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Alzheimer's Disease Analysis Model (ADAM) is a multi-agent reasoning large language model (LLM) framework designed to integrate and analyze multimodal data, including microbiome profiles, clinical datasets, and external knowledge bases, to…

Artificial Intelligence · Computer Science 2025-08-22 Ziyuan Huang , Vishaldeep Kaur Sekhon , Roozbeh Sadeghian , Maria L. Vaida , Cynthia Jo , Doyle Ward , Vanni Bucci , John P. Haran

Reasoning lies at the heart of intelligence, shaping the ability to make decisions, draw conclusions, and generalize across domains. In artificial intelligence, as systems increasingly operate in open, uncertain, and multimodal…

Large Reasoning Models (LRMs) often suffer from the ``over-thinking'' problem, generating unnecessarily long reasoning on simple tasks. Some strategies have been proposed to mitigate this issue, such as length penalties or routing…

Computation and Language · Computer Science 2025-10-16 Jian Xie , Zhendong Chu , Aoxiao Zhong , Kai Zhang , Mingzhe Han , Xing Fan , Jialie Shen , Qingsong Wen

Large language models (LLMs) have recently gained significant attention as a promising approach to accelerate scientific discovery. However, their application in open-ended scientific domains such as biology remains limited, primarily due…

Machine Learning · Computer Science 2026-05-21 Yunhui Jang , Lu Zhu , Jake Fawkes , Alisandra Kaye Denton , Dominique Beaini , Emmanuel Noutahi

Predicting how cells respond to genetic perturbations is fundamental to understanding gene function, disease mechanisms, and therapeutic development. While recent deep learning approaches have shown promise in modeling single-cell…

Machine Learning · Computer Science 2026-03-10 Andrea Giuseppe Di Francesco , Andrea Rubbi , Pietro Liò

Reinforcement learning (RL) has recently shown promise in predicting Alzheimer's disease (AD) progression due to its unique ability to model domain knowledge. However, it is not clear which RL algorithms are well-suited for this task.…

Recent healthcare foundation models have achieved strong predictive performance through large scale self supervised learning, yet their latent representations frequently entangle physiologic severity, intervention intensity, observational…

Machine Learning · Computer Science 2026-05-19 Yuanyun Zhang , Shi Li

Reinforcement Learning has significantly advanced the reasoning capabilities of Multimodal Large Language Models (MLLMs), yet the resulting policies remain brittle against real-world visual degradations such as blur, compression artifacts,…

Computer Vision and Pattern Recognition · Computer Science 2026-05-12 Rui Liu , Dian Yu , Haolin Liu , Yucheng Shi , Tong Zheng , Runpeng Dai , Haitao Mi , Pratap Tokekar , Leoweiliang

Although Vision Language Models (VLMs) have shown strong generalization in medical imaging, pathology presents unique challenges due to ultra-high resolution, complex tissue structures, and nuanced clinical semantics. These factors make…

Computer Vision and Pattern Recognition · Computer Science 2026-03-24 Wenchuan Zhang , Jingru Guo , Hengzhe Zhang , Penghao Zhang , Jie Chen , Shuwan Zhang , Zhang Zhang , Yuhao Yi , Hong Bu

Predicting the responses of a cell under perturbations may bring important benefits to drug discovery and personalized therapeutics. In this work, we propose a novel graph variational Bayesian causal inference framework to predict a cell's…

We train a neural network to predict distributional responses in gene expression following genetic perturbations. This is an essential task in early-stage drug discovery, where such responses can offer insights into gene function and inform…

Despite the success of large vision and language models (VLMs) in many downstream applications, it is unclear how well they encode compositional information. Here, we create the Attribution, Relation, and Order (ARO) benchmark to…

Computer Vision and Pattern Recognition · Computer Science 2023-03-27 Mert Yuksekgonul , Federico Bianchi , Pratyusha Kalluri , Dan Jurafsky , James Zou

Visual reasoning models (VRMs) have recently shown strong cross-modal reasoning capabilities by integrating visual perception with language reasoning. However, they often suffer from overthinking, producing unnecessarily long reasoning…

Computer Vision and Pattern Recognition · Computer Science 2026-04-17 Yixu Huang , Tinghui Zhu , Muhao Chen

Reduced Order Models (ROMs) are of considerable importance in many areas of engineering in which computational time presents difficulties. Established approaches employ projection-based reduction such as Proper Orthogonal Decomposition,…

Numerical Analysis · Mathematics 2023-04-26 Thomas Simpson , Konstantinos Vlachas , Anthony Garland , Nikolaos Dervilis , Eleni Chatzi

Unified multimodal models (UMMs) aim to integrate multimodal understanding and generation within a unified architecture, yet it remains unclear to what extent their representations are truly aligned across modalities. To investigate this…

Computation and Language · Computer Science 2026-04-08 Cheng Yang , Chufan Shi , Bo Shui , Yaokang Wu , Muzi Tao , Huijuan Wang , Ivan Yee Lee , Yong Liu , Xuezhe Ma , Taylor Berg-Kirkpatrick

Recent advances in embodied AI highlight the potential of vision language models (VLMs) as agents capable of perception, reasoning, and interaction in complex environments. However, top-performing systems rely on large-scale models that are…

Autonomous science promises to augment scientific discovery, particularly in complex fields like biomedicine. However, this requires AI systems that can consistently generate novel and diverse solutions to open-ended problems. We evaluate…

Artificial Intelligence · Computer Science 2026-05-13 Andrew Shen , Shaul Druckmann , James Zou

Inhibiting a signalling pathway concerns controlling the cellular processes of a cancer cell's viability, cell division, and death. Assay protocols created to see if the molecular structures of the drugs being tested have the desired…

Quantitative Methods · Quantitative Biology 2022-07-19 Roumen Anguelov , G Manjunath , Avulundiah E Phiri , Trevor T Nyakudya , Priyesh Bipath , June C Serem , Yvette N Hlophe

We consider the problem of predicting perturbation effects via causal models. In many applications, it is a priori unknown which mechanisms of a system are modified by an external perturbation, even though the features of the perturbation…

Machine Learning · Computer Science 2025-07-02 Nora Schneider , Lars Lorch , Niki Kilbertus , Bernhard Schölkopf , Andreas Krause

Instruction-guided image editing offers an intuitive way for users to edit images with natural language. However, diffusion-based editing models often struggle to accurately interpret complex user instructions, especially those involving…

Computer Vision and Pattern Recognition · Computer Science 2026-02-26 Ziyun Zeng , Hang Hua , Jiebo Luo