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Molecular Relational Learning (MRL) aims to understand interactions between molecular pairs, playing a critical role in advancing biochemical research. With the recent development of large language models (LLMs), a growing number of studies…

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers…

3D structural Magnetic Resonance Imaging (MRI) brain scans are commonly acquired in clinical settings to monitor a wide range of neurological conditions, including neurodegenerative disorders and stroke. While deep learning models have…

In language processing, training data with extremely large variance may lead to difficulty in the language model's convergence. It is difficult for the network parameters to adapt sentences with largely varied semantics or grammatical…

Tables stored in databases and tables which are present in web pages and articles account for a large part of semi-structured data that is available on the internet. It then becomes pertinent to develop a modeling approach with large…

The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding. Despite the success of LLMs in NLP, their effectiveness in…

Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…

In computational biophysics, where molecular data is expanding rapidly and system complexity is increasing exponentially, large language models (LLMs) and agent-based systems are fundamentally reshaping the field. This perspective article…

Language model (LM) pre-training is useful in many language processing tasks. But can pre-trained LMs be further leveraged for more general machine learning problems? We propose an approach for using LMs to scaffold learning and…

Active learning (AL) accelerates scientific discovery by prioritizing the most informative experiments, but traditional machine learning (ML) models used in AL suffer from cold-start limitations and domain-specific feature engineering,…

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…

Anatomy evaluation is crucial for understanding the physiological state, diagnosing abnormalities, and guiding medical interventions. Statistical shape modeling (SSM) is vital in this process. By enabling the extraction of quantitative…

Automated disease diagnosis using medical image analysis relies on deep learning, often requiring large labeled datasets for supervised model training. Diseases like Acute Myeloid Leukemia (AML) pose challenges due to scarce and costly…

Randomized controlled trials are a cornerstone of medicine and the social sciences as they enable reliable estimates of causal effects. However, they are costly and time-consuming to conduct, motivating interest in predicting causal effects…

Protein-specific large language models (Protein LLMs) are revolutionizing protein science by enabling more efficient protein structure prediction, function annotation, and design. While existing surveys focus on specific aspects or…

Identifying drug-target interactions is essential for developing effective therapeutics. Binding affinity quantifies these interactions, and traditional approaches rely on computationally intensive 3D structural data. In contrast, language…

Sequence-to-sequence models provide a simple and elegant solution for building speech recognition systems by folding separate components of a typical system, namely acoustic (AM), pronunciation (PM) and language (LM) models into a single…

The emergence of Large Language Models (LLMs) presents unprecedented opportunities to revolutionize medical contrastive vision-language pre-training. In this paper, we show how LLMs can facilitate large-scale supervised pre-training,…

Computational prediction of the interaction of T cell receptors (TCRs) and their ligands is a grand challenge in immunology. Despite advances in high-throughput assays, specificity-labelled TCR data remains sparse. In other domains, the…

Forecasting the short-term spread of an ongoing disease outbreak is a formidable challenge due to the complexity of contributing factors, some of which can be characterized through interlinked, multi-modality variables such as…