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Related papers: APPA : Agentic Preformulation Pathway Assistant

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Biology has changed radically in the last two decades, transitioning from a descriptive science into a design science. Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable biofuels or…

Quantitative Methods · Quantitative Biology 2021-01-27 Tijana Radivojević , Zak Costello , Kenneth Workman , Hector Garcia Martin

Building biological models by inferring functional dependencies from experimental data is an im- portant issue in Molecular Biology. To relieve the biologist from this traditionally manual process, various approaches have been proposed to…

Machine Learning · Computer Science 2011-07-29 Max Ostrowski , Torsten Schaub , Markus Durzinsky , Wolfgang Marwan , Annegret Wagler

Modern therapeutic antibody design often involves composing multi-part assemblages of individual functional domains, each of which may be derived from a different source or engineered independently. While these complex formats can expand…

Machine Learning · Computer Science 2025-09-25 Jiayi Xin , Aniruddh Raghu , Nick Bhattacharya , Adam Carr , Melanie Montgomery , Hunter Elliott

Molecular simulations are essential tools in computational chemistry, enabling the prediction and understanding of molecular interactions and thermodynamic properties of biomolecules. However, traditional force fields face significant…

Chemical Physics · Physics 2024-06-17 Junhan Chang , Duo Zhang , Yuqing Deng , Hongrui Lin , Zhirong Liu , Linfeng Zhang , Hang Zheng , Xinyan Wang

The delivery of traditional substance education has remained problematic due to challenges in scalability, personalization, and the currency of information in a rapidly evolving substance use landscape. While artificial intelligence (AI)…

Computation and Language · Computer Science 2026-05-04 Kosar Haghani , Zahra Kolagar , Mohammed Atiquzzaman

Researchers and experts are taking efforts in delivering an optimal user experience from a long time. Computer interfaces are being developed to keep user 'in the flow' as well as for making users more connected to the real world wile using…

Human-Computer Interaction · Computer Science 2015-08-19 Pushkar Joshi

Summary: The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make modeling simpler, but largely exclude users from the process. We present an…

Biomolecules · Quantitative Biology 2017-02-08 Rowan Hatherley , David K. Brown , Özlem Tastan Bishop

We introduce an emerging AI-based approach and prototype system for assisting team formation when researchers respond to calls for proposals from funding agencies. This is an instance of the general problem of building teams when demand…

Information Retrieval · Computer Science 2022-11-29 Biplav Srivastava , Tarmo Koppel , Sai Teja Paladi , Siva Likitha Valluru , Rohit Sharma , Owen Bond

Accurate prediction of drug response in precision medicine requires models that capture how specific chemical substructures interact with cellular pathway states. However, most existing deep learning approaches treat chemical and…

Machine Learning · Computer Science 2026-04-14 Yewon Han , Sunghyun Kim , Eunyi Jeong , Sungkyung Lee , Seokwoo Yun , Sangsoo Lim

Drug discovery is a lengthy and resource-intensive process composed of multiple stages. Among these stages, lead optimization plays a critical role in transforming early hit compounds into viable drug candidates. This stage requires…

Machine Learning · Computer Science 2026-05-29 Lingxiao Li , Haobo Zhang , Ruohao Fan , Bin Chen , Jiayu Zhou

We present Experiment Automation Agents (EAA), a vision-language-model-driven agentic system designed to automate complex experimental microscopy workflows. EAA integrates multimodal reasoning, tool-augmented action, and optional long-term…

Artificial Intelligence · Computer Science 2026-02-18 Ming Du , Yanqi Luo , Srutarshi Banerjee , Michael Wojcik , Jelena Popovic , Mathew J. Cherukara

This paper studies a difference operator for stochastic systems whose specifications are represented by Abstract Probabilistic Automata (APAs). In the case refinement fails between two specifications, the target of this operator is to…

Logic in Computer Science · Computer Science 2015-07-01 Benoît Delahaye , Uli Fahrenberg , Kim G. Larsen , Axel Legay

Generative recommendation has recently emerged as a promising paradigm for sequential recommendation. It formulates the task as an autoregressive generation process, predicting tokens of the next item conditioned on user interaction…

Information Retrieval · Computer Science 2026-05-29 Yuanqing Yu , Yifan Wang , Weizhi Ma , Zhiqiang Guo , Min Zhang

Drug discovery is adapting to novel technologies such as data science, informatics, and artificial intelligence (AI) to accelerate effective treatment development while reducing costs and animal experiments. AI is transforming drug…

Artificial Intelligence · Computer Science 2023-07-14 Catrin Hasselgren , Tudor I. Oprea

In this work, we introduce a Self-Aware Polymorphic Architecture (SAPA) design approach to support emerging context-aware applications and mitigate the programming challenges caused by the ever-increasing complexity and heterogeneity of…

Hardware Architecture · Computer Science 2018-02-15 Michel A. Kinsy , Mihailo Isakov , Alan Ehret , Donato Kava

Pharmaceutical three-dimensional (3D) printing is an advanced fabrication technology with the potential to enable truly personalised dosage forms. Recent studies have integrated artificial intelligence (AI) to accelerate formulation and…

Artificial Intelligence · Computer Science 2026-05-19 Adeshola Okubena , Yusuf Ali Mohammed , Moe Elbadawi

Recent progress in large language model (LLM)-based multi-agent collaboration highlights the power of structured communication in enabling collective intelligence. However, existing methods largely rely on static or graph-based inter-agent…

Artificial Intelligence · Computer Science 2025-11-04 Song Wang , Zhen Tan , Zihan Chen , Shuang Zhou , Tianlong Chen , Jundong Li

Discovering new drug molecules is a pivotal yet challenging process due to the near-infinitely large chemical space and notorious demands on time and resources. Numerous generative models have recently been introduced to accelerate the drug…

Computational Engineering, Finance, and Science · Computer Science 2025-12-23 Shitong Luo , Wenhao Gao , Zuofan Wu , Jian Peng , Connor W. Coley , Jianzhu Ma

Scientific publication compresses a branching, iterative research process into a linear narrative, discarding the majority of what was discovered along the way. This compilation imposes two structural costs: a Storytelling Tax, where failed…

Drug combination therapy is a well-established strategy for disease treatment with better effectiveness and less safety degradation. However, identifying novel drug combinations through wet-lab experiments is resource intensive due to the…

Machine Learning · Computer Science 2023-01-18 Zhihang Hu , Qinze Yu , Yucheng Guo , Taifeng Wang , Irwin King , Xin Gao , Le Song , Yu Li