style, in order to gain a better understanding of the styles. Then, we develop automatic classifiers based on (a) standardized questionnaire responses; (b) basic text features, i.e., TF-IDF scores of words and word sequences; (c) more advanced text features, using LIWC (linguistic inquiry and word count) and context-aware features using BERT (bidirectional encoder representations from transformers); (d) audio features. We find that automated classification with language-derived features (i.e., based on LIWC) significantly outperforms questionnaire-based classification models. Furthermore, the best performance is achieved by combining LIWC with the questionnaire features. This suggests that more work should be put into developing linguistically based automated techniques for characterizing personality, however questionnaires still to some extent complement such methods.

We introduce methods for discovering and applying sparse feature circuits. These are causally implicated subnetworks of human-interpretable features for explaining language model behaviors. Circuits identified in prior work consist of polysemantic and difficult-to-interpret units like attention heads or neurons, rendering them unsuitable for many downstream applications. In contrast, sparse feature circuits enable detailed understanding of unanticipated mechanisms. Because they are based on fine-grained units, sparse feature circuits are useful for downstream tasks: We introduce SHIFT, where we improve the generalization of a classifier by ablating features that a human judges to be task-irrelevant. Finally, we demonstrate an entirely unsupervised and scalable interpretability pipeline by discovering thousands of sparse feature circuits for automatically discovered model behaviors.

Large Language Models (LLMs) are huge artificial neural networks which primarily serve to generate text, but also provide a very sophisticated probabilistic model of language use. Since generating a semantically consistent text requires a form of effective memory, we investigate the memory properties of LLMs and find surprising similarities with key characteristics of human memory. We argue that the human-like memory properties of the Large Language Model do not follow automatically from the LLM architecture but are rather learned from the statistics of the training textual data. These results strongly suggest that the biological features of human memory leave an imprint on the way that we structure our textual narratives.

Retrieval-augmented language models are being increasingly tasked with subjective, contentious, and conflicting queries such as "is aspartame linked to cancer". To resolve these ambiguous queries, one must search through a large range of websites and consider "which, if any, of this evidence do I find convincing?". In this work, we study how LLMs answer this question. In particular, we construct ConflictingQA, a dataset that pairs controversial queries with a series of real-world evidence documents that contain different facts (e.g., quantitative results), argument styles (e.g., appeals to authority), and answers (Yes or No). We use this dataset to perform sensitivity and counterfactual analyses to explore which text features most affect LLM predictions. Overall, we find that current models rely heavily on the relevance of a website to the query, while largely ignoring stylistic features that humans find important such as whether a text contains scientific references or is written with a neutral tone. Taken together, these results highlight the importance of RAG corpus quality (e.g., the need to filter misinformation), and possibly even a shift in how LLMs are trained to better align with human judgements.

Retrieval Augmented Generation (RAG) is a widely used approach for leveraging external context in several natural language applications such as question answering and information retrieval. Yet, the exact nature in which a Language Model (LM) leverages this non-parametric memory or retrieved context isn't clearly understood. This paper mechanistically examines the RAG pipeline to highlight that LMs demonstrate a "shortcut'' effect and have a strong bias towards utilizing the retrieved context to answer questions, while relying minimally on model priors. We propose (a) Causal Mediation Analysis; for proving that parametric memory is minimally utilized when answering a question and (b) Attention Contributions and Knockouts for showing the last token residual stream do not get enriched from the subject token in the question, but gets enriched from tokens of RAG-context. We find this pronounced "shortcut'' behaviour to be true across both LLMs (e.g.,LlaMa) and SLMs (e.g., Phi)

Argumentation is one of society's foundational pillars, and, sparked by advances in NLP and the vast availability of text data, automated mining of arguments receives increasing attention. A decisive property of arguments is their strength or quality. While there are works on the automated estimation of argument strength, their scope is narrow: they focus on isolated datasets and neglect the interactions with related argument mining tasks, such as argument identification, evidence detection, or emotional appeal. In this work, we close this gap by approaching argument quality estimation from multiple different angles: Grounded on rich results from thorough empirical evaluations, we assess the generalization capabilities of argument quality estimation across diverse domains, the interplay with related argument mining tasks, and the impact of emotions on perceived argument strength. We find that generalization depends on a sufficient representation of different domains in the training part. In zero-shot transfer and multi-task experiments, we reveal that argument quality is among the more challenging tasks but can improve others. Finally, we show that emotions play a minor role in argument quality than is often assumed.

