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SiT: Self-supervised vIsion Transformer

Self-supervised learning methods are gaining increasing traction in computer vision due to their recent success in reducing the gap with supervised learning. In natural language processing (NLP) self-supervised learning and transformers are already the methods of choice. The recent literature suggests that the transformers are becoming increasingly popular also in computer vision. So far, the vision transformers have been shown to work well when pretrained either using a large scale supervised data or with some kind of co-supervision, e.g. in terms of teacher network. These supervised pretrained vision transformers achieve very good results in downstream tasks with minimal changes. In this work we investigate the merits of self-supervised learning for pretraining image/vision transformers and then using them for downstream classification tasks. We propose Self-supervised vIsion Transformers (SiT) and discuss several self-supervised training mechanisms to obtain a pretext model. The architectural flexibility of SiT allows us to use it as an autoencoder and work with multiple self-supervised tasks seamlessly. We show that a pretrained SiT can be finetuned for a downstream classification task on small scale datasets, consisting of a few thousand images rather than several millions. The proposed approach is evaluated on standard datasets using common protocols. The results demonstrate the strength of the transformers and their suitability for self-supervised learning. We outperformed existing self-supervised learning methods by large margin. We also observed that SiT is good for few shot learning and also showed that it is learning useful representation by simply training a linear classifier on top of the learned features from SiT. Pretraining, finetuning, and evaluation codes will be available under: https://github.com/Sara-Ahmed/SiT.

SITTA: A Semantic Image-Text Alignment for Image Captioning

Textual and semantic comprehension of images is essential for generating proper captions. The comprehension requires detection of objects, modeling of relations between them, an assessment of the semantics of the scene and, finally, representing the extracted knowledge in a language space. To achieve rich language capabilities while ensuring good image-language mappings, pretrained language models (LMs) were conditioned on pretrained multi-modal (image-text) models that allow for image inputs. This requires an alignment of the image representation of the multi-modal model with the language representations of a generative LM. However, it is not clear how to best transfer semantics detected by the vision encoder of the multi-modal model to the LM. We introduce two novel ways of constructing a linear mapping that successfully transfers semantics between the embedding spaces of the two pretrained models. The first aligns the embedding space of the multi-modal language encoder with the embedding space of the pretrained LM via token correspondences. The latter leverages additional data that consists of image-text pairs to construct the mapping directly from vision to language space. Using our semantic mappings, we unlock image captioning for LMs without access to gradient information. By using different sources of data we achieve strong captioning performance on MS-COCO and Flickr30k datasets. Even in the face of limited data, our method partly exceeds the performance of other zero-shot and even finetuned competitors. Our ablation studies show that even LMs at a scale of merely 250M parameters can generate decent captions employing our semantic mappings. Our approach makes image captioning more accessible for institutions with restricted computational resources.

Situation Awareness for Driver-Centric Driving Style Adaptation

There is evidence that the driving style of an autonomous vehicle is important to increase the acceptance and trust of the passengers. The driving situation has been found to have a significant influence on human driving behavior. However, current driving style models only partially incorporate driving environment information, limiting the alignment between an agent and the given situation. Therefore, we propose a situation-aware driving style model based on different visual feature encoders pretrained on fleet data, as well as driving behavior predictors, which are adapted to the driving style of a specific driver. Our experiments show that the proposed method outperforms static driving styles significantly and forms plausible situation clusters. Furthermore, we found that feature encoders pretrained on our dataset lead to more precise driving behavior modeling. In contrast, feature encoders pretrained supervised and unsupervised on different data sources lead to more specific situation clusters, which can be utilized to constrain and control the driving style adaptation for specific situations. Moreover, in a real-world setting, where driving style adaptation is happening iteratively, we found the MLP-based behavior predictors achieve good performance initially but suffer from catastrophic forgetting. In contrast, behavior predictors based on situationdependent statistics can learn iteratively from continuous data streams by design. Overall, our experiments show that important information for driving behavior prediction is contained within the visual feature encoder. The dataset is publicly available at huggingface.co/datasets/jHaselberger/SADC-Situation-Awareness-for-Driver-Centric-Driving-Style-Adaptation.

