Daily Papers

Protein-protein interactions (PPIs) are fundamental to numerous cellular processes, and their characterization is vital for understanding disease mechanisms and guiding drug discovery. While protein language models (PLMs) have demonstrated remarkable success in predicting protein structure and function, their application to sequence-based PPI binding affinity prediction remains relatively underexplored. This gap is often attributed to the scarcity of high-quality, rigorously refined datasets and the reliance on simple strategies for concatenating protein representations. In this work, we address these limitations. First, we introduce a meticulously curated version of the PPB-Affinity dataset of a total of 8,207 unique protein-protein interaction entries, by resolving annotation inconsistencies and duplicate entries for multi-chain protein interactions. This dataset incorporates a stringent, less than or equal to 30%, sequence identity threshold to ensure robust splitting into training, validation, and test sets, minimizing data leakage. Second, we propose and systematically evaluate four architectures for adapting PLMs to PPI binding affinity prediction: embeddings concatenation (EC), sequences concatenation (SC), hierarchical pooling (HP), and pooled attention addition (PAD). These architectures were assessed using two training methods: full fine-tuning and a lightweight approach employing ConvBERT heads over frozen PLM features. Our comprehensive experiments across multiple leading PLMs (ProtT5, ESM2, Ankh, Ankh2, and ESM3) demonstrated that the HP and PAD architectures consistently outperform conventional concatenation methods, achieving up to 12% increase in terms of Spearman correlation. These results highlight the necessity of sophisticated architectural designs to fully exploit the capabilities of PLMs for nuanced PPI binding affinity prediction.

Pretrained contextualized embeddings are powerful word representations for structured prediction tasks. Recent work found that better word representations can be obtained by concatenating different types of embeddings. However, the selection of embeddings to form the best concatenated representation usually varies depending on the task and the collection of candidate embeddings, and the ever-increasing number of embedding types makes it a more difficult problem. In this paper, we propose Automated Concatenation of Embeddings (ACE) to automate the process of finding better concatenations of embeddings for structured prediction tasks, based on a formulation inspired by recent progress on neural architecture search. Specifically, a controller alternately samples a concatenation of embeddings, according to its current belief of the effectiveness of individual embedding types in consideration for a task, and updates the belief based on a reward. We follow strategies in reinforcement learning to optimize the parameters of the controller and compute the reward based on the accuracy of a task model, which is fed with the sampled concatenation as input and trained on a task dataset. Empirical results on 6 tasks and 21 datasets show that our approach outperforms strong baselines and achieves state-of-the-art performance with fine-tuned embeddings in all the evaluations.

Laboratory test results are an important and generally high dimensional component of a patient's Electronic Health Record (EHR). We train embedding representations (via Word2Vec and GloVe) for LOINC codes of laboratory tests from the EHRs of about 80,000 patients at a cancer center. To include information about lab test outcomes, we also train embeddings on the concatenation of a LOINC code with a symbol indicating normality or abnormality of the result. We observe several clinically meaningful similarities among LOINC embeddings trained over our data. For the embeddings of the concatenation of LOINCs with abnormality codes, we evaluate the performance for mortality prediction tasks and the ability to preserve ordinality properties: i.e. a lab test with normal outcome should be more similar to an abnormal one than to the a very abnormal one.

Tables are a popular and efficient means of presenting structured information. They are used extensively in various kinds of documents including web pages. Tables display information as a two-dimensional matrix, the semantics of which is conveyed by a mixture of structure (rows, columns), headers, caption, and content. Recent research has started to consider tables as first class objects, not just as an addendum to texts, yielding interesting results for problems like table matching, table completion, or value imputation. All of these problems inherently rely on an accurate measure for the semantic similarity of two tables. We present TabSim, a novel method to compute table similarity scores using deep neural networks. Conceptually, TabSim represents a table as a learned concatenation of embeddings of its caption, its content, and its structure. Given two tables in this representation, a Siamese neural network is trained to compute a score correlating with the tables' semantic similarity. To train and evaluate our method, we created a gold standard corpus consisting of 1500 table pairs extracted from biomedical articles and manually scored regarding their degree of similarity, and adopted two other corpora originally developed for a different yet similar task. Our evaluation shows that TabSim outperforms other table similarity measures on average by app. 7% pp F1-score in a binary similarity classification setting and by app. 1.5% pp in a ranking scenario.

Multi-label text classification is a critical task in the industry. It helps to extract structured information from large amount of textual data. We propose Text to Topic (Text2Topic), which achieves high multi-label classification performance by employing a Bi-Encoder Transformer architecture that utilizes concatenation, subtraction, and multiplication of embeddings on both text and topic. Text2Topic also supports zero-shot predictions, produces domain-specific text embeddings, and enables production-scale batch-inference with high throughput. The final model achieves accurate and comprehensive results compared to state-of-the-art baselines, including large language models (LLMs). In this study, a total of 239 topics are defined, and around 1.6 million text-topic pairs annotations (in which 200K are positive) are collected on approximately 120K texts from 3 main data sources on Booking.com. The data is collected with optimized smart sampling and partial labeling. The final Text2Topic model is deployed on a real-world stream processing platform, and it outperforms other models with 92.9% micro mAP, as well as a 75.8% macro mAP score. We summarize the modeling choices which are extensively tested through ablation studies, and share detailed in-production decision-making steps.

We introduce ObjectAdd, a training-free diffusion modification method to add user-expected objects into user-specified area. The motive of ObjectAdd stems from: first, describing everything in one prompt can be difficult, and second, users often need to add objects into the generated image. To accommodate with real world, our ObjectAdd maintains accurate image consistency after adding objects with technical innovations in: (1) embedding-level concatenation to ensure correct text embedding coalesce; (2) object-driven layout control with latent and attention injection to ensure objects accessing user-specified area; (3) prompted image inpainting in an attention refocusing & object expansion fashion to ensure rest of the image stays the same. With a text-prompted image, our ObjectAdd allows users to specify a box and an object, and achieves: (1) adding object inside the box area; (2) exact content outside the box area; (3) flawless fusion between the two areas

Any-to-any singing voice conversion is confronted with a significant challenge of ``timbre leakage'' issue caused by inadequate disentanglement between the content and the speaker timbre. To address this issue, this study introduces a novel neural concatenative singing voice conversion (NeuCoSVC) framework. The NeuCoSVC framework comprises a self-supervised learning (SSL) representation extractor, a neural harmonic signal generator, and a waveform synthesizer. Specifically, the SSL extractor condenses the audio into a sequence of fixed-dimensional SSL features. The harmonic signal generator produces both raw and filtered harmonic signals as the pitch information by leveraging a linear time-varying (LTV) filter. Finally, the audio generator reconstructs the audio waveform based on the SSL features, as well as the harmonic signals and the loudness information. During inference, the system performs voice conversion by substituting source SSL features with their nearest counterparts from a matching pool, which comprises SSL representations extracted from the target audio, while the raw harmonic signals and the loudness are extracted from the source audio and are kept unchanged. Since the utilized SSL features in the conversion stage are directly from the target audio, the proposed framework has great potential to address the ``timbre leakage'' issue caused by previous disentanglement-based approaches. Experimental results confirm that the proposed system delivers much better performance than the speaker embedding approach (disentanglement-based) in the context of one-shot SVC across intra-language, cross-language, and cross-domain evaluations.

While large language models (LLMs) excel on generation tasks, their decoder-only architecture often limits their potential as embedding models if no further representation finetuning is applied. Does this contradict their claim of generalists? To answer the question, we take a closer look at Mixture-of-Experts (MoE) LLMs. Our study shows that the expert routers in MoE LLMs can serve as an off-the-shelf embedding model with promising performance on a diverse class of embedding-focused tasks, without requiring any finetuning. Moreover, our extensive analysis shows that the MoE routing weights (RW) is complementary to the hidden state (HS) of LLMs, a widely-used embedding. Compared to HS, we find that RW is more robust to the choice of prompts and focuses on high-level semantics. Motivated by the analysis, we propose MoEE combining RW and HS, which achieves better performance than using either separately. Our exploration of their combination and prompting strategy shed several novel insights, e.g., a weighted sum of RW and HS similarities outperforms the similarity on their concatenation. Our experiments are conducted on 6 embedding tasks with 20 datasets from the Massive Text Embedding Benchmark (MTEB). The results demonstrate the significant improvement brought by MoEE to LLM-based embedding without further finetuning.

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.

This paper concerns the research problem of point cloud registration to find the rigid transformation to optimally align the source point set with the target one. Learning robust point cloud registration models with deep neural networks has emerged as a powerful paradigm, offering promising performance in predicting the global geometric transformation for a pair of point sets. Existing methods firstly leverage an encoder to regress a latent shape embedding, which is then decoded into a shape-conditioned transformation via concatenation-based conditioning. However, different regions of a 3D shape vary in their geometric structures which makes it more sense that we have a region-conditioned transformation instead of the shape-conditioned one. In this paper we present a Region-Aware point cloud Registration, denoted as RAR, to predict transformation for pairwise point sets in the self-supervised learning fashion. More specifically, we develop a novel region-aware decoder (RAD) module that is formed with an implicit neural region representation parameterized by neural networks. The implicit neural region representation is learned with a self-supervised 3D shape reconstruction loss without the need for region labels. Consequently, the region-aware decoder (RAD) module guides the training of the region-aware transformation (RAT) module and region-aware weight (RAW) module, which predict the transforms and weights for different regions respectively. The global geometric transformation from source point set to target one is then formed by the weighted fusion of region-aware transforms. Compared to the state-of-the-art approaches, our experiments show that our RAR achieves superior registration performance over various benchmark datasets (e.g. ModelNet40).

We are creating multimedia contents everyday and everywhere. While automatic content generation has played a fundamental challenge to multimedia community for decades, recent advances of deep learning have made this problem feasible. For example, the Generative Adversarial Networks (GANs) is a rewarding approach to synthesize images. Nevertheless, it is not trivial when capitalizing on GANs to generate videos. The difficulty originates from the intrinsic structure where a video is a sequence of visually coherent and semantically dependent frames. This motivates us to explore semantic and temporal coherence in designing GANs to generate videos. In this paper, we present a novel Temporal GANs conditioning on Captions, namely TGANs-C, in which the input to the generator network is a concatenation of a latent noise vector and caption embedding, and then is transformed into a frame sequence with 3D spatio-temporal convolutions. Unlike the naive discriminator which only judges pairs as fake or real, our discriminator additionally notes whether the video matches the correct caption. In particular, the discriminator network consists of three discriminators: video discriminator classifying realistic videos from generated ones and optimizes video-caption matching, frame discriminator discriminating between real and fake frames and aligning frames with the conditioning caption, and motion discriminator emphasizing the philosophy that the adjacent frames in the generated videos should be smoothly connected as in real ones. We qualitatively demonstrate the capability of our TGANs-C to generate plausible videos conditioning on the given captions on two synthetic datasets (SBMG and TBMG) and one real-world dataset (MSVD). Moreover, quantitative experiments on MSVD are performed to validate our proposal via Generative Adversarial Metric and human study.