15 accepted papers
Retrieving molecular structures from tandem mass spectra is a crucial step in rapid compound identification. Existing retrieval methods, such as traditional mass spectral library matching, suffer from limited spectral library coverage, while recent cross-modal representation learning frameworks ofte
While chain-of-thought (CoT) distillation from advanced large language models (LLMs) has proven effective in general reasoning tasks, it struggles in scientific domains where even advanced models often produce incorrect or superficial reasoning due to high complexity and specialized knowledge requir…
The rapid evolution of Large Language Models has catalyzed a surge in scientific idea production, yet this leap has not been accompanied by a matching advance in idea evaluation. The fundamental nature of scientific evaluation needs knowledgeable grounding, collective deliberation, and multi-criteri…
Molecular structure elucidation involves deducing a molecule’s structure from various types of spectral data, which is crucial in chemical experimental analysis. While large language models (LLMs) have shown remarkable proficiency in analyzing and reasoning through complex tasks, they still encounte…
Protein language models have emerged as powerful tools for sequence generation, offering substantial advantages in functional optimization and *denovo* design. However, these models also present significant risks of generating harmful protein sequences, such as those that enhance viral transmissibil…
Retrieval-augmented generation (RAG) systems often struggle with narrative-rich documents and event-centric reasoning, particularly when synthesizing information across multiple sources. We present EventRAG, a novel framework that enhances text generation through structured event representations. We…
Parameter-efficient fine-tuning (PEFT) methods, such as LoRA, have enabled the efficient adaptation of large language models (LLMs) by updating only a small subset of parameters. However, their robustness under out-of-distribution (OOD) conditions remains insufficiently studied. In this paper, we id…
Evaluating the response quality of large language models (LLMs) for open-ended questions poses a significant challenge, especially given the subjectivity and multi-dimensionality of "quality" in natural language generation. Existing LLM evaluators often neglect that different scenarios require disti…
The past years have witnessed a proliferation of large language models (LLMs). Yet, reliable evaluation of LLMs is challenging due to the inaccuracy of standard metrics in human perception of text quality and the inefficiency in sampling informative test examples for human evaluation. This paper pre…
Protein optimization is a fundamental biological task aimed at enhancing theperformance of proteins by modifying their sequences. Computational methodsprimarily rely on evolutionary information (EI) encoded by protein languagemodels (PLMs) to predict fitness landscape for optimization. However, thes…
The development of Large Language Models (LLMs) has greatly advanced the field of drug discovery, with the belief that natural language can enhance human control over molecule design. However, the scarcity of high-quality labeled data remains a challenge for cross text-molecule learning. Existing da…
Large Language Models (LLMs) have revolutionized the field of natural language processing, but they fall short in comprehending biological sequences such as proteins. To address this challenge, we propose InstructProtein, an innovative LLM that possesses bidirectional generation capabilities in both…
Directed evolution, a cornerstone of protein optimization, is to harness natural mutational processes to enhance protein functionality. Existing Machine Learning-assisted Directed Evolution (MLDE) methodologies typically rely on data-driven strategies and often overlook the profound domain knowledge…
Molecular property is usually observed with a limited number of samples, and researchers have considered property prediction as a few-shot problem. One important fact that has been ignored by prior works is that each molecule can be recorded with several different properties simultaneously. To effec…
Molecular representation learning lays the foundation for drug discovery. However, existing methods suffer from poor out-of-distribution (OOD) generalization, particularly when data for training and testing originate from different environments. To address this issue, we propose a new framework for…