Large language models (LLMs) are capable of generating coherent summaries from very long contexts given a user query. Extracting and properly citing evidence spans could help improve the transparency and reliability of these summaries. At the same time, LLMs suffer from positional biases in terms of which information they understand and attend to, which could affect evidence citation. Whereas previous work has focused on evidence citation with predefined levels of granularity (e.g. sentence, paragraph, document, etc.), we propose the task of long-context query focused summarization with unstructured evidence citation. We show how existing systems struggle to generate and properly cite unstructured evidence from their context, and that evidence tends to be "lost-in-the-middle". To help mitigate this, we create the Summaries with Unstructured Evidence Text dataset (SUnsET), a synthetic dataset generated using a novel domain-agnostic pipeline which can be used as supervision to adapt LLMs to this task. We demonstrate across 5 LLMs of different sizes and 4 datasets with varying document types and lengths that LLMs adapted with SUnsET data generate more relevant and factually consistent evidence than their base models, extract evidence from more diverse locations in their context, and can generate more relevant and consistent summaries.

As mental health care systems worldwide struggle to meet demand, there is increasing focus on using language models to infer neuropsychiatric conditions or psychopathological traits from language production. Yet, so far, this research has only delivered solutions with limited clinical applicability, due to insufficient consideration of ethical questions crucial to ensuring the synergy between possible applications and model design. To accelerate progress towards clinically applicable models, our paper charts the ethical landscape of research on language-based inference of psychopathology and provides a practical tool for researchers to navigate it. We identify seven core ethical principles that should guide model development and deployment in this domain, translate them into ELLIPS, an ethical toolkit operationalizing these principles into questions that can guide researchers' choices with respect to data selection, architectures, evaluation, and model deployment, and provide a case study exemplifying its use. With this, we aim to facilitate the emergence of model technology with concrete potential for real-world applicability.

We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials. Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the `PICO' elements). These spans are further annotated at a more granular level, e.g., individual interventions within them are marked and mapped onto a structured medical vocabulary. We acquired annotations from a diverse set of workers with varying levels of expertise and cost. We describe our data collection process and the corpus itself in detail. We then outline a set of challenging NLP tasks that would aid searching of the medical literature and the practice of evidence-based medicine.

As language models become more powerful, training and evaluation are increasingly bottlenecked by the data and metrics used for a particular task. For example, summarization models are often trained to predict human reference summaries and evaluated using ROUGE, but both of these metrics are rough proxies for what we really care about -- summary quality. In this work, we show that it is possible to significantly improve summary quality by training a model to optimize for human preferences. We collect a large, high-quality dataset of human comparisons between summaries, train a model to predict the human-preferred summary, and use that model as a reward function to fine-tune a summarization policy using reinforcement learning. We apply our method to a version of the TL;DR dataset of Reddit posts and find that our models significantly outperform both human reference summaries and much larger models fine-tuned with supervised learning alone. Our models also transfer to CNN/DM news articles, producing summaries nearly as good as the human reference without any news-specific fine-tuning. We conduct extensive analyses to understand our human feedback dataset and fine-tuned models We establish that our reward model generalizes to new datasets, and that optimizing our reward model results in better summaries than optimizing ROUGE according to humans. We hope the evidence from our paper motivates machine learning researchers to pay closer attention to how their training loss affects the model behavior they actually want.

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce BEND, a Benchmark for DNA language models, featuring a collection of realistic and biologically meaningful downstream tasks defined on the human genome. We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features. BEND is available at https://github.com/frederikkemarin/BEND.

In the field of language modeling, models augmented with retrieval components have emerged as a promising solution to address several challenges faced in the natural language processing (NLP) field, including knowledge grounding, interpretability, and scalability. Despite the primary focus on NLP, we posit that the paradigm of retrieval-enhancement can be extended to a broader spectrum of machine learning (ML) such as computer vision, time series prediction, and computational biology. Therefore, this work introduces a formal framework of this paradigm, Retrieval-Enhanced Machine Learning (REML), by synthesizing the literature in various domains in ML with consistent notations which is missing from the current literature. Also, we found that while a number of studies employ retrieval components to augment their models, there is a lack of integration with foundational Information Retrieval (IR) research. We bridge this gap between the seminal IR research and contemporary REML studies by investigating each component that comprises the REML framework. Ultimately, the goal of this work is to equip researchers across various disciplines with a comprehensive, formally structured framework of retrieval-enhanced models, thereby fostering interdisciplinary future research.

