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Accurately quantifying uncertainty in large language models (LLMs) is crucial for their reliable deployment, especially in high-stakes applications. Current state-of-the-art methods for measuring semantic uncertainty in LLMs rely on strict…

Machine Learning · Computer Science 2024-10-31 Yashvir S. Grewal , Edwin V. Bonilla , Thang D. Bui

Large language models (LLMs) often necessitate extensive labeled datasets and training compute to achieve impressive performance across downstream tasks. This paper explores a self-training paradigm, where the LLM autonomously curates its…

Computation and Language · Computer Science 2024-11-13 Wei Jie Yeo , Teddy Ferdinan , Przemyslaw Kazienko , Ranjan Satapathy , Erik Cambria

Sentence embedding is essential for many NLP tasks, with contrastive learning methods achieving strong performance using annotated datasets like NLI. Yet, the reliance on manual labels limits scalability. Recent studies leverage large…

Computation and Language · Computer Science 2025-06-05 Liyang He , Chenglong Liu , Rui Li , Zhenya Huang , Shulan Ruan , Jun Zhou , Enhong Chen

Purpose: Large Language Models (LLMs) like GPT (Generative Pre-trained Transformer) from OpenAI and LLaMA (Large Language Model Meta AI) from Meta AI are increasingly recognized for their potential in the field of cheminformatics,…

Biomolecules · Quantitative Biology 2024-05-22 Shaghayegh Sadeghi , Alan Bui , Ali Forooghi , Jianguo Lu , Alioune Ngom

Domain-specific text embeddings are critical for clinical natural language processing, yet systematic comparisons across model architectures remain limited. This study evaluates ten transformer-based embedding models adapted for cardiology…

Computation and Language · Computer Science 2025-11-26 Richard J. Young , Alice M. Matthews

Objective and scalable measurement of teaching quality is a persistent challenge in education. While Large Language Models (LLMs) offer potential, general-purpose models have struggled to reliably apply complex, authentic classroom…

Computation and Language · Computer Science 2025-11-07 Michael Hardy

Retrieval-augmented generation improves large language models by grounding outputs in external knowledge sources, reducing hallucinations and addressing knowledge cutoffs. However, standard embedding-based retrieval fails to capture the…

Information Retrieval · Computer Science 2025-12-23 Markus Ekvall , Ludvig Bergenstråhle , Patrick Truong , Ben Murrell , Joakim Lundeberg

Representation learning offers a conduit to elucidate distinctive features within the latent space and interpret the deep models. However, the randomness of lesion distribution and the complexity of low-quality factors in medical images…

Computer Vision and Pattern Recognition · Computer Science 2024-04-09 Qingshan Hou , Shuai Cheng , Peng Cao , Jinzhu Yang , Xiaoli Liu , Osmar R. Zaiane , Yih Chung Tham

Large-scale volumetric medical images with annotation are rare, costly, and time prohibitive to acquire. Self-supervised learning (SSL) offers a promising pre-training and feature extraction solution for many downstream tasks, as it only…

Computer Vision and Pattern Recognition · Computer Science 2023-03-16 Ke Yu , Li Sun , Junxiang Chen , Max Reynolds , Tigmanshu Chaudhary , Kayhan Batmanghelich

One-hot CNN (convolutional neural network) has been shown to be effective for text categorization (Johnson & Zhang, 2015). We view it as a special case of a general framework which jointly trains a linear model with a non-linear feature…

Machine Learning · Statistics 2016-05-27 Rie Johnson , Tong Zhang

Understanding how the human brain progresses from processing simple linguistic inputs to performing high-level reasoning is a fundamental challenge in neuroscience. While modern large language models (LLMs) are increasingly used to model…

Computation and Language · Computer Science 2026-01-27 Linyang He , Tianjun Zhong , Richard Antonello , Gavin Mischler , Micah Goldblum , Nima Mesgarani

Recently, using large language models (LLMs) for data augmentation has led to considerable improvements in unsupervised sentence embedding models. However, existing methods encounter two primary challenges: limited data diversity and high…

Computation and Language · Computer Science 2025-10-07 Peichao Lai , Zhengfeng Zhang , Wentao Zhang , Fangcheng Fu , Bin Cui

A new trend uses LLMs as dense text encoders via contrastive learning. However, since LLM embeddings predict the probability distribution of the next token, they are inherently generative and distributive, conflicting with contrastive…

Computation and Language · Computer Science 2025-10-17 Jingcheng Deng , Zhongtao Jiang , Liang Pang , Liwei Chen , Kun Xu , Zihao Wei , Huawei Shen , Xueqi Cheng

Large language models (LLMs) exhibit remarkable generative capabilities but often suffer from hallucinations. Retrieval-augmented generation (RAG) offers an effective solution by incorporating external knowledge, but existing methods still…

Computation and Language · Computer Science 2024-12-17 Xiaoxi Li , Jiajie Jin , Yujia Zhou , Yongkang Wu , Zhonghua Li , Qi Ye , Zhicheng Dou

Transcriptome foundation models TFMs hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale single-cell gene expression data, and ultimately unraveling…

Machine Learning · Computer Science 2025-03-03 Xinyu Yuan , Zhihao Zhan , Zuobai Zhang , Manqi Zhou , Jianan Zhao , Boyu Han , Yue Li , Jian Tang

Large language models (LLMs) are transforming cellular biology by enabling the development of "virtual cells"--computational systems that represent, predict, and reason about cellular states and behaviors. This work provides a comprehensive…

Computation and Language · Computer Science 2025-10-10 Krinos Li , Xianglu Xiao , Shenglong Deng , Lucas He , Zijun Zhong , Yuanjie Zou , Zhonghao Zhan , Zheng Hui , Weiye Bao , Guang Yang

Large language models (LLMs) excel in natural language processing but adapting these LLMs to speech processing tasks efficiently is not straightforward. Direct task-specific fine-tuning is limited by overfitting risks, data requirements,…

Computation and Language · Computer Science 2025-06-02 Maike Züfle , Jan Niehues

Recent advancements in machine learning (ML), natural language processing (NLP), and foundational models have shown promise for real-life applications in critical, albeit compute-constrainted fields like healthcare. In such areas, combining…

Machine Learning · Computer Science 2025-02-05 Georgios Margaritis , Periklis Petridis , Dimitris J. Bertsimas

Transcriptomic foundation models pretrained with masked language modeling can achieve low pretraining loss yet produce poor cell representations for downstream tasks. We introduce whole-cell expression decoding (WCED), where models…

Contrastive learning has been demonstrated to be effective in enhancing pre-trained language models (PLMs) to derive superior universal sentence embeddings. However, existing contrastive methods still have two limitations. Firstly, previous…

Computation and Language · Computer Science 2022-10-11 Yuxin Jiang , Linhan Zhang , Wei Wang