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Large Language Models (LLMs) have revolutionized the field of natural language processing, but they fall short in comprehending biological sequences such as proteins. To address this challenge, we propose InstructProtein, an innovative LLM…

Biomolecules · Quantitative Biology 2023-10-06 Zeyuan Wang , Qiang Zhang , Keyan Ding , Ming Qin , Xiang Zhuang , Xiaotong Li , Huajun Chen

We address the problem of Bayesian structure learning for domains with hundreds of variables by employing non-parametric bootstrap, recursively. We propose a method that covers both model averaging and model selection in the same framework.…

Machine Learning · Statistics 2018-09-14 Raanan Y. Rohekar , Yaniv Gurwicz , Shami Nisimov , Guy Koren , Gal Novik

Recent years have seen a paradigm shift in NLP towards using pretrained language models ({PLM}) for a wide range of tasks. However, there are many difficult design decisions to represent structures (e.g. tagged text, coreference chains) in…

Computation and Language · Computer Science 2022-11-18 Tianyu Liu , Yuchen Jiang , Nicholas Monath , Ryan Cotterell , Mrinmaya Sachan

Large language models (LLMs) excel at generating code from natural language (NL) descriptions. However, the plain textual descriptions are inherently ambiguous and often fail to capture complex requirements like intricate system behaviors,…

Artificial Intelligence · Computer Science 2025-11-06 Wenxin Mao , Zhitao Wang , Long Wang , Sirong Chen , Cuiyun Gao , Luyang Cao , Ziming Liu , Qiming Zhang , Jun Zhou , Zhi Jin

Human cognition excels at transcending sensory input and forming latent representations that structure our understanding of the world. While Large Language Model (LLM) agents demonstrate emergent reasoning and decision-making abilities,…

Machine Learning · Computer Science 2026-01-22 Hengguan Huang , Xing Shen , Songtao Wang , Lingfa Meng , Dianbo Liu , David Alejandro Duchene , Hao Wang , Samir Bhatt

In statistics and machine learning, detecting dependencies in datasets is a central challenge. We propose a novel neural network model for supervised graph structure learning, i.e., the process of learning a mapping between observational…

Machine Learning · Statistics 2024-02-14 Philipp Froehlich , Heinz Koeppl

A Bayesian network is a widely used probabilistic graphical model with applications in knowledge discovery and prediction. Learning a Bayesian network (BN) from data can be cast as an optimization problem using the well-known…

Artificial Intelligence · Computer Science 2020-09-01 Zhenyu A. Liao , Charupriya Sharma , James Cussens , Peter van Beek

Large language models (LLMs) are becoming attractive as few-shot reasoners to solve Natural Language (NL)-related tasks. However, the understanding of their capability to process structured data like tables remains an under-explored area.…

Computation and Language · Computer Science 2024-07-18 Yuan Sui , Mengyu Zhou , Mingjie Zhou , Shi Han , Dongmei Zhang

Current statistical models for structured prediction make simplifying assumptions about the underlying output graph structure, such as assuming a low-order Markov chain, because exact inference becomes intractable as the tree-width of the…

Machine Learning · Computer Science 2010-03-26 Xu Miao , Rajesh P. N. Rao

Large language models (LLMs) can be seen as atomic units of computation mapping sequences to a distribution over sequences. Thus, they can be seen as stochastic language layers in a language network, where the learnable parameters are the…

Effective decision-making on networks often relies on learning from graph-structured data, where Graph Neural Networks (GNNs) play a central role, but they take efforts to configure and tune. In this demo, we propose LLMNet, showing how to…

Machine Learning · Computer Science 2025-06-18 Xiaohan Zheng , Lanning Wei , Yong Li , Quanming Yao

Bayesian networks (BNs) are widely used graphical models usable to draw statistical inference about Directed acyclic graphs (DAGs). We presented here Graph_sampler a fast free C language software for structural inference on BNs.…

Computation · Statistics 2016-02-05 Sagnik Datta , Ghislaine Gayraud , Eric Leclerc , Frederic Y. Bois

Large Language Models (LLMs) have demonstrated strong performance across a wide range of tasks, yet they still struggle with complex mathematical reasoning, a challenge fundamentally rooted in deep structural dependencies. To address this…

Artificial Intelligence · Computer Science 2025-12-01 Lei Zan , Keli Zhang , Ruichu Cai , Lujia Pan

Large language models (LLMs) have demonstrated remarkable in-context reasoning capabilities across a wide range of tasks, particularly with unstructured inputs such as language or images. However, LLMs struggle to handle structured data,…

Machine Learning · Computer Science 2025-02-20 Jintang Li , Ruofan Wu , Yuchang Zhu , Huizhe Zhang , Liang Chen , Zibin Zheng

Bayesian networks in their Factor Graph Reduced Normal Form (FGrn) are a powerful paradigm for implementing inference graphs. Unfortunately, the computational and memory costs of these networks may be considerable, even for relatively small…

Machine Learning · Statistics 2021-06-22 Giovanni Di Gennaro , Amedeo Buonanno , Francesco A. N. Palmieri

Large Language Models (LLMs) are known for their expensive and time-consuming training. Thus, oftentimes, LLMs are fine-tuned to address a specific task, given the pretrained weights of a pre-trained LLM considered a foundation model. In…

Computation and Language · Computer Science 2025-12-05 Eshed Gal , Moshe Eliasof , Javier Turek , Uri Ascher , Eran Treister , Eldad Haber

Large language models (LLMs) have exhibited remarkable capabilities across diverse open-domain tasks, yet their application in specialized domains such as civil engineering remains largely unexplored. This paper starts bridging this gap by…

Computation and Language · Computer Science 2025-07-08 Jiachen Liu , Ziheng Geng , Ran Cao , Lu Cheng , Paolo Bocchini , Minghui Cheng

In recent years, the rapid advancement of large language models (LLMs) in natural language processing has sparked significant interest among researchers to understand their mechanisms and functional characteristics. Although prior studies…

Neurons and Cognition · Quantitative Biology 2026-01-08 Yiheng Liu , Zhengliang Liu , Zihao Wu , Junhao Ning , Haiyang Sun , Sichen Xia , Yang Yang , Xiaohui Gao , Ning Qiang , Bao Ge , Tianming Liu , Junwei Han , Xintao Hu

Analyzing network topologies and communication graphs plays a crucial role in contemporary network management. However, the absence of a cohesive approach leads to a challenging learning curve, heightened errors, and inefficiencies. In this…

Networking and Internet Architecture · Computer Science 2023-08-14 Sathiya Kumaran Mani , Yajie Zhou , Kevin Hsieh , Santiago Segarra , Ranveer Chandra , Srikanth Kandula

Distilling underlying principles from data has historically driven scientific breakthroughs. However, conventional data-driven machine learning often produces complex models that lack interpretability and generalization due to insufficient…

Materials Science · Physics 2025-07-28 Zhilong Song , Qionghua Zhou , Chunjin Ren , Chongyi Ling , Minggang Ju , Jinlan Wang