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Despite advances in machine learning (ML) and large language models (LLMs), rule-based natural language processing (NLP) systems remain active in clinical settings due to their interpretability and operational efficiency. However, their…

Computation and Language · Computer Science 2025-06-23 Jianlin Shi , Brian T. Bucher

Understanding cell identity and function through single-cell level sequencing data remains a key challenge in computational biology. We present a novel framework that leverages gene-specific textual annotations from the NCBI Gene database…

Genomics · Quantitative Biology 2025-05-14 Douglas Jiang , Zilin Dai , Luxuan Zhang , Qiyi Yu , Haoqi Sun , Feng Tian

Understanding the structural and functional characteristics of proteins are crucial for developing preventative and curative strategies that impact fields from drug discovery to policy development. An important and popular technique for…

Machine Learning · Computer Science 2024-10-17 Sarwan Ali , Taslim Murad , Prakash Chourasia , Haris Mansoor , Imdad Ullah Khan , Pin-Yu Chen , Murray Patterson

Designing controllers for complex industrial electronic systems is challenging due to nonlinearities and parameter uncertainties, and traditional methods are often slow and costly. To address this, we propose a novel autonomous design…

Systems and Control · Electrical Eng. & Systems 2025-07-23 Chenggang Cui , Jiaming Liu , Peifeng Hui , Pengfeng Lin , Chuanlin Zhang

The firing dynamics of biological neurons in mathematical models is often determined by the model's parameters, representing the neurons' underlying properties. The parameter estimation problem seeks to recover those parameters of a single…

Neurons and Cognition · Quantitative Biology 2022-10-05 Long Le , Yao Li

Natural language is hierarchically structured: smaller units (e.g., phrases) are nested within larger units (e.g., clauses). When a larger constituent ends, all of the smaller constituents that are nested within it must also be closed.…

Computation and Language · Computer Science 2019-05-09 Yikang Shen , Shawn Tan , Alessandro Sordoni , Aaron Courville

Information encoding in the nervous system is supported through the precise spike-timings of neurons; however, an understanding of the underlying processes by which such representations are formed in the first place remains unclear. Here we…

Neural and Evolutionary Computing · Computer Science 2015-12-01 Brian Gardner , Ioana Sporea , André Grüning

A central goal for mechanistic interpretability has been to identify the right units of analysis in large language models (LLMs) that causally explain their outputs. While early work focused on individual neurons, evidence that neurons…

Computation and Language · Computer Science 2026-05-05 Or Shafran , Atticus Geiger , Mor Geva

As large language models (LLMs) advance in their linguistic capacity, understanding how they capture aspects of language competence remains a significant challenge. This study therefore employs psycholinguistic paradigms in English, which…

Computation and Language · Computer Science 2024-12-12 Xufeng Duan , Xinyu Zhou , Bei Xiao , Zhenguang G. Cai

Microwell microfluidics has been utilized for single-cell analysis to reveal heterogeneity in gene expression, signaling pathways, and phenotypic responses for identifying rare cell types, understanding disease progression, and developing…

Neurons and Cognition · Quantitative Biology 2025-10-17 Dinh-Nguyen Nguyen , Sadia Shakil , Raymond Kai-Yu Tong , Ngoc-Duy Dinh

Machine learning practitioners often face significant challenges in formally integrating their prior knowledge and beliefs into predictive models, limiting the potential for nuanced and context-aware analyses. Moreover, the expertise needed…

Machine Learning · Statistics 2024-12-23 James Requeima , John Bronskill , Dami Choi , Richard E. Turner , David Duvenaud

Understanding the function of individual neurons within language models is essential for mechanistic interpretability research. We propose $\textbf{Neuron to Graph (N2G)}$, a tool which takes a neuron and its dataset examples, and…

Machine Learning · Computer Science 2023-04-26 Alex Foote , Neel Nanda , Esben Kran , Ionnis Konstas , Fazl Barez

The prediction of protein structures from sequences is an important task for function prediction, drug design, and related biological processes understanding. Recent advances have proved the power of language models (LMs) in processing the…

Quantitative Methods · Quantitative Biology 2022-12-01 Bozhen Hu , Jun Xia , Jiangbin Zheng , Cheng Tan , Yufei Huang , Yongjie Xu , Stan Z. Li

Neural machine translation (NMT) models learn representations containing substantial linguistic information. However, it is not clear if such information is fully distributed or if some of it can be attributed to individual neurons. We…

Computation and Language · Computer Science 2018-11-06 Anthony Bau , Yonatan Belinkov , Hassan Sajjad , Nadir Durrani , Fahim Dalvi , James Glass

Recent advancements in specialized large-scale architectures for training image and language have profoundly impacted the field of computer vision and natural language processing (NLP). Language models, such as the recent ChatGPT and GPT4…

Biomolecules · Quantitative Biology 2023-05-04 Sergio Romero-Romero , Sebastian Lindner , Noelia Ferruz

Pre-trained language models learn informative word representations on a large-scale text corpus through self-supervised learning, which has achieved promising performance in fields of natural language processing (NLP) after fine-tuning.…

Computation and Language · Computer Science 2023-10-31 Jian Yang , Xinyu Hu , Gang Xiao , Yulong Shen

Enabling humanoid robots to perform autonomously loco-manipulation in unstructured environments is crucial and highly challenging for achieving embodied intelligence. This involves robots being able to plan their actions and behaviors in…

Robotics · Computer Science 2024-08-16 Jin Wang , Arturo Laurenzi , Nikos Tsagarakis

Word segmentation stands as a cornerstone of Natural Language Processing (NLP). Based on the concept of "comprehend first, segment later", we propose a new framework to explore the limit of unsupervised word segmentation with Large Language…

Computation and Language · Computer Science 2025-05-27 Zihong Zhang , Liqi He , Zuchao Li , Lefei Zhang , Hai Zhao , Bo Du

Despite the superior performance of large language models to generate natural language texts, it is hard to generate texts with correct logic according to a given task, due to the difficulties for neural models to capture implied rules from…

Computation and Language · Computer Science 2024-07-08 Fan Zhang , Kebing Jin , Hankz Hankui Zhuo

We propose a neural language model capable of unsupervised syntactic structure induction. The model leverages the structure information to form better semantic representations and better language modeling. Standard recurrent neural networks…

Computation and Language · Computer Science 2018-02-20 Yikang Shen , Zhouhan Lin , Chin-Wei Huang , Aaron Courville