Situated Language Learning via Interactive Narratives

This paper provides a roadmap that explores the question of how to imbue learning agents with the ability to understand and generate contextually relevant natural language in service of achieving a goal. We hypothesize that two key components in creating such agents are interactivity and environment grounding, shown to be vital parts of language learning in humans, and posit that interactive narratives should be the environments of choice for such training these agents. These games are simulations in which an agent interacts with the world through natural language -- "perceiving", "acting upon", and "talking to" the world using textual descriptions, commands, and dialogue -- and as such exist at the intersection of natural language processing, storytelling, and sequential decision making. We discuss the unique challenges a text games' puzzle-like structure combined with natural language state-and-action spaces provides: knowledge representation, commonsense reasoning, and exploration. Beyond the challenges described so far, progress in the realm of interactive narratives can be applied in adjacent problem domains. These applications provide interesting challenges of their own as well as extensions to those discussed so far. We describe three of them in detail: (1) evaluating AI system's commonsense understanding by automatically creating interactive narratives; (2) adapting abstract text-based policies to include other modalities such as vision; and (3) enabling multi-agent and human-AI collaboration in shared, situated worlds.

Multimodal Situational Safety

Multimodal Large Language Models (MLLMs) are rapidly evolving, demonstrating impressive capabilities as multimodal assistants that interact with both humans and their environments. However, this increased sophistication introduces significant safety concerns. In this paper, we present the first evaluation and analysis of a novel safety challenge termed Multimodal Situational Safety, which explores how safety considerations vary based on the specific situation in which the user or agent is engaged. We argue that for an MLLM to respond safely, whether through language or action, it often needs to assess the safety implications of a language query within its corresponding visual context. To evaluate this capability, we develop the Multimodal Situational Safety benchmark (MSSBench) to assess the situational safety performance of current MLLMs. The dataset comprises 1,820 language query-image pairs, half of which the image context is safe, and the other half is unsafe. We also develop an evaluation framework that analyzes key safety aspects, including explicit safety reasoning, visual understanding, and, crucially, situational safety reasoning. Our findings reveal that current MLLMs struggle with this nuanced safety problem in the instruction-following setting and struggle to tackle these situational safety challenges all at once, highlighting a key area for future research. Furthermore, we develop multi-agent pipelines to coordinately solve safety challenges, which shows consistent improvement in safety over the original MLLM response. Code and data: mssbench.github.io.

In-situ graph reasoning and knowledge expansion using Graph-PReFLexOR

The pursuit of automated scientific discovery has fueled progress from symbolic logic to modern AI, forging new frontiers in reasoning and pattern recognition. Transformers function as potential systems, where every possible relationship remains latent potentiality until tasks impose constraints, akin to measurement. Yet, refining their sampling requires more than probabilistic selection: solutions must conform to specific structures or rules, ensuring consistency and the invocation of general principles. We present Graph-PReFLexOR (Graph-based Preference-based Recursive Language Modeling for Exploratory Optimization of Reasoning), a framework that combines graph reasoning with symbolic abstraction to dynamically expand domain knowledge. Inspired by reinforcement learning, Graph-PReFLexOR defines reasoning as a structured mapping, where tasks yield knowledge graphs, abstract patterns, and ultimately, final answers. Inspired by category theory, it encodes concepts as nodes and their relationships as edges, supporting hierarchical inference and adaptive learning through isomorphic representations. Demonstrations include hypothesis generation, materials design, and creative reasoning, such as discovering relationships between mythological concepts like 'thin places' with materials science. We propose a 'knowledge garden growth' strategy that integrates insights across domains, promoting interdisciplinary connections. Results with a 3-billion-parameter Graph-PReFLexOR model show superior reasoning depth and adaptability, underscoring the potential for transparent, multidisciplinary AI-driven discovery. It lays the groundwork for general autonomous reasoning solutions.

Towards A Holistic Landscape of Situated Theory of Mind in Large Language Models

Large Language Models (LLMs) have generated considerable interest and debate regarding their potential emergence of Theory of Mind (ToM). Several recent inquiries reveal a lack of robust ToM in these models and pose a pressing demand to develop new benchmarks, as current ones primarily focus on different aspects of ToM and are prone to shortcuts and data leakage. In this position paper, we seek to answer two road-blocking questions: (1) How can we taxonomize a holistic landscape of machine ToM? (2) What is a more effective evaluation protocol for machine ToM? Following psychological studies, we taxonomize machine ToM into 7 mental state categories and delineate existing benchmarks to identify under-explored aspects of ToM. We argue for a holistic and situated evaluation of ToM to break ToM into individual components and treat LLMs as an agent who is physically situated in environments and socially situated in interactions with humans. Such situated evaluation provides a more comprehensive assessment of mental states and potentially mitigates the risk of shortcuts and data leakage. We further present a pilot study in a grid world setup as a proof of concept. We hope this position paper can facilitate future research to integrate ToM with LLMs and offer an intuitive means for researchers to better position their work in the landscape of ToM. Project page: https://github.com/Mars-tin/awesome-theory-of-mind

