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Benchmarks underpin how progress in large language models (LLMs) is measured and trusted. Yet our analyses reveal that apparent convergence in benchmark accuracy can conceal deep epistemic divergence. Using two major reasoning benchmarks -…

Computation and Language · Computer Science 2026-02-13 Eddie Yang , Dashun Wang

Large language models (LLMs) are increasingly used in situations where human values are at stake, such as decision-making tasks that involve reasoning when performed by humans. We investigate the so-called reasoning capabilities of LLMs…

Computation and Language · Computer Science 2025-12-25 Nathaniël de Leeuw , Marceau Nahon , Mathis Reymond , Raja Chatila , Mehdi Khamassi

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

A range of studies have concluded that neural word prediction models can distinguish grammatical from ungrammatical sentences with high accuracy. However, these studies are based primarily on monolingual evidence from English. To…

Computation and Language · Computer Science 2020-05-22 Aaron Mueller , Garrett Nicolai , Panayiota Petrou-Zeniou , Natalia Talmina , Tal Linzen

Language Confusion is a phenomenon where Large Language Models (LLMs) generate text that is neither in the desired language, nor in a contextually appropriate language. This phenomenon presents a critical challenge in text generation by…

Computation and Language · Computer Science 2025-02-11 Yiyi Chen , Qiongxiu Li , Russa Biswas , Johannes Bjerva

We propose a method to teach multiple large language models (LLM) to collaborate by interleaving their generations at the token level. We model the decision of which LLM generates the next token as a latent variable. By optimizing the…

Computation and Language · Computer Science 2024-08-28 Shannon Zejiang Shen , Hunter Lang , Bailin Wang , Yoon Kim , David Sontag

Multilingual Large Language Models (LLMs) can process many languages, yet how they internally represent this diversity remains unclear. Do they form shared multilingual representations with language-specific decoding, and if so, why does…

Computation and Language · Computer Science 2026-02-10 Abir Harrasse , Florent Draye , Punya Syon Pandey , Zhijing Jin , Bernhard Schölkopf

Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal…

Machine Learning · Computer Science 2025-05-23 Ziqing Wang , Kexin Zhang , Zihan Zhao , Yibo Wen , Abhishek Pandey , Han Liu , Kaize Ding

Large language models (LLMs) reason over discrete token ID sequences, yet modern subword tokenizers routinely produce non-unique encodings: multiple token ID sequences can detokenize to identical surface strings. This representational…

Computation and Language · Computer Science 2026-01-22 Navid Ayoobi , Marcus I Armstrong , Arjun Mukherjee

Large Language Models (LLMs) are increasingly deployed to automatically label and analyze educational dialogue at scale, yet current pipelines lack reliable ways to detect when models are wrong. We investigate whether reasoning generated by…

Computation and Language · Computer Science 2026-02-11 Bakhtawar Ahtisham , Kirk Vanacore , Zhuqian Zhou , Jinsook Lee , Rene F. Kizilcec

Character-level patterns have been widely used as features in English Named Entity Recognition (NER) systems. However, to date there has been no direct investigation of the inherent differences between name and non-name tokens in text, nor…

Computation and Language · Computer Science 2018-09-21 Xiaodong Yu , Stephen Mayhew , Mark Sammons , Dan Roth

The capabilities of large language models (LLMs) have expanded beyond natural language processing to scientific prediction tasks, including molecular property prediction. However, their effectiveness in in-context learning remains…

This paper shows how one can directly apply natural language processing (NLP) methods to classification problems in cheminformatics. Connection between these seemingly separate fields is shown by considering standard textual representation…

Computation and Language · Computer Science 2018-03-09 Stanisław Jastrzębski , Damian Leśniak , Wojciech Marian Czarnecki

Complex chemical structures, like drugs, are usually defined by SMILES strings as a sequence of molecules and bonds. These SMILES strings are used in different complex machine learning-based drug-related research and representation works.…

Biomolecules · Quantitative Biology 2024-03-29 Azmine Toushik Wasi , Šerbetar Karlo , Raima Islam , Taki Hasan Rafi , Dong-Kyu Chae

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and…

Machine Learning · Computer Science 2024-03-11 Zhiqiang Zhong , Kuangyu Zhou , Davide Mottin

With the widespread application of multimodal large language models in scientific intelligence, there is an urgent need for more challenging evaluation benchmarks to assess their ability to understand complex scientific data. Scientific…

Artificial Intelligence · Computer Science 2025-12-12 Yitong Zhou , Mingyue Cheng , Qingyang Mao , Yucong Luo , Qi Liu , Yupeng Li , Xiaohan Zhang , Deguang Liu , Xin Li , Enhong Chen

Concept Bottleneck Models (CBMs) provide inherent interpretability by first mapping input samples to high-level semantic concepts, followed by a combination of these concepts for the final classification. However, the annotation of…

Machine Learning · Computer Science 2026-03-02 Yangyi Li , Mengdi Huai

Large Language Models (LLMs) have revolutionised the field of Natural Language Processing (NLP) and have achieved state-of-the-art performance in practically every task in this field. However, the prevalent approach used in text generation,…

Computation and Language · Computer Science 2024-08-12 Nicolo Micheletti , Samuel Belkadi , Lifeng Han , Goran Nenadic

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

One of the long-standing goals in optimisation and constraint programming is to describe a problem in natural language and automatically obtain an executable, efficient model. Large language models appear to bring this vision closer,…

Artificial Intelligence · Computer Science 2025-11-20 Alessio Pellegrino , Jacopo Mauro