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Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…

Quantitative Methods · Quantitative Biology 2023-06-09 Francesco Ceccarelli , Lorenzo Giusti , Sean B. Holden , Pietro Liò

Proteins are essential to life's processes, underpinning evolution and diversity. Advances in sequencing technology have revealed millions of proteins, underscoring the need for sophisticated pre-trained protein models for biological…

Biomolecules · Quantitative Biology 2024-04-25 Shujian Jiao , Bingxuan Li , Lei Wang , Xiaojin Zhang , Wei Chen , Jiajie Peng , Zhongyu Wei

Word embedding methods revolve around learning continuous distributed vector representations of words with neural networks, which can capture semantic and/or syntactic cues, and in turn be used to induce similarity measures among words,…

Computation and Language · Computer Science 2016-07-25 Kuan-Yu Chen , Shih-Hung Liu , Berlin Chen , Hsin-Min Wang , Hsin-Hsi Chen

The representation of knowledge based on first-order logic captures the richness of natural language and supports multiple probabilistic inference models. Although symbolic representation enables quantitative reasoning with statistical…

Artificial Intelligence · Computer Science 2018-09-25 Jingchi Jiang , Huanzheng Wang , Jing Xie , Xitong Guo , Yi Guan , Qiubin Yu

Natural language is an appealing medium for explaining how large language models process and store information, but evaluating the faithfulness of such explanations is challenging. To help address this, we develop two modes of evaluation…

Computation and Language · Computer Science 2023-09-20 Jing Huang , Atticus Geiger , Karel D'Oosterlinck , Zhengxuan Wu , Christopher Potts

We introduce a framework for reasoning about what meaning is captured by the neurons in a trained neural network. We provide a strategy for discovering meaning by training a second model (referred to as an observer model) to classify the…

Machine Learning · Computer Science 2021-03-16 Eric E. Allen

Neural methods for embedding entities are typically extrinsically evaluated on downstream tasks and, more recently, intrinsically using probing tasks. Downstream task-based comparisons are often difficult to interpret due to differences in…

Computation and Language · Computer Science 2020-11-19 Andrew Runge , Eduard Hovy

Large language models (LLMs) exhibit social biases that reinforce harmful stereotypes, limiting their safe deployment. Most existing debiasing methods adopt a suppressive paradigm by modifying parameters, prompts, or neurons associated with…

Artificial Intelligence · Computer Science 2026-01-30 Jinhao Pan , Chahat Raj , Anjishnu Mukherjee , Sina Mansouri , Bowen Wei , Shloka Yada , Ziwei Zhu

Neural network models have achieved state-of-the-art performances in a wide range of natural language processing (NLP) tasks. However, a long-standing criticism against neural network models is the lack of interpretability, which not only…

Computation and Language · Computer Science 2021-10-26 Xiaofei Sun , Diyi Yang , Xiaoya Li , Tianwei Zhang , Yuxian Meng , Han Qiu , Guoyin Wang , Eduard Hovy , Jiwei Li

Sentence Embedding stands as a fundamental task within the realm of Natural Language Processing, finding extensive application in search engines, expert systems, and question-and-answer platforms. With the continuous evolution of large…

Computation and Language · Computer Science 2024-05-16 Bowen Zhang , Kehua Chang , Chunping Li

Recent advances in natural language processing (NLP) owe their success to pre-training language models on large amounts of unstructured data. Still, there is an increasing effort to combine the unstructured nature of LMs with structured…

Computation and Language · Computer Science 2023-12-22 Juraj Vladika , Alexander Fichtl , Florian Matthes

Motivation: Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are…

Quantitative Methods · Quantitative Biology 2017-05-01 Mona Alshahrani , Mohammed Asif Khan , Omar Maddouri , Akira R Kinjo , Núria Queralt-Rosinach , Robert Hoehndorf

The ability of machine learning models to store input information in hidden layer vector embeddings, analogous to the concept of `memory', is widely employed but not well characterized. We find that language model embeddings typically…

Computation and Language · Computer Science 2026-05-20 Benjamin L. Badger

Providing textual concept-based explanations for neurons in deep neural networks (DNNs) is of importance in understanding how a DNN model works. Prior works have associated concepts with neurons based on examples of concepts or a…

Computer Vision and Pattern Recognition · Computer Science 2024-06-14 Nhat Hoang-Xuan , Minh Vu , My T. Thai

This paper presents a Kernel Entity Salience Model (KESM) that improves text understanding and retrieval by better estimating entity salience (importance) in documents. KESM represents entities by knowledge enriched distributed…

Information Retrieval · Computer Science 2018-05-04 Chenyan Xiong , Zhengzhong Liu , Jamie Callan , Tie-Yan Liu

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

Understanding the internal mechanisms by which multi-modal large language models (LLMs) interpret different modalities and integrate cross-modal representations is becoming increasingly critical for continuous improvements in both academia…

Computation and Language · Computer Science 2024-06-12 Haowen Pan , Yixin Cao , Xiaozhi Wang , Xun Yang , Meng Wang

We present a method for extracting \emph{monosemantic} neurons, defined as latent dimensions that align with coherent and interpretable concepts, from user and item embeddings in recommender systems. Our approach employs a Sparse…

Information Retrieval · Computer Science 2025-11-25 Dor Arviv , Yehonatan Elisha , Oren Barkan , Noam Koenigstein

End-to-end neural models for intelligent dialogue systems suffer from the problem of generating uninformative responses. Various methods were proposed to generate more informative responses by leveraging external knowledge. However, few…

Computation and Language · Computer Science 2019-05-22 Rongzhong Lian , Min Xie , Fan Wang , Jinhua Peng , Hua Wu

Neural network based approaches for sentence relation modeling automatically generate hidden matching features from raw sentence pairs. However, the quality of matching feature representation may not be satisfied due to complex semantic…

Computation and Language · Computer Science 2016-04-01 Peng Li , Heng Huang
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