Enhancing Large Language Models' Situated Faithfulness to External Contexts

Large Language Models (LLMs) are often augmented with external information as contexts, but this external information can sometimes be inaccurate or even intentionally misleading. We argue that robust LLMs should demonstrate situated faithfulness, dynamically calibrating their trust in external information based on their confidence in the internal knowledge and the external context. To benchmark this capability, we evaluate LLMs across several QA datasets, including a newly created dataset called RedditQA featuring in-the-wild incorrect contexts sourced from Reddit posts. We show that when provided with both correct and incorrect contexts, both open-source and proprietary models tend to overly rely on external information, regardless of its factual accuracy. To enhance situated faithfulness, we propose two approaches: Self-Guided Confidence Reasoning (SCR) and Rule-Based Confidence Reasoning (RCR). SCR enables models to self-access the confidence of external information relative to their own internal knowledge to produce the most accurate answer. RCR, in contrast, extracts explicit confidence signals from the LLM and determines the final answer using predefined rules. Our results show that for LLMs with strong reasoning capabilities, such as GPT-4o and GPT-4o mini, SCR outperforms RCR, achieving improvements of up to 24.2% over a direct input augmentation baseline. Conversely, for a smaller model like Llama-3-8B, RCR outperforms SCR. Fine-tuning SCR with our proposed Confidence Reasoning Direct Preference Optimization (CR-DPO) method improves performance on both seen and unseen datasets, yielding an average improvement of 8.9% on Llama-3-8B. In addition to quantitative results, we offer insights into the relative strengths of SCR and RCR. Our findings highlight promising avenues for improving situated faithfulness in LLMs. The data and code are released.

Vision-based Situational Graphs Generating Optimizable 3D Scene Representations

3D scene graphs offer a more efficient representation of the environment by hierarchically organizing diverse semantic entities and the topological relationships among them. Fiducial markers, on the other hand, offer a valuable mechanism for encoding comprehensive information pertaining to environments and the objects within them. In the context of Visual SLAM (VSLAM), especially when the reconstructed maps are enriched with practical semantic information, these markers have the potential to enhance the map by augmenting valuable semantic information and fostering meaningful connections among the semantic objects. In this regard, this paper exploits the potential of fiducial markers to incorporate a VSLAM framework with hierarchical representations that generates optimizable multi-layered vision-based situational graphs. The framework comprises a conventional VSLAM system with low-level feature tracking and mapping capabilities bolstered by the incorporation of a fiducial marker map. The fiducial markers aid in identifying walls and doors in the environment, subsequently establishing meaningful associations with high-level entities, including corridors and rooms. Experimental results are conducted on a real-world dataset collected using various legged robots and benchmarked against a Light Detection And Ranging (LiDAR)-based framework (S-Graphs) as the ground truth. Consequently, our framework not only excels in crafting a richer, multi-layered hierarchical map of the environment but also shows enhancement in robot pose accuracy when contrasted with state-of-the-art methodologies.

Towards Collaborative Plan Acquisition through Theory of Mind Modeling in Situated Dialogue

Collaborative tasks often begin with partial task knowledge and incomplete initial plans from each partner. To complete these tasks, agents need to engage in situated communication with their partners and coordinate their partial plans towards a complete plan to achieve a joint task goal. While such collaboration seems effortless in a human-human team, it is highly challenging for human-AI collaboration. To address this limitation, this paper takes a step towards collaborative plan acquisition, where humans and agents strive to learn and communicate with each other to acquire a complete plan for joint tasks. Specifically, we formulate a novel problem for agents to predict the missing task knowledge for themselves and for their partners based on rich perceptual and dialogue history. We extend a situated dialogue benchmark for symmetric collaborative tasks in a 3D blocks world and investigate computational strategies for plan acquisition. Our empirical results suggest that predicting the partner's missing knowledge is a more viable approach than predicting one's own. We show that explicit modeling of the partner's dialogue moves and mental states produces improved and more stable results than without. These results provide insight for future AI agents that can predict what knowledge their partner is missing and, therefore, can proactively communicate such information to help their partner acquire such missing knowledge toward a common understanding of joint tasks.

