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RESEARCH PAPER · npj Systems Biology and Applications · 2021

Nobel Turing Challenge: creating the engine for scientific discovery

Hiroaki Kitano

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Nobel Turing Challenge: creating the engine for scientific discoveryOriginalToward Building Science Discovery Machines0AI Descartes: Combining Data and Theory for Derivable Scientific Discovery1Rawls’s Original Position and Algorithmic Fairness17Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs4A WAY TO SUSTAINABLE CROP PRODUCTION THROUGH SCIENTIST−FARMER ENGAGEMENT4From materials discovery to system optimization by integrating combinatorial electrochemistry and data science37Robotic search for optimal cell culture in regenerative medicine99Social impact and governance of AI and neurotechnologies43Automated Rational Design of Metal–Organic Polyhedra45Automation of yeast spot assays using an affordable liquid handling robot1Brokering between tenants for an international materials acceleration platform5Using natural language processing to find research topics in Living Machines conferences and their intersections with Bioinspiration & Biomimetics publications3SCICERO: A deep learning and NLP approach for generating scientific knowledge graphs in the computer science domain51On scientific understanding with artificial intelligence372Automation of yeast spot assays using an affordable liquid handling robot15Knowledge Engineering in Chemistry: From Expert Systems to Agents of Creation23What is missing in autonomous discovery: open challenges for the community44Enabling technology and core theory of synthetic biology65Biological research and self-driving labs in deep space supported by artificial intelligence49Modelplasticity and abductive decision making3Autonomous experimental systems in materials science22Artificial intelligence adoption in the physical sciences, natural sciences, life sciences, social sciences and the arts and humanities: A bibliometric analysis of research publications from 1960-2021140Artificial intelligence for science and engineering: A priority for public investment in research and development2Eroom’s Law and the decline in the productivity of biopharmaceutical R&D0High-performance computing leadership to enable advances in artificial intelligence and a thriving compute ecosystem0Interpretability: Should – and can – we understand the reasoning of machine-learning systems?0Lessons from shortcomings in machine learning for medical imaging1Preface0Quantifying the “cognitive extent” of science and how it has changed over time and across countries0The end of Moore’s Law? Innovation in computer systems continues at a high pace0Leveraging pre-trained language models for mining microbiome-disease relationships41Chemical Species Ontology for Data Integration and Knowledge Discovery38How do clinical researchers generate data-driven scientific hypotheses? Cognitive events using think-aloud protocol4Curiosity-driven AI for Science : Automated Discovery of Self-Organized Structures0Formalizing chemical physics using the Lean theorem prover6Hypotheses devised by AI could find ‘blind spots’ in research23Asking the right questions for mutagenicity prediction from BioMedical text3Data-driven hypothesis generation among inexperienced clinical researchers: A comparison of secondary data analyses with visualization (VIADS) and other tools8Data-Driven Hypothesis Generation in Clinical Research: What We Learned from a Human Subject Study?5Revisiting Self-Operating Mathematical Universe (SOMU) as a Theory for Artificial General Intelligence, AGI and G+ Consciousness2Using think-aloud protocol to identify cognitive events while generating data-driven scientific hypotheses by inexperienced clinical researchers.1A dynamic knowledge graph approach to distributed self-driving laboratories108Towards AI Research Agents in the Chemical Sciences3Hacking decarbonization with a community-operated CreatorSpace8CRISPR-Based Therapies: Revolutionizing Drug Development and Precision Medicine23Transforming research laboratories with connected digital twins19Intrinsic and post-hoc XAI approaches for fingerprint identification and response prediction in smart manufacturing processes32Artificial intelligence and illusions of understanding in scientific research681Replicating a High-Impact Scientific Publication Using Systems of Large Language Models4The automated lab of tomorrow15Towards Machine-FAIR: Representing software and datasets to facilitate reuse and scientific discovery by machines2The digital lab manager: Automating research support14Dynamic knowledge graph applications for augmented built environments through “The World Avatar”15Artificial Intelligence in the Digital Economy: Intellectual Property Protection Challenges0Desafios da IA responsável na pesquisa científica5Towards End-to-End Prompt-Vision-Physics Neural Network for Fast Design Discovery2Machine learning in drug delivery82Evolving scientific discovery by unifying data and background knowledge with AI Hilbert21Beyond protein lists: AI-assisted interpretation of proteomic investigations in the context of evolving scientific knowledge13Investigating questionable research practices among Iranian applied linguists: Prevalence, severity, and the role of artificial intelligence tools18Link prediction for hypothesis generation: an active curriculum learning infused temporal graph-based approach7Self-Driving Laboratories for Chemistry and Materials Science674The Digital Lab Facility Manager: Automating operations of research laboratories through “The World Avatar”15Autonomous materials research and design: Characterization6Autonomous research and development of structural materials – An introduction and vision21Human Rights and Ethics Guiding Human-Machine Teaming2Towards next-gen smart manufacturing systems: the explainability revolution27Redefining Roles: A Paradigm Shift in Tryptophan–Kynurenine Metabolism for