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Multimodal learning typically relies on the assumption that all modalities are fully available during both the training and inference phases. However, in real-world scenarios, consistently acquiring complete multimodal data presents…

Pre-trained Large Language Models (LLMs) encapsulate large amounts of knowledge and take enormous amounts of compute to train. We make use of this resource, together with the observation that LLMs are able to transfer knowledge and…

Recent advancements in immune sequencing and experimental techniques are generating extensive T cell receptor (TCR) repertoire data, enabling the development of models to predict TCR binding specificity. Despite the computational challenges…

Pre-trained protein language models have demonstrated significant applicability in different protein engineering task. A general usage of these pre-trained transformer models latent representation is to use a mean pool across residue…

Medical report generation from imaging data remains a challenging task in clinical practice. While large language models (LLMs) show great promise in addressing this challenge, their effective integration with medical imaging data still…

Large Multimodal Models (LMMs), or Vision-Language Models (VLMs), have shown impressive capabilities in a wide range of visual tasks. However, they often struggle with fine-grained visual reasoning, failing to identify domain-specific…

The adoption of large language models (LLMs) in healthcare has attracted significant research interest. However, their performance in healthcare remains under-investigated and potentially limited, due to i) they lack rich domain-specific…

Biomedical data is inherently multimodal, consisting of electronic health records, medical imaging, digital pathology, genome sequencing, wearable sensors, and more. The application of artificial intelligence tools to these multifaceted…

Artificial intelligence (AI) technology has advanced rapidly in recent years, with large language models (LLMs) emerging as a significant breakthrough. LLMs are increasingly making an impact across various industries, with the medical field…

Fine-tuning-as-a-service introduces a threat to Large Language Models' safety when service providers fine-tune their models on poisoned user-submitted datasets, a process known as harmful fine-tuning attacks. In this work, we show that by…

Medical Decision-Making (MDM) is a multi-faceted process that requires clinicians to assess complex multi-modal patient data patient, often collaboratively. Large Language Models (LLMs) promise to streamline this process by synthesizing…

Medical diagnosis requires the effective synthesis of visual manifestations and clinical metadata. However, existing methods often treat metadata as isolated tags, failing to exploit the rich semantic knowledge embedded in clinical…

When nanoparticles (NPs) are introduced into a biological solution, layers of biomolecules form on their surface, creating a corona. Understanding how the structure of the protein evolves into the corona is essential for evaluating the…

Safety aligned Large Language Models (LLMs) are vulnerable to harmful fine-tuning attacks -- a few harmful data mixed in the fine-tuning dataset can break the LLMs's safety alignment. While several defenses have been proposed, our…

Feature transformation aims to reconstruct the feature space of raw features to enhance the performance of downstream models. However, the exponential growth in the combinations of features and operations poses a challenge, making it…

Artificial intelligence (AI) is accelerating progress in modeling T and B cell receptors by enabling predictive and generative frameworks grounded in sequence data and immune context. This chapter surveys recent advances in the use of…

As a prominent direction of Artificial General Intelligence (AGI), Multimodal Large Language Models (MLLMs) have garnered increased attention from both industry and academia. Building upon pre-trained LLMs, this family of models further…

Deep learning has transformed protein design, enabling accurate structure prediction, sequence optimization, and de novo protein generation. Advances in single-chain protein structure prediction via AlphaFold2, RoseTTAFold, ESMFold, and…

Prompt-based learning has been demonstrated as a compelling paradigm contributing to large language models' tremendous success (LLMs). Inspired by their success in language tasks, existing research has leveraged LLMs in embodied instruction…

Medical decision-making requires integrating diverse medical information, from imaging to clinical narratives. These medical modalities are often acquired in a many-to-many manner. However, current medical vision-language pretraining models…