DOROTHIE: Spoken Dialogue for Handling Unexpected Situations in Interactive Autonomous Driving Agents

In the real world, autonomous driving agents navigate in highly dynamic environments full of unexpected situations where pre-trained models are unreliable. In these situations, what is immediately available to vehicles is often only human operators. Empowering autonomous driving agents with the ability to navigate in a continuous and dynamic environment and to communicate with humans through sensorimotor-grounded dialogue becomes critical. To this end, we introduce Dialogue On the ROad To Handle Irregular Events (DOROTHIE), a novel interactive simulation platform that enables the creation of unexpected situations on the fly to support empirical studies on situated communication with autonomous driving agents. Based on this platform, we created the Situated Dialogue Navigation (SDN), a navigation benchmark of 183 trials with a total of 8415 utterances, around 18.7 hours of control streams, and 2.9 hours of trimmed audio. SDN is developed to evaluate the agent's ability to predict dialogue moves from humans as well as generate its own dialogue moves and physical navigation actions. We further developed a transformer-based baseline model for these SDN tasks. Our empirical results indicate that language guided-navigation in a highly dynamic environment is an extremely difficult task for end-to-end models. These results will provide insight towards future work on robust autonomous driving agents. The DOROTHIE platform, SDN benchmark, and code for the baseline model are available at https://github.com/sled-group/DOROTHIE.

Singapore Soundscape Site Selection Survey (S5): Identification of Characteristic Soundscapes of Singapore via Weighted k-means Clustering

The ecological validity of soundscape studies usually rests on a choice of soundscapes that are representative of the perceptual space under investigation. For example, a soundscape pleasantness study might investigate locations with soundscapes ranging from "pleasant" to "annoying". The choice of soundscapes is typically researcher-led, but a participant-led process can reduce selection bias and improve result reliability. Hence, we propose a robust participant-led method to pinpoint characteristic soundscapes possessing arbitrary perceptual attributes. We validate our method by identifying Singaporean soundscapes spanning the perceptual quadrants generated from the "Pleasantness" and "Eventfulness" axes of the ISO 12913-2 circumplex model of soundscape perception, as perceived by local experts. From memory and experience, 67 participants first selected locations corresponding to each perceptual quadrant in each major planning region of Singapore. We then performed weighted k-means clustering on the selected locations, with weights for each location derived from previous frequencies and durations spent in each location by each participant. Weights hence acted as proxies for participant confidence. In total, 62 locations were thereby identified as suitable locations with characteristic soundscapes for further research utilizing the ISO 12913-2 perceptual quadrants. Audio-visual recordings and acoustic characterization of the soundscapes will be made in a future study.

Autonomous In-Situ Soundscape Augmentation via Joint Selection of Masker and Gain

The selection of maskers and playback gain levels in a soundscape augmentation system is crucial to its effectiveness in improving the overall acoustic comfort of a given environment. Traditionally, the selection of appropriate maskers and gain levels has been informed by expert opinion, which may not representative of the target population, or by listening tests, which can be time-consuming and labour-intensive. Furthermore, the resulting static choices of masker and gain are often inflexible to the dynamic nature of real-world soundscapes. In this work, we utilized a deep learning model to perform joint selection of the optimal masker and its gain level for a given soundscape. The proposed model was designed with highly modular building blocks, allowing for an optimized inference process that can quickly search through a large number of masker and gain combinations. In addition, we introduced the use of feature-domain soundscape augmentation conditioned on the digital gain level, eliminating the computationally expensive waveform-domain mixing process during inference time, as well as the tedious pre-calibration process required for new maskers. The proposed system was validated on a large-scale dataset of subjective responses to augmented soundscapes with more than 440 participants, ensuring the ability of the model to predict combined effect of the masker and its gain level on the perceptual pleasantness level.