Innovative Clinical Applications58Automating care by self-maintainability for full laboratory automation9Conceptual Models of the AI-Materials Scientist Interface — From Tool to Collaborator: A Review Study0Harnessing the leading edge: machine learning ventures in chemistry and materials science3Multi-objective Bayesian optimization: a case study in material extrusion15Science-Gym: A Simple Testbed for AI-Driven Scientific Discovery0Science: logos, intellectual intuition, and first principles0Blurring the boundaries between living and non-living? Examining and mapping the living properties of engineered matter and systems4Automating the practice of science: Opportunities, challenges, and implications47Dehumanizing the human, humanizing the machine: organic consciousness as a hallmark of the persistence of the human against the backdrop of artificial intelligence11A comprehensive large-scale biomedical knowledge graph for AI-powered data-driven biomedical research51An out-of-hours cell culture autopilot proof of concept based on a modular architecture using the SiLA2 open standard2When ChatGPT Writes Your Research Proposal: Scientific Creativity in the Age of Generative AI6GeoFactory: an LLM performance enhancement framework for geoscience factual and inferential tasks6Self-Driving Laboratories: Translating Materials Science from Laboratory to Factory9A large-scale replication of scenario-based experiments in psychology and management using large language models35Exploring the role of large language models in the scientific method: from hypothesis to discovery89Is Automated Discovery Expanding Human Understanding? On the Role of Machine Learning in the Increase of Scientific Understanding1AI-Assisted Tools for Scientific Review Writing: Opportunities and Cautions21BioLab: End-to-End Autonomous Life Sciences Research with Multi-Agents System Integrating Biological Foundation Models3Leveraging 3D Cell Culture and Artificial Intelligence Technologies for Regenerative Medicine1Does ChatGPT know what robots are thinking? - Evaluation of human-created vs. AI-generated scientific ideas0Will AI ever win its own Nobel? Some predict a prize-worthy science discovery soon2Autonomous alloy composition optimization using molecular dynamics guided by a large language model5Credence, attribution, and creativity in the construction of literary meaning with generative artificial intelligence1BioLabAgents: A Multi-Agent Framework for Scientific Idea Generation and Evaluation on Biomedical Research Trajectories0Collaborative AI-Integrated Model for Reviewing Educational Literature1Pareto-Optimal Experimentation: Human-Guided Multi-Objective Bayesian Optimization in Scanning Probe Microscopy4A Survey on Agentic AI: Applications, Challenges and Evaluation Frameworks0Combinatorial to autonomous experimentation0Multi-stage Bayesian optimisation for dynamic decision-making in self-driving labs1Science-Gym: a simple testbed for AI-driven scientific discovery1Shifting the educational paradigm: Discovering concepts and connections0Artificial Intelligence Nanocomposite Synergy for Next-Generation Fuel Desulfurization0Automated Discovery of Multicellular Behavior for Optimized Plant Growth and Climate Resilience0Bringing ML to the real world: Rewards are all we need1The future of fundamental science led by generative closed-loop artificial intelligence11How Artificial Intelligence is Shaping Life Sciences: Systematic Qualitative Review with a Future-oriented Analytical Framework0Expanding diversity in chemical space1Agentic AI for autonomous discovery of radiation-tolerant CoCrFeMnNi high entropy alloys3New tools drive scientific discovery: evidence from all nobel-prize and major non-nobel breakthroughs1Creating an engine of scientific discovery, an Indo-Japan perspective: learnings from IJNTC 2025 workshop1Convenience AI0A Neutrosophic Topological Approach to Scientific Decision Architectures: Structural Stability, Convergence, and Information Dynamics1A restricted GRN for the exploration of regulatory subnetworks for COVID-19 and CXCR40A schematic view of the modeling and type of results for COVID-190An inferred pathway correlating ACE2 and COVID-190An instance of report.txt for CREB-phosphorylation0Evaluation of names recognition in biopatternsg (level 1)0Evaluation of pairs-like relations generation in biopatternsg (level 2)0Evaluation of pairs-like relations generation in Biopatternsg with small molecules0Evaluation of pairs-like relations generation in Biopatternsg without small molecules0Evaluation of relations extraction in biopatternsg (level 3)0Evaluation of relations extraction in Biopatternsg with small molecules0Evaluation of relations extraction in Biopatternsg without small molecules0KBs organized following the steps in Fig. 1 and Fig. 6 (Part 1)0KBs organized following the steps in Fig. 1 and Fig. 6 (Part 2)0Pathways Commons sif file of the reactome’s pathway named creb phosphorylation (prolog format)0Regulatory events knowledge base (KB)0Restricted GRN to explore subnetworks for COVID-19 and CXCR40Subnetworks for the regulation of COVID-19 and CXCR4 (Part 1)0Subnetworks for the regulation of COVID-19 and CXCR4 (Part 2)0Work-flow for the semantic modeling and analyzing of a GRN0Конвейер обработки данных с использованием искусственного интеллекта для моделирования и анализа сетей регуляции генов0IA para los datos, Ciencia para el criterio: un modelo de trabajo para la investigación científica0From Black Box to Clarity: A Systematic Review of Explainability Methods in Deep Convolutional Neural Networks0Regulatory Integration, Multistability, and Organizational-State Transitions in Biological Systems0AI is Sustainable. Scientific Knowledge Isn't? Reconsidering Human Intellect in the Age of Artificial Intelligence0Core AI and Machine Learning Architectures for Biological Sequence and Structure Modelling0Self-driving labs: A new paradigm in cell culture0From environmental sensing to societal listening0KI in der Sportpsychologie: Chancