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Multimodal scientific reasoning remains a significant challenge for large language models (LLMs), particularly in chemistry, where problem-solving relies on symbolic diagrams, molecular structures, and structured visual data. Here, we…

Computation and Language · Computer Science 2025-12-18 Yiming Cui , Xin Yao , Yuxuan Qin , Xin Li , Shijin Wang , Guoping Hu

We describe our strategy for the 2025 edition of the BabyLM Challenge. Our main contribution is that of an improved form of Masked Language Modeling (MLM), which adapts the probabilities of the tokens masked according to the model's ability…

Computation and Language · Computer Science 2025-10-24 Lukas Edman , Alexander Fraser

We present a modular framework powered by large language models (LLMs) that automates and streamlines key tasks across the early-stage computational drug discovery pipeline. By combining LLM reasoning with domain-specific tools, the…

This work introduces an approach to assessing phrase break in ESL learners' speech with pre-trained language models (PLMs). Different with traditional methods, this proposal converts speech to token sequences, and then leverages the power…

Computation and Language · Computer Science 2022-10-31 Zhiyi Wang , Shaoguang Mao , Wenshan Wu , Yan Xia

Speech Language Models (SLMs) aim to learn language from raw audio, without textual resources. Despite significant advances, our current models exhibit weak syntax and semantic abilities. However, if the scaling properties of neural…

Audio and Speech Processing · Electrical Eng. & Systems 2024-12-13 Santiago Cuervo , Ricard Marxer

Large Language Models (LLMs) have demonstrated great performance in few-shot In-Context Learning (ICL) for a variety of generative and discriminative chemical design tasks. The newly expanded context windows of LLMs can further improve ICL…

Current Large Language Models (LLMs) are primarily based on large-scale dense matrix multiplications. Inspired by the brain's information processing mechanism, we explore the fundamental question: how to effectively integrate the brain's…

Neural and Evolutionary Computing · Computer Science 2026-04-21 Han Xu , Xuerui Qiu , Baiyu Chen , Xinhao Luo , Xingrun Xing , Jiahong Zhang , Bo Lei , Tiejun Huang , Bo Xu , Guoqi Li

This paper tackles the challenge of teaching code semantics to Large Language Models (LLMs) for program analysis by incorporating code symmetries into the model architecture. We introduce a group-theoretic framework that defines code…

Machine Learning · Computer Science 2024-09-10 Kexin Pei , Weichen Li , Qirui Jin , Shuyang Liu , Scott Geng , Lorenzo Cavallaro , Junfeng Yang , Suman Jana

Language models require tokenized inputs. However, tokenization strategies for continuous data like audio and vision are often based on simple heuristics such as fixed sized convolutions or discrete clustering, which do not necessarily…

Computation and Language · Computer Science 2024-10-08 Alan Baade , Puyuan Peng , David Harwath

Several machine learning methods aim to learn or reason about complex physical systems. A common first-step towards reasoning is to infer system parameters from observations of its behavior. In this paper, we investigate the performance of…

Computation and Language · Computer Science 2024-02-07 Sean Memery , Mirella Lapata , Kartic Subr

Large language models (LLMs) have made impressive progress in chemistry applications. However, the community lacks an LLM specifically designed for chemistry. The main challenges are two-fold: firstly, most chemical data and scientific…

We present ReaderLM-v2, a compact 1.5 billion parameter language model designed for efficient web content extraction. Our model processes documents up to 512K tokens, transforming messy HTML into clean Markdown or JSON formats with high…

Computation and Language · Computer Science 2025-03-04 Feng Wang , Zesheng Shi , Bo Wang , Nan Wang , Han Xiao

Pre-trained LLMs have demonstrated substantial capabilities across a range of conventional natural language processing (NLP) tasks, such as summarization and entity recognition. In this paper, we explore the application of LLMs in the…

Quantitative Methods · Quantitative Biology 2024-08-14 Kamyar Zeinalipour , Neda Jamshidi , Monica Bianchini , Marco Maggini , Marco Gori

Pretrained masked language models (MLMs) require finetuning for most NLP tasks. Instead, we evaluate MLMs out of the box via their pseudo-log-likelihood scores (PLLs), which are computed by masking tokens one by one. We show that PLLs…

Computation and Language · Computer Science 2021-01-05 Julian Salazar , Davis Liang , Toan Q. Nguyen , Katrin Kirchhoff

Chemistry plays a crucial role in many domains, such as drug discovery and material science. While large language models (LLMs) such as GPT-4 exhibit remarkable capabilities on natural language processing tasks, existing research indicates…

Artificial Intelligence · Computer Science 2024-08-13 Botao Yu , Frazier N. Baker , Ziqi Chen , Xia Ning , Huan Sun

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…

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

While large language models (LLM) have made impressive progress in natural language processing, it remains unclear how to utilize them in improving automatic speech recognition (ASR). In this work, we propose to train a single multilingual…

Computation and Language · Computer Science 2023-02-20 Ke Hu , Tara N. Sainath , Bo Li , Nan Du , Yanping Huang , Andrew M. Dai , Yu Zhang , Rodrigo Cabrera , Zhifeng Chen , Trevor Strohman

We propose SLOT (Sample-specific Language Model Optimization at Test-time), a novel and parameter-efficient test-time inference approach that enhances a language model's ability to more accurately respond to individual prompts. Existing…

Computation and Language · Computer Science 2025-05-27 Yang Hu , Xingyu Zhang , Xueji Fang , Zhiyang Chen , Xiao Wang , Huatian Zhang , Guojun Qi

This paper investigates the logical reasoning capabilities of large language models (LLMs). For a precisely defined yet tractable formulation, we choose the conceptually simple but technically complex task of constructing proofs in Boolean…

Machine Learning · Computer Science 2025-04-30 Yuan Xia , Akanksha Atrey , Fadoua Khmaissia , Kedar S. Namjoshi