DREAM: Improving Situational QA by First Elaborating the Situation

When people answer questions about a specific situation, e.g., "I cheated on my mid-term exam last week. Was that wrong?", cognitive science suggests that they form a mental picture of that situation before answering. While we do not know how language models (LMs) answer such questions, we conjecture that they may answer more accurately if they are also provided with additional details about the question situation, elaborating the "scene". To test this conjecture, we train a new model, DREAM, to answer questions that elaborate the scenes that situated questions are about, and then provide those elaborations as additional context to a question-answering (QA) model. We find that DREAM is able to create better scene elaborations (more accurate, useful, and consistent) than a representative state-of-the-art, zero-shot model (Macaw). We also find that using the scene elaborations as additional context improves the answer accuracy of a downstream QA system, including beyond that obtainable by simply further finetuning the QA system on DREAM's training data. These results suggest that adding focused elaborations about a situation can improve a system's reasoning about it, and may serve as an effective way of injecting new scenario based knowledge into QA models. Finally, our approach is dataset-neutral; we observe improved QA performance across different models, with even bigger gains on models with fewer parameters. We make our dataset and model publicly available at https://github.com/allenai/dream.

Predicting sepsis in multi-site, multi-national intensive care cohorts using deep learning

Despite decades of clinical research, sepsis remains a global public health crisis with high mortality, and morbidity. Currently, when sepsis is detected and the underlying pathogen is identified, organ damage may have already progressed to irreversible stages. Effective sepsis management is therefore highly time-sensitive. By systematically analysing trends in the plethora of clinical data available in the intensive care unit (ICU), an early prediction of sepsis could lead to earlier pathogen identification, resistance testing, and effective antibiotic and supportive treatment, and thereby become a life-saving measure. Here, we developed and validated a machine learning (ML) system for the prediction of sepsis in the ICU. Our analysis represents the largest multi-national, multi-centre in-ICU study for sepsis prediction using ML to date. Our dataset contains 156,309 unique ICU admissions, which represent a refined and harmonised subset of five large ICU databases originating from three countries. Using the international consensus definition Sepsis-3, we derived hourly-resolved sepsis label annotations, amounting to 26,734 (17.1%) septic stays. We compared our approach, a deep self-attention model, to several clinical baselines as well as ML baselines and performed an extensive internal and external validation within and across databases. On average, our model was able to predict sepsis with an AUROC of 0.847 pm 0.050 (internal out-of sample validation) and 0.761 pm 0.052 (external validation). For a harmonised prevalence of 17%, at 80% recall our model detects septic patients with 39% precision 3.7 hours in advance.

WildFeedback: Aligning LLMs With In-situ User Interactions And Feedback

As large language models (LLMs) continue to advance, aligning these models with human preferences has emerged as a critical challenge. Traditional alignment methods, relying on human or LLM annotated datasets, are limited by their resource-intensive nature, inherent subjectivity, and the risk of feedback loops that amplify model biases. To overcome these limitations, we introduce WildFeedback, a novel framework that leverages real-time, in-situ user interactions to create preference datasets that more accurately reflect authentic human values. WildFeedback operates through a three-step process: feedback signal identification, preference data construction, and user-guided evaluation. We applied this framework to a large corpus of user-LLM conversations, resulting in a rich preference dataset that reflects genuine user preferences. This dataset captures the nuances of user preferences by identifying and classifying feedback signals within natural conversations, thereby enabling the construction of more representative and context-sensitive alignment data. Our extensive experiments demonstrate that LLMs fine-tuned on WildFeedback exhibit significantly improved alignment with user preferences, as evidenced by both traditional benchmarks and our proposed user-guided evaluation. By incorporating real-time feedback from actual users, WildFeedback addresses the scalability, subjectivity, and bias challenges that plague existing approaches, marking a significant step toward developing LLMs that are more responsive to the diverse and evolving needs of their users. In summary, WildFeedback offers a robust, scalable solution for aligning LLMs with true human values, setting a new standard for the development and evaluation of user-centric language models.

Immunohistochemistry guided segmentation of benign epithelial cells, in situ lesions, and invasive epithelial cells in breast cancer slides

Digital pathology enables automatic analysis of histopathological sections using artificial intelligence (AI). Automatic evaluation could improve diagnostic efficiency and help find associations between morphological features and clinical outcome. For development of such prediction models, identifying invasive epithelial cells, and separating these from benign epithelial cells and in situ lesions would be the first step. In this study, we aimed to develop an AI model for segmentation of epithelial cells in sections from breast cancer. We generated epithelial ground truth masks by restaining hematoxylin and eosin (HE) sections with cytokeratin (CK) AE1/AE3, and by pathologists' annotations. HE/CK image pairs were used to train a convolutional neural network, and data augmentation was used to make the model more robust. Tissue microarrays (TMAs) from 839 patients, and whole slide images from two patients were used for training and evaluation of the models. The sections were derived from four cohorts of breast cancer patients. TMAs from 21 patients from a fifth cohort was used as a second test set. In quantitative evaluation, a mean Dice score of 0.70, 0.79, and 0.75 for invasive epithelial cells, benign epithelial cells, and in situ lesions, respectively, were achieved. In qualitative scoring (0-5) by pathologists, results were best for all epithelium and invasive epithelium, with scores of 4.7 and 4.4. Scores for benign epithelium and in situ lesions were 3.7 and 2.0. The proposed model segmented epithelial cells in HE stained breast cancer slides well, but further work is needed for accurate division between the classes. Immunohistochemistry, together with pathologists' annotations, enabled the creation of accurate ground truths. The model is made freely available in FastPathology and the code is available at https://github.com/AICAN-Research/breast-epithelium-segmentation

