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Existing machine learning methods for molecular (e.g., gene) embeddings are restricted to specific tasks or data modalities, limiting their effectiveness within narrow domains. As a result, they fail to capture the full breadth of gene…

Concept Bottleneck Models (CBMs) aim to enhance interpretability by predicting human-understandable concepts as intermediates for decision-making. However, these models often face challenges in ensuring reliable concept representations,…

The rapid advancement of Multimodal Large Language Models (MLLMs) has extended CLIP-based frameworks to produce powerful, universal embeddings for retrieval tasks. However, existing methods primarily focus on natural images, offering…

Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…

Protein language models (PLMs) have revolutionised computational biology through their ability to generate powerful sequence representations for diverse prediction tasks. However, their black-box nature limits biological interpretation and…

Representation learning for protein biochemical space faces a difficult trade-off: protein language models excel at capturing long-range biological semantics but often miss fine-grained chemical details. Conversely, chemical language models…

Foundation models have established unified representations for natural language processing, yet this paradigm remains largely unexplored for tabular data. Existing methods face fundamental limitations: LLM-based approaches lack…

Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology. However, existing…

The Bond Graph approach and the Chemical Reaction Network approach to modelling biomolecular systems developed independently. This paper brings together the two approaches by providing a bond graph interpretation of the chemical reaction…

Recent advances in large language models (LLMs) and biomedical foundation models (BioFMs) have achieved strong results in biological text reasoning, molecular modeling, and single-cell analysis, yet they remain siloed in disjoint embedding…

Unified models (UMs) hold promise for their ability to understand and generate content across heterogeneous modalities. Compared to merely generating visual content, the use of UMs for interleaved cross-modal reasoning is more promising and…

With the rise of data-driven reaction prediction models, effective reaction descriptors are crucial for bridging the gap between real-world chemistry and digital representations. However, general-purpose, reaction-wise descriptors remain…

Chemical reactions are the fundamental building blocks of drug design and organic chemistry research. In recent years, there has been a growing need for a large-scale deep-learning framework that can efficiently capture the basic rules of…

The polarizable embedding (PE) model is a fragment-based quantum-classical approach aimed at accurate inclusion of environment effects in quantum-mechanical response property calculations. The aim of this tutorial is to give insight into…

In this paper, we introduce ReasonEmbed, a novel text embedding model developed for reasoning-intensive document retrieval. Our work includes three key technical contributions. First, we propose ReMixer, a new data synthesis method that…

Revealing the functional sites of biological sequences, such as evolutionary conserved, structurally interacting or co-evolving protein sites, is a fundamental, and yet challenging task. Different frameworks and models were developed to…

Universal multimodal embedding models have achieved great success in capturing semantic relevance between queries and candidates. However, current methods either condense queries and candidates into a single vector, potentially limiting the…

The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…

Learning high-quality feature embeddings efficiently and effectively is critical for the performance of web-scale machine learning systems. A typical model ingests hundreds of features with vocabularies on the order of millions to billions…

Many processes in biology and drug discovery involve various 3D interactions between molecules, such as protein and protein, protein and small molecule, etc. Given that different molecules are usually represented in different granularity,…