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Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based…

Large language models (LLMs) have substantially advanced machine learning research, including natural language processing, computer vision, data mining, etc., yet they still exhibit critical limitations in explainability, reliability,…

Molecular property prediction integrates quantum chemistry, cheminformatics, and deep learning to connect molecular structure with physicochemical and biological behavior. This survey traces four complementary paradigms, including Quantum,…

Graph Neural Networks (GNNs) have been widely employed for feature representation learning in molecular graphs. Therefore, it is crucial to enhance the expressiveness of feature representation to ensure the effectiveness of GNNs. However, a…

Deep learning models have become fundamental tools in drug design. In particular, large language models trained on biochemical sequences learn feature vectors that guide drug discovery through virtual screening. However, such models do not…

The prediction of molecular properties is a crucial task in the field of material and drug discovery. The potential benefits of using deep learning techniques are reflected in the wealth of recent literature. Still, these techniques are…

Molecular property prediction is crucial for drug discovery and materials science, yet existing approaches suffer from limited interpretability, poor cross-task generalization, and lack of chemical reasoning capabilities. Traditional…

Multimodal molecular representation learning, which jointly models molecular graphs and their textual descriptions, enhances predictive accuracy and interpretability by enabling more robust and reliable predictions of drug toxicity,…

Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…

Predicting molecular properties with data-driven methods has drawn much attention in recent years. Particularly, Graph Neural Networks (GNNs) have demonstrated remarkable success in various molecular generation and prediction tasks. In…

Large language models (LLMs) have shown strong empirical performance across pharmacology and drug discovery tasks, yet the internal mechanisms by which they encode pharmacological knowledge remain poorly understood. In this work, we…

Large language models (LLMs) have demonstrated their instruction-following capabilities and achieved powerful performance on various tasks. Inspired by their success, recent works in the molecular domain have led to the development of large…

A prior-informed large language model (LLM) driven multi-task learning framework is proposed for the unified description of multiple nuclear observables. By fine-tuning the pre-trained DeepSeek-R1-1.5B model with Low-Rank Adaptation (LoRA),…

Pre-trained large language models (LMs) struggle to perform logical reasoning reliably despite advances in scale and compositionality. In this work, we tackle this challenge through the lens of symbolic programming. We propose DSR-LM, a…

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…

Machine learning (ML) is a promising approach for predicting small molecule properties in drug discovery. Here, we provide a comprehensive overview of various ML methods introduced for this purpose in recent years. We review a wide range of…

Virtual screening plays a critical role in modern drug discovery by enabling the identification of promising candidate molecules for experimental validation. Traditional machine learning methods such, as Support Vector Machines (SVM) and…

This paper presents a study on the integration of domain-specific knowledge in prompt engineering to enhance the performance of large language models (LLMs) in scientific domains. A benchmark dataset is curated to encapsulate the intricate…

The recent success of graph neural networks has significantly boosted molecular property prediction, advancing activities such as drug discovery. The existing deep neural network methods usually require large training dataset for each…

Due to an exponential increase in published research articles, it is impossible for individual scientists to read all publications, even within their own research field. In this work, we investigate the use of large language models (LLMs)…