Tracing the cosmological origin of gas that fuels in situ star formation in TNG50 galaxies

Based on their cosmological origin, the stars of a galaxy can be divided into two categories: those that enter through merger events (ex situ) and those born in the main progenitor (in situ). We used the TNG50 cosmological magnetohydrodynamical simulation and its Lagrangian tracer particles to explore and quantify the origin of gas that ultimately forms the in situ stars of galaxies. We tracked back the baryonic mass contributing to the z=0 in situ stellar populations of galaxies, studying trends in mass from dwarfs to group-scale halos. We find that more massive halos acquire this matter earlier than lower-mass halos, reflecting an overall earlier assembly of their in situ stellar mass. Defining the Lagrangian half-mass radius R_{rm L, 1/2} of a galaxy as the distance containing half of the mass that will form its in situ stars by z=0, we find that R_{rm L, 1/2} is larger for more massive halos at early times, reflecting larger "in situ Lagrangian regions." However, the dependence of this radius on halo mass becomes flat at z simeq 3 and then inverts toward z=0. In addition, R_{rm L, 1/2} increases rapidly with redshift, surpassing the virial radii of halos at z sim 2. This marks the cosmic epoch at which most of the gas that eventually forms the in situ stars of galaxies leaves the intergalactic medium (IGM) and enters halos, a transition that occurs earlier for more massive halos. The formation redshift of the in situ stellar component increases with halo mass, while the formation redshift of the dark matter halo decreases, indicative of a differential assembly history between these two components. Finally, we decomposed the z=0 in situ stellar mass into its distinct modes of accretion. Smooth accretion from the IGM is the most important for low-mass galaxies, while mergers and satellite-stripped gas become relevant and even dominant only for high-mass galaxies.

When Neural Code Completion Models Size up the Situation: Attaining Cheaper and Faster Completion through Dynamic Model Inference

Leveraging recent advancements in large language models, modern neural code completion models have demonstrated the capability to generate highly accurate code suggestions. However, their massive size poses challenges in terms of computational costs and environmental impact, hindering their widespread adoption in practical scenarios. Dynamic inference emerges as a promising solution, as it allocates minimal computation during inference while maintaining the model's performance. In this research, we explore dynamic inference within the context of code completion. Initially, we conducted an empirical investigation on GPT-2, focusing on the inference capabilities of intermediate layers for code completion. We found that 54.4% of tokens can be accurately generated using just the first layer, signifying significant computational savings potential. Moreover, despite using all layers, the model still fails to predict 14.5% of tokens correctly, and the subsequent completions continued from them are rarely considered helpful, with only a 4.2% Acceptance Rate. These findings motivate our exploration of dynamic inference in code completion and inspire us to enhance it with a decision-making mechanism that stops the generation of incorrect code. We thus propose a novel dynamic inference method specifically tailored for code completion models. This method aims not only to produce correct predictions with largely reduced computation but also to prevent incorrect predictions proactively. Our extensive evaluation shows that it can averagely skip 1.7 layers out of 16 layers in the models, leading to an 11.2% speedup with only a marginal 1.1% reduction in ROUGE-L.

