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Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…

Machine Learning · Computer Science 2025-10-01 Yogesh Verma , Markus Heinonen , Vikas Garg

To operate reliably under changing conditions, complex systems require feedback on how effectively they use resources, not just whether objectives are met. Current AI systems process vast information to produce sophisticated predictions,…

Artificial Intelligence · Computer Science 2026-03-10 Wael Hafez , Chenan Wei , Rodrigo Pena , Amir Nazeri , Cameron Reid

Motivation: We explored how explainable artificial intelligence (XAI) can help to shed light into the inner workings of neural networks for protein function prediction, by extending the widely used XAI method of integrated gradients such…

Machine Learning · Computer Science 2024-02-12 Markus Wenzel , Erik Grüner , Nils Strodthoff

Over the past decades, cognitive neuroscientists and behavioral economists have recognized the value of describing the process of decision making in detail and modeling the emergence of decisions over time. For example, the time it takes to…

Neurons and Cognition · Quantitative Biology 2025-07-24 Mrugsen Nagsen Gopnarayan , Jaan Aru , Sebastian Gluth

The recent surge in AI agents that autonomously communicate, collaborate with humans and use diverse tools has unlocked promising opportunities in various real-world settings. However, a vital aspect remains underexplored: how agents handle…

Machine Learning · Computer Science 2025-11-04 Nabeel Seedat , Jiashuo Liu , Mihaela van der Schaar

Engineering new molecules with desirable functions and properties has the potential to extend our ability to engineer proteins beyond what nature has so far evolved. Advances in the so-called "de novo" design problem have recently been…

Machine Learning · Computer Science 2023-10-17 Adam Winnifrith , Carlos Outeiral , Brian Hie

Cognitive Psychology and related disciplines have identified several critical mechanisms that enable intelligent biological agents to learn to solve complex problems. There exists pressing evidence that the cognitive mechanisms that enable…

Artificial Intelligence · Computer Science 2022-08-19 Manfred Eppe , Christian Gumbsch , Matthias Kerzel , Phuong D. H. Nguyen , Martin V. Butz , Stefan Wermter

Graphical models are widely used to study complex multivariate biological systems. Network inference algorithms aim to reverse-engineer such models from noisy experimental data. It is common to assess such algorithms using techniques from…

Methodology · Statistics 2014-03-03 Chris J. Oates , Richard Amos , Simon E. F. Spencer

Artificial intelligence built on large foundation models has transformed language understanding, vision and reasoning, yet these systems remain isolated and cannot readily share their capabilities. Integrating the complementary strengths of…

Artificial Intelligence · Computer Science 2026-02-17 Siyang Li , Chenhao Liu , Dongrui Wu , Zhigang Zeng , Lieyun Ding

Multi-agent systems powered by large language models have demonstrated remarkable capabilities across diverse domains, yet existing automated design approaches seek monolithic solutions that fail to adapt resource allocation based on query…

Artificial Intelligence · Computer Science 2025-10-06 Bo Ma , Hang Li , ZeHua Hu , XiaoFan Gui , LuYao Liu , Simon Liu

Biological data are extremely diverse, complex but also quite sparse. The recent developments in deep learning methods are offering new possibilities for the analysis of complex data. However, it is easy to be get a deep learning model that…

Machine Learning · Computer Science 2019-01-21 Florian Richoux , Charlène Servantie , Cynthia Borès , Stéphane Téletchéa

Biomarker discovery is vital in advancing personalized medicine, offering insights into disease diagnosis, prognosis, and therapeutic efficacy. Traditionally, the identification and validation of biomarkers heavily depend on extensive…

Machine Learning · Computer Science 2024-09-25 Wangyang Ying , Dongjie Wang , Xuanming Hu , Ji Qiu , Jin Park , Yanjie Fu

With the advent of large multimodal language models, science is now at a threshold of an AI-based technological transformation. An emerging ecosystem of models and tools aims to support researchers throughout the scientific lifecycle,…

Artificial Intelligence (AI) technologies could be broadly categorised into Analytics and Autonomy. Analytics focuses on algorithms offering perception, comprehension, and projection of knowledge gleaned from sensorial data. Autonomy…

Artificial Intelligence · Computer Science 2018-12-24 Hussein Abbass , John Harvey , Kate Yaxley

High-precision CNC machining of free-form aerospace components requires bounded compensations informed by inspection, simulation, and process knowledge. Off-the-shelf large language model (LLM) assistants can generate text, but they do not…

Agent based systems are more common than we may think. A Promise Theory perspective on cooperation, in systems of human-machine agents, offers a unified perspective on organization and functional design with semi-automated efforts, in terms…

Artificial Intelligence · Computer Science 2026-04-14 M. Burgess

Generative AI models are increasingly being integrated into human task workflows, enabling the production of expressive content across a wide range of contexts. Unlike traditional human-AI design methods, the new approach to designing…

Human-Computer Interaction · Computer Science 2025-04-01 Hari Subramonyam , Divy Thakkar , Andrew Ku , Jürgen Dieber , Anoop Sinha

The field of prompt engineering is becoming an essential phenomenon in artificial intelligence. It is altering how data scientists interact with large language models (LLMs) for analytics applications. This research paper shares empirical…

Digital Libraries · Computer Science 2026-02-03 Snehasish Paul , Rohit Kumar , Laxman Das

Introduction: Artificial intelligence (AI) is exhibiting tremendous potential to reduce the massive costs and long timescales of drug discovery. There are however important challenges currently limiting the impact and scope of AI models.…

Other Quantitative Biology · Quantitative Biology 2024-09-25 Ghita Ghislat , Saiveth Hernandez-Hernandez , Chayanit Piyawajanusorn , Pedro J. Ballester

Many promising-looking ideas in AI research fail to deliver, but their validation takes substantial human labor and compute. Predicting an idea's chance of success is thus crucial for accelerating empirical AI research, a skill that even…

Artificial Intelligence · Computer Science 2025-06-03 Jiaxin Wen , Chenglei Si , Yueh-han Chen , He He , Shi Feng