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Language models for biological and chemical sequences enable crucial applications such as drug discovery, protein engineering, and precision medicine. Currently, these language models are predominantly based on Transformer architectures.…

The ability to design molecules while preserving similarity to a target molecule and/or property is crucial for various applications in drug discovery, chemical design, and biology. We introduce in this paper an efficient training-free…

Machine Learning · Computer Science 2025-11-18 Jiri Navratil , Jarret Ross , Payel Das , Youssef Mroueh , Samuel C Hoffman , Vijil Chenthamarakshan , Brian Belgodere

There is a growing interest in applying large language models (LLMs) in robotic tasks, due to their remarkable reasoning ability and extensive knowledge learned from vast training corpora. Grounding LLMs in the physical world remains an…

Robotics · Computer Science 2024-04-11 Wenqiang Lai , Yuan Gao , Tin Lun Lam

In the intersection of molecular science and deep learning, tasks like virtual screening have driven the need for a high-throughput molecular representation generator on large chemical databases. However, as SMILES strings are the most…

Computational Engineering, Finance, and Science · Computer Science 2021-12-28 Wenhao Zhu , Ziyao Li , Lingsheng Cai , Guojie Song

Large Language Models (LLMs) and AI assistants driven by these models are experiencing exponential growth in usage among both expert and amateur users. In this work, we focus on evaluating the reliability of current LLMs as science…

Computation and Language · Computer Science 2024-09-24 Prasoon Bajpai , Niladri Chatterjee , Subhabrata Dutta , Tanmoy Chakraborty

Large language models (LLMs) like ChatGPT have shown significant advancements across diverse natural language understanding (NLU) tasks, including intelligent dialogue and autonomous agents. Yet, lacking widely acknowledged testing…

Computation and Language · Computer Science 2024-05-10 Jinyang Wu , Feihu Che , Xinxin Zheng , Shuai Zhang , Ruihan Jin , Shuai Nie , Pengpeng Shao , Jianhua Tao

Since the release of ChatGPT and GPT-4, large language models (LLMs) and multimodal large language models (MLLMs) have attracted widespread attention for their exceptional capabilities in understanding, reasoning, and generation,…

Computation and Language · Computer Science 2024-12-31 Hanguang Xiao , Feizhong Zhou , Xingyue Liu , Tianqi Liu , Zhipeng Li , Xin Liu , Xiaoxuan Huang

Deep learning has significantly advanced molecular modeling and design, enabling efficient understanding and discovery of novel molecules. In particular, large language models (LLMs) introduce a fresh research paradigm to tackle scientific…

Machine Learning · Computer Science 2025-01-06 Pengfei Liu , Jun Tao , Zhixiang Ren

Background: The potential of large language models (LLMs) to automate and support pharmacoepidemiologic study design is an emerging area of interest, yet their reliability remains insufficiently characterized. General-purpose LLMs often…

Computation and Language · Computer Science 2026-04-21 Xinyao Zhang , Nicole Sonne Heckmann , Manuela Del Castillo Suero , Francesco Paolo Speca , Maurizio Sessa

This paper explores the use of large language models (LLMs) as research tools in the history, philosophy, and sociology of science (HPSS). LLMs are remarkably effective at processing unstructured text and inferring meaning from context,…

Computation and Language · Computer Science 2025-06-17 Arno Simons , Michael Zichert , Adrian Wüthrich

Large Language Models (LLMs) have emerged as a transformative power in enhancing natural language comprehension, representing a significant stride toward artificial general intelligence. The application of LLMs extends beyond conventional…

Deep learning has been a prevalence in computational chemistry and widely implemented in molecule property predictions. Recently, self-supervised learning (SSL), especially contrastive learning (CL), gathers growing attention for the…

Machine Learning · Computer Science 2022-06-01 Yuyang Wang , Rishikesh Magar , Chen Liang , Amir Barati Farimani

The rise of large language models (LLMs) has significantly impacted various domains, including natural language processing (NLP) and image generation, by making complex computational tasks more accessible. While LLMs demonstrate impressive…

Databases · Computer Science 2024-10-15 Ananya Rahaman , Anny Zheng , Mostafa Milani , Fei Chiang , Rachel Pottinger

Predicting cancer treatment outcomes requires models that are both accurate and interpretable, particularly in the presence of heterogeneous clinical data. While large language models (LLMs) have shown strong performance in biomedical NLP,…

Computation and Language · Computer Science 2025-10-21 Raghu Vamshi Hemadri , Geetha Krishna Guruju , Kristi Topollai , Anna Ewa Choromanska

Molecular property prediction is an increasingly critical task within drug discovery and development. Typically, neural networks can learn molecular properties using graph-based, language-based or feature-based methods. Recent advances in…

Machine Learning · Computer Science 2025-07-31 Philip Spence , Brooks Paige , Anne Osbourn

Large Language Models have taken the cognitive science world by storm. It is perhaps timely now to take stock of the various research paradigms that have been used to make scientific inferences about ``cognition" in these models or about…

Artificial Intelligence · Computer Science 2024-06-17 Desmond C. Ong

Mathematical equations have been unreasonably effective in describing complex natural phenomena across various scientific disciplines. However, discovering such insightful equations from data presents significant challenges due to the…

Machine Learning · Computer Science 2025-03-21 Parshin Shojaee , Kazem Meidani , Shashank Gupta , Amir Barati Farimani , Chandan K Reddy

Large Language Models (LLMs) are being employed widely to automate tasks across the software development life-cycle. It is, however, unclear whether these tasks are performed consistently with respect to the semantics of the artefacts being…

Software Engineering · Computer Science 2026-05-15 Mohammad Reza Mousavi

Large language models (LLMs) have made significant progress in various domains, including healthcare. However, the specialized nature of clinical language understanding tasks presents unique challenges and limitations that warrant further…

Computation and Language · Computer Science 2023-08-01 Yuqing Wang , Yun Zhao , Linda Petzold

Recent advancements in natural language processing, particularly with large language models (LLMs), are transforming how scientists engage with the literature. While the adoption of LLMs is increasing, concerns remain regarding potential…

Computation and Language · Computer Science 2025-10-23 Jian Zhang