Machine learning applications to DNA subsequence and restriction site analysis

Based on the BioBricks standard, restriction synthesis is a novel catabolic iterative DNA synthesis method that utilizes endonucleases to synthesize a query sequence from a reference sequence. In this work, the reference sequence is built from shorter subsequences by classifying them as applicable or inapplicable for the synthesis method using three different machine learning methods: Support Vector Machines (SVMs), random forest, and Convolution Neural Networks (CNNs). Before applying these methods to the data, a series of feature selection, curation, and reduction steps are applied to create an accurate and representative feature space. Following these preprocessing steps, three different pipelines are proposed to classify subsequences based on their nucleotide sequence and other relevant features corresponding to the restriction sites of over 200 endonucleases. The sensitivity using SVMs, random forest, and CNNs are 94.9%, 92.7%, 91.4%, respectively. Moreover, each method scores lower in specificity with SVMs, random forest, and CNNs resulting in 77.4%, 85.7%, and 82.4%, respectively. In addition to analyzing these results, the misclassifications in SVMs and CNNs are investigated. Across these two models, different features with a derived nucleotide specificity visually contribute more to classification compared to other features. This observation is an important factor when considering new nucleotide sensitivity features for future studies.

Wearable data from subjects playing Super Mario, sitting university exams, or performing physical exercise help detect acute mood episodes via self-supervised learning

Personal sensing, leveraging data passively and near-continuously collected with wearables from patients in their ecological environment, is a promising paradigm to monitor mood disorders (MDs), a major determinant of worldwide disease burden. However, collecting and annotating wearable data is very resource-intensive. Studies of this kind can thus typically afford to recruit only a couple dozens of patients. This constitutes one of the major obstacles to applying modern supervised machine learning techniques to MDs detection. In this paper, we overcome this data bottleneck and advance the detection of MDs acute episode vs stable state from wearables data on the back of recent advances in self-supervised learning (SSL). This leverages unlabelled data to learn representations during pre-training, subsequently exploited for a supervised task. First, we collected open-access datasets recording with an Empatica E4 spanning different, unrelated to MD monitoring, personal sensing tasks -- from emotion recognition in Super Mario players to stress detection in undergraduates -- and devised a pre-processing pipeline performing on-/off-body detection, sleep-wake detection, segmentation, and (optionally) feature extraction. With 161 E4-recorded subjects, we introduce E4SelfLearning, the largest to date open access collection, and its pre-processing pipeline. Second, we show that SSL confidently outperforms fully-supervised pipelines using either our novel E4-tailored Transformer architecture (E4mer) or classical baseline XGBoost: 81.23% against 75.35% (E4mer) and 72.02% (XGBoost) correctly classified recording segments from 64 (half acute, half stable) patients. Lastly, we illustrate that SSL performance is strongly associated with the specific surrogate task employed for pre-training as well as with unlabelled data availability.

Can You Follow Me? Testing Situational Understanding in ChatGPT

Understanding sentence meanings and updating information states appropriately across time -- what we call "situational understanding" (SU) -- is a critical ability for human-like AI agents. SU is essential in particular for chat models, such as ChatGPT, to enable consistent, coherent, and effective dialogue between humans and AI. Previous works have identified certain SU limitations in non-chatbot Large Language models (LLMs), but the extent and causes of these limitations are not well understood, and capabilities of current chat-based models in this domain have not been explored. In this work we tackle these questions, proposing a novel synthetic environment for SU testing which allows us to do controlled and systematic testing of SU in chat-oriented models, through assessment of models' ability to track and enumerate environment states. Our environment also allows for close analysis of dynamics of model performance, to better understand underlying causes for performance patterns. We apply our test to ChatGPT, the state-of-the-art chatbot, and find that despite the fundamental simplicity of the task, the model's performance reflects an inability to retain correct environment states across time. Our follow-up analyses suggest that performance degradation is largely because ChatGPT has non-persistent in-context memory (although it can access the full dialogue history) and it is susceptible to hallucinated updates -- including updates that artificially inflate accuracies. Our findings suggest overall that ChatGPT is not currently equipped for robust tracking of situation states, and that trust in the impressive dialogue performance of ChatGPT comes with risks. We release the codebase for reproducing our test environment, as well as all prompts and API responses from ChatGPT, at https://github.com/yangalan123/SituationalTesting.

Learning Disentangled Identifiers for Action-Customized Text-to-Image Generation

This study focuses on a novel task in text-to-image (T2I) generation, namely action customization. The objective of this task is to learn the co-existing action from limited data and generalize it to unseen humans or even animals. Experimental results show that existing subject-driven customization methods fail to learn the representative characteristics of actions and struggle in decoupling actions from context features, including appearance. To overcome the preference for low-level features and the entanglement of high-level features, we propose an inversion-based method Action-Disentangled Identifier (ADI) to learn action-specific identifiers from the exemplar images. ADI first expands the semantic conditioning space by introducing layer-wise identifier tokens, thereby increasing the representational richness while distributing the inversion across different features. Then, to block the inversion of action-agnostic features, ADI extracts the gradient invariance from the constructed sample triples and masks the updates of irrelevant channels. To comprehensively evaluate the task, we present an ActionBench that includes a variety of actions, each accompanied by meticulously selected samples. Both quantitative and qualitative results show that our ADI outperforms existing baselines in action-customized T2I generation. Our project page is at https://adi-t2i.github.io/ADI.