Large language models (LLMs) are trained from vast repositories of text authored by millions of distinct authors, reflecting an enormous diversity of human traits. While these models bear the potential to be used as approximations of human subjects in behavioral studies, prior efforts have been limited in steering model responses to match individual human users. In this work, we introduce "Anthology", a method for conditioning LLMs to particular virtual personas by harnessing open-ended life narratives, which we refer to as "backstories." We show that our methodology enhances the consistency and reliability of experimental outcomes while ensuring better representation of diverse sub-populations. Across three nationally representative human surveys conducted as part of Pew Research Center's American Trends Panel (ATP), we demonstrate that Anthology achieves up to 18% improvement in matching the response distributions of human respondents and 27% improvement in consistency metrics. Our code and generated backstories are available at https://github.com/CannyLab/anthology.

We investigate the internal structure of language model computations using causal analysis and demonstrate two motifs: (1) a form of adaptive computation where ablations of one attention layer of a language model cause another layer to compensate (which we term the Hydra effect) and (2) a counterbalancing function of late MLP layers that act to downregulate the maximum-likelihood token. Our ablation studies demonstrate that language model layers are typically relatively loosely coupled (ablations to one layer only affect a small number of downstream layers). Surprisingly, these effects occur even in language models trained without any form of dropout. We analyse these effects in the context of factual recall and consider their implications for circuit-level attribution in language models.

Loneliness has been associated with negative outcomes for physical and mental health. Understanding how people express and cope with various forms of loneliness is critical for early screening and targeted interventions to reduce loneliness, particularly among vulnerable groups such as young adults. To examine how different forms of loneliness and coping strategies manifest in loneliness self-disclosure, we built a dataset, FIG-Loneliness (FIne-Grained Loneliness) by using Reddit posts in two young adult-focused forums and two loneliness related forums consisting of a diverse age group. We provided annotations by trained human annotators for binary and fine-grained loneliness classifications of the posts. Trained on FIG-Loneliness, two BERT-based models were used to understand loneliness forms and authors' coping strategies in these forums. Our binary loneliness classification achieved an accuracy above 97%, and fine-grained loneliness category classification reached an average accuracy of 77% across all labeled categories. With FIG-Loneliness and model predictions, we found that loneliness expressions in the young adults related forums were distinct from other forums. Those in young adult-focused forums were more likely to express concerns pertaining to peer relationship, and were potentially more sensitive to geographical isolation impacted by the COVID-19 pandemic lockdown. Also, we showed that different forms of loneliness have differential use in coping strategies.

In domains with high stakes such as law, recruitment, and healthcare, learning models frequently rely on sensitive user data for inference, necessitating the complete set of features. This not only poses significant privacy risks for individuals but also demands substantial human effort from organizations to verify information accuracy. This paper asks whether it is necessary to use all input features for accurate predictions at inference time. The paper demonstrates that, in a personalized setting, individuals may only need to disclose a small subset of their features without compromising decision-making accuracy. The paper also provides an efficient sequential algorithm to determine the appropriate attributes for each individual to provide. Evaluations across various learning tasks show that individuals can potentially report as little as 10\% of their information while maintaining the same accuracy level as a model that employs the full set of user information.

Summarization of clinical narratives is a long-standing research problem. Here, we introduce the task of hospital-course summarization. Given the documentation authored throughout a patient's hospitalization, generate a paragraph that tells the story of the patient admission. We construct an English, text-to-text dataset of 109,000 hospitalizations (2M source notes) and their corresponding summary proxy: the clinician-authored "Brief Hospital Course" paragraph written as part of a discharge note. Exploratory analyses reveal that the BHC paragraphs are highly abstractive with some long extracted fragments; are concise yet comprehensive; differ in style and content organization from the source notes; exhibit minimal lexical cohesion; and represent silver-standard references. Our analysis identifies multiple implications for modeling this complex, multi-document summarization task.

Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a novel numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including 3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at https://github.com/QizhiPei/BioT5.

We introduce a dataset of high-quality human-authored summaries of news articles in Norwegian. The dataset is intended for benchmarking the abstractive summarisation capabilities of generative language models. Each document in the dataset is provided with three different candidate gold-standard summaries written by native Norwegian speakers, and all summaries are provided in both of the written variants of Norwegian -- Bokm{\aa}l and Nynorsk. The paper describes details on the data creation effort as well as an evaluation of existing open LLMs for Norwegian on the dataset. We also provide insights from a manual human evaluation, comparing human-authored to model-generated summaries. Our results indicate that the dataset provides a challenging LLM benchmark for Norwegian summarisation capabilities