Related papers: Quantifying Cross-Attention Interaction in Transfo…

In silico prediction of drug-target interactions (DTI) is significant for drug discovery because it can largely reduce timelines and costs in the drug development process. Specifically, deep learning-based DTI approaches have been shown…

Human-object interaction (HOI) detection as a downstream of object detection tasks requires localizing pairs of humans and objects and extracting the semantic relationships between humans and objects from an image. Recently, one-stage…

Accurate and robust drug response prediction is of utmost importance in precision medicine. Although many models have been developed to utilize the representations of drugs and cancer cell lines for predicting cancer drug responses (CDR),…

T cells are central to the adaptive immune response, capable of detecting pathogenic antigens while ignoring healthy tissues with remarkable specificity and sensitivity. Quantitatively understanding how T cell receptors (TCRs) discriminate…

Explainable Artificial Intelligence (XAI) is essential for the transparency and clinical adoption of Clinical Decision Support Systems (CDSS). However, the real-world effectiveness of existing XAI methods remains limited and is…

Transformer networks have achieved remarkable success across diverse domains, leveraging a variety of architectural innovations, including residual connections. However, traditional residual connections, which simply sum the outputs of…

T cells monitor the health status of cells by identifying foreign peptides displayed on their surface. T-cell receptors (TCRs), which are protein complexes found on the surface of T cells, are able to bind to these peptides. This process is…

Motivation: The activity of the adaptive immune system is governed by T-cells and their specific T-cell receptors (TCR), which selectively recognize foreign antigens. Recent advances in experimental techniques have enabled sequencing of…

Recently, machine learning (ML) has gained popularity in the early stages of drug discovery. This trend is unsurprising given the increasing volume of relevant experimental data and the continuous improvement of ML algorithms. However,…

While deep learning models play a crucial role in predicting antibody-antigen interactions (AAI), the scarcity of publicly available sequence-structure pairings constrains their generalization. Current AAI methods often focus on…

T cell receptors (TCRs) bind foreign or self-peptides attached to major histocompatibility complex (MHC) molecules, and the strength of this interaction determines T cell activation. Optimizing the ability of T cells to recognize a…

Following the major successes of self-attention and Transformers for image analysis, we investigate the use of such attention mechanisms in the context of Image Quality Assessment (IQA) and propose a novel full-reference IQA method, Vision…

The attention module is the key component in Transformers. While the global attention mechanism offers high expressiveness, its excessive computational cost restricts its applicability in various scenarios. In this paper, we propose a novel…

Understanding cellular mechanisms requires integrating information across DNA, RNA, and protein - the three molecular systems linked by the Central Dogma of molecular biology. While domain-specific foundation models have achieved success…

The anti-cancer immune response relies on the bindings between T-cell receptors (TCRs) and antigens, which elicits adaptive immunity to eliminate tumor cells. This ability of the immune system to respond to novel various neoantigens arises…

Attention is fundamental to cognition, yet it remains a challenge to understand attention in tasks approaching real-world complexity. Here, we approached this problem by modeling gaze patterns of monkeys playing Pac-Man. We first show a…

International Classification of Disease (ICD) coding procedure which refers to tagging medical notes with diagnosis codes has been shown to be effective and crucial to the billing system in medical sector. Currently, ICD codes are assigned…

Survival prediction, utilizing pathological images and genomic profiles, is increasingly important in cancer analysis and prognosis. Despite significant progress, precise survival analysis still faces two main challenges: (1) The massive…

Major histocompatibility complex class two (MHC-II) molecules are trans-membrane proteins and key components of the cellular immune system. Upon recognition of foreign peptides expressed on the MHC-II binding groove, helper T cells mount an…

Multimodal Diffusion Transformers (MM-DiTs) have achieved remarkable progress in text-driven visual generation. However, even state-of-the-art MM-DiT models like FLUX struggle with achieving precise alignment between text prompts and…