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Large language models (LLMs) have shown strong knowledge reserves and task-solving capabilities, but still face the challenge of severe hallucination, hindering their practical application. Though scientific theories and rules can…

Computation and Language · Computer Science 2026-04-09 Maotian Ma , Zheni Zeng , Zhenghao Liu , Yukun Yan

The simplified molecular-input line-entry system (SMILES) is the most popular representation of chemical compounds. Therefore, many SMILES-based molecular property prediction models have been developed. In particular, transformer-based…

Quantitative Methods · Quantitative Biology 2022-05-03 Ingoo Lee , Hojung Nam

Large Language Models (LLMs) are capable of successfully performing many language processing tasks zero-shot (without training data). If zero-shot LLMs can also reliably classify and explain social phenomena like persuasiveness and…

Computation and Language · Computer Science 2024-02-27 Caleb Ziems , William Held , Omar Shaikh , Jiaao Chen , Zhehao Zhang , Diyi Yang

Large language models (LLMs) have shown great promise in generating structured diagrams from natural language descriptions, particularly Mermaid sequence diagrams for software engineering. However, the lack of existing benchmarks to assess…

Software Engineering · Computer Science 2026-04-28 Basel Shbita , Farhan Ahmed , Chad DeLuca

Large language models (LLMs) have achieved impressive performance in code generation. However, due to the long-tail distribution of LLMs' training data, low-frequency terms are typically underrepresented in the training process.…

Computation and Language · Computer Science 2024-10-22 Lishui Fan , Mouxiang Chen , Zhongxin Liu

Large language models (LLMs) are known to struggle with consistently generating truthful responses. While various representation intervention techniques have been proposed, these methods typically apply a universal representation correction…

Computation and Language · Computer Science 2025-02-10 Hanyu Wang , Bochuan Cao , Yuanpu Cao , Jinghui Chen

Molecule representation learning (MRL) methods aim to embed molecules into a real vector space. However, existing SMILES-based (Simplified Molecular-Input Line-Entry System) or GNN-based (Graph Neural Networks) MRL methods either take…

Machine Learning · Computer Science 2021-09-23 Hongwei Wang , Weijiang Li , Xiaomeng Jin , Kyunghyun Cho , Heng Ji , Jiawei Han , Martin D. Burke

Test collections play a vital role in evaluation of information retrieval (IR) systems. Obtaining a diverse set of user queries for test collection construction can be challenging, and acquiring relevance judgments, which indicate the…

Information Retrieval · Computer Science 2024-05-14 Hossein A. Rahmani , Nick Craswell , Emine Yilmaz , Bhaskar Mitra , Daniel Campos

Current SMILES-based diffusion models for molecule generation typically support only unimodal constraint. They inject conditioning signals at the start of the training process and require retraining a new model from scratch whenever the…

Machine Learning · Computer Science 2025-08-21 Yunzhe Zhang , Yifei Wang , Khanh Vinh Nguyen , Pengyu Hong

Large language models (LLMs) are a class of artificial intelligence models based on deep learning, which have great performance in various tasks, especially in natural language processing (NLP). Large language models typically consist of…

Quantitative Methods · Quantitative Biology 2025-02-04 Jiajia Liu , Mengyuan Yang , Yankai Yu , Haixia Xu , Tiangang Wang , Kang Li , Xiaobo Zhou

The ability to automatically generate accurate protocols for scientific experiments would represent a major step towards the automation of science. Large Language Models (LLMs) have impressive capabilities on a wide range of tasks, such as…

Computation and Language · Computer Science 2023-10-17 Odhran O'Donoghue , Aleksandar Shtedritski , John Ginger , Ralph Abboud , Ali Essa Ghareeb , Justin Booth , Samuel G Rodriques

Large Language Models (LLMs) are deployed as powerful tools for several natural language processing (NLP) applications. Recent works show that modern LLMs can generate self-explanations (SEs), which elicit their intermediate reasoning steps…

Computation and Language · Computer Science 2024-03-15 Chirag Agarwal , Sree Harsha Tanneru , Himabindu Lakkaraju

Large language models (LLMs) have demonstrated powerful text generation capabilities, bringing unprecedented innovation to the healthcare field. While LLMs hold immense promise for applications in healthcare, applying them to real clinical…

Computation and Language · Computer Science 2023-10-16 Rui Yang , Edison Marrese-Taylor , Yuhe Ke , Lechao Cheng , Qingyu Chen , Irene Li

Recently, large language models (LLMs) have emerged as a groundbreaking technology and their unparalleled text generation capabilities have sparked interest in their application to the fundamental sentence representation learning task.…

Computation and Language · Computer Science 2024-05-20 Huiming Wang , Zhaodonghui Li , Liying Cheng , Soh De Wen , Lidong Bing

Geometric representation-conditioned molecule generation provides an effective paradigm that decouples molecule representation modeling from structure generation. By decoupling molecule generation into two stages-first generating a…

Machine Learning · Computer Science 2026-05-11 Shaoheng Yan , Zian Li , Cai Zhou , Qiaojing Huang , Kai Liu , Muhan Zhang

Molecular representation learning is fundamental for many drug related applications. Most existing molecular pre-training models are limited in using single molecular modality, either SMILES or graph representation. To effectively leverage…

Machine Learning · Computer Science 2024-11-05 Shikun Feng , Lixin Yang , Yanwen Huang , Yuyan Ni , Weiying Ma , Yanyan Lan

Chemical reaction prediction, involving forward synthesis and retrosynthesis prediction, is a fundamental problem in organic synthesis. A popular computational paradigm formulates synthesis prediction as a sequence-to-sequence translation…

Machine Learning · Computer Science 2022-08-15 Zipeng Zhong , Jie Song , Zunlei Feng , Tiantao Liu , Lingxiang Jia , Shaolun Yao , Min Wu , Tingjun Hou , Mingli Song

Can a large language model (LLM) improve at code generation using only its own raw outputs, without a verifier, a teacher model, or reinforcement learning? We answer in the affirmative with simple self-distillation (SSD): sample solutions…

Computation and Language · Computer Science 2026-04-02 Ruixiang Zhang , Richard He Bai , Huangjie Zheng , Navdeep Jaitly , Ronan Collobert , Yizhe Zhang

With the growing popularity of Large Language Models (LLMs) in software engineers' daily practices, it is important to ensure that the code generated by these tools is not only functionally correct but also free of vulnerabilities. Although…

Software Engineering · Computer Science 2024-09-06 Mohammed Latif Siddiq , Joanna C. S. Santos , Sajith Devareddy , Anna Muller

This survey reviews how large language models (LLMs) are transforming synthetic training data generation in both natural language and code domains. By producing artificial but task-relevant examples, these models can significantly augment…

Computation and Language · Computer Science 2025-11-21 Mihai Nadas , Laura Diosan , Andreea Tomescu