Jatmo: Prompt Injection Defense by Task-Specific Finetuning

Large Language Models (LLMs) are attracting significant research attention due to their instruction-following abilities, allowing users and developers to leverage LLMs for a variety of tasks. However, LLMs are vulnerable to prompt-injection attacks: a class of attacks that hijack the model's instruction-following abilities, changing responses to prompts to undesired, possibly malicious ones. In this work, we introduce Jatmo, a method for generating task-specific models resilient to prompt-injection attacks. Jatmo leverages the fact that LLMs can only follow instructions once they have undergone instruction tuning. It harnesses a teacher instruction-tuned model to generate a task-specific dataset, which is then used to fine-tune a base model (i.e., a non-instruction-tuned model). Jatmo only needs a task prompt and a dataset of inputs for the task: it uses the teacher model to generate outputs. For situations with no pre-existing datasets, Jatmo can use a single example, or in some cases none at all, to produce a fully synthetic dataset. Our experiments on six tasks show that Jatmo models provide the same quality of outputs on their specific task as standard LLMs, while being resilient to prompt injections. The best attacks succeeded in less than 0.5% of cases against our models, versus over 90% success rate against GPT-3.5-Turbo. We release Jatmo at https://github.com/wagner-group/prompt-injection-defense.

PubDef: Defending Against Transfer Attacks From Public Models

Adversarial attacks have been a looming and unaddressed threat in the industry. However, through a decade-long history of the robustness evaluation literature, we have learned that mounting a strong or optimal attack is challenging. It requires both machine learning and domain expertise. In other words, the white-box threat model, religiously assumed by a large majority of the past literature, is unrealistic. In this paper, we propose a new practical threat model where the adversary relies on transfer attacks through publicly available surrogate models. We argue that this setting will become the most prevalent for security-sensitive applications in the future. We evaluate the transfer attacks in this setting and propose a specialized defense method based on a game-theoretic perspective. The defenses are evaluated under 24 public models and 11 attack algorithms across three datasets (CIFAR-10, CIFAR-100, and ImageNet). Under this threat model, our defense, PubDef, outperforms the state-of-the-art white-box adversarial training by a large margin with almost no loss in the normal accuracy. For instance, on ImageNet, our defense achieves 62% accuracy under the strongest transfer attack vs only 36% of the best adversarially trained model. Its accuracy when not under attack is only 2% lower than that of an undefended model (78% vs 80%). We release our code at https://github.com/wagner-group/pubdef.

Require Process Control? LSTMc is all you need!

Over the past three decades, numerous controllers have been developed to regulate complex chemical processes, but they have certain limitations. Traditional PI/PID controllers often require customized tuning for various set-point scenarios. On the other hand, MPC frameworks involve resource-intensive steps, and the utilization of black-box machine learning (ML) models can lead to issues such as local minima and infeasibility. Thus, there is a need for an alternative controller paradigm that combines the simplicity of a PI controller with the grade-to-grade (G2G) transferability of an MPC approach. To this end, we developed a novel LSTM controller (LSTMc) as a model-free data-driven controller framework. The LSTMc considers an augmented input tensor that incorporates information on state evolution and error dynamics for the current and previous W time steps, to predict the manipulated input at the next step (u_{t+1}). To demonstrate LSTMc, batch crystallization of dextrose was taken as a representative case study. The desired output for set-point tracking was the mean crystal size (L), with the manipulated input being the jacket temperature (T_j). Extensive training data, encompassing 7000+ different operating conditions, was compiled to ensure comprehensive training of LSTMc across a wide state space region. For comparison, we also designed a PI controller and an LSTM-MPC for different set-point tracking cases. The results consistently showed that LSTMc achieved the lowest set-point deviation (<2\%), three times lower than the MPC. Remarkably, LSTMc maintained this superior performance across all set points, even when sensor measurements contained noise levels of 10\% to 15\%. In summary, by effectively leveraging process data and utilizing sequential ML models, LSTMc offers a superior controller design approach.