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Large language models (LLMs) have achieved great success in many fields, and recent works have studied exploring LLMs for graph discriminative tasks such as node classification. However, the abilities of LLMs for graph generation remain…

Molecular property prediction (MPP) is a fundamental and crucial task in drug discovery. However, prior methods are limited by the requirement for a large number of labeled molecules and their restricted ability to generalize for unseen and…

Significant interests have recently risen in leveraging sequence-based large language models (LLMs) for drug design. However, most current applications of LLMs in drug discovery lack the ability to comprehend three-dimensional (3D)…

Molecular relational learning (MRL) is crucial for understanding the interaction behaviors between molecular pairs, a critical aspect of drug discovery and development. However, the large feasible model space of MRL poses significant…

We present MeshLLM, a novel framework that leverages large language models (LLMs) to understand and generate text-serialized 3D meshes. Our approach addresses key limitations in existing methods, including the limited dataset scale when…

Recent large language models (LLMs) have demonstrated promising capabilities in modeling real-world knowledge and enhancing knowledge-based generation tasks. In this paper, we further explore the potential of using LLMs to aid in the design…

In real-world drug design, molecule optimization requires selectively improving multiple molecular properties up to pharmaceutically relevant levels, while maintaining others that already meet such criteria. However, existing computational…

We introduce Directional Stimulus Prompting, a novel framework for guiding black-box large language models (LLMs) toward specific desired outputs. Instead of directly adjusting LLMs, our method employs a small tunable policy model (e.g.,…

The synthesis of inorganic crystalline materials is essential for modern technology, especially in quantum materials development. However, designing efficient synthesis workflows remains a significant challenge due to the precise…

In the field of chemistry, the objective is to create novel molecules with desired properties, facilitating accurate property predictions for applications such as material design and drug screening. However, existing graph deep learning…

Contemporary large language models (LLMs), such as GPT-4 and Llama, have harnessed extensive computational power and diverse text corpora to achieve remarkable proficiency in interpreting and generating domain-specific content, including…

Recovering the structure of causal graphical models from observational data is an essential yet challenging task for causal discovery in scientific scenarios. Domain-specific causal discovery usually relies on expert validation or prior…

Large Language Models (LLMs) are rapidly reshaping machine translation (MT), particularly by introducing instruction-following, in-context learning, and preference-based alignment into what has traditionally been a supervised…

Large language models (LLMs), especially Explicit Long Chain-of-Thought (CoT) reasoning models like DeepSeek-R1 and QWQ, have demonstrated powerful reasoning capabilities, achieving impressive performance in commonsense reasoning and…

Machine learning (ML) is revolutionising drug discovery by expediting the prediction of small molecule properties essential for developing new drugs. These properties -- including absorption, distribution, metabolism and excretion (ADME)--…

A drug molecule is a substance that changes the organism's mental or physical state. Every approved drug has an indication, which refers to the therapeutic use of that drug for treating a particular medical condition. While the Large…

Large Language Models (LLMs) are increasingly being integrated into various components of Ontology Matching pipelines. This paper investigates the capability of LLMs to perform ontology matching directly on ontology modules and generate the…

Molecular optimization is a crucial yet complex and time-intensive process that often acts as a bottleneck for drug development. Traditional methods rely heavily on trial and error, making multi-objective optimization both time-consuming…

Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Traditional physics-based simulation methods often struggle with…

Effectively integrating molecular graph structures with Large Language Models (LLMs) is a key challenge in drug discovery. Most existing multi-modal alignment methods typically process these structures by fine-tuning the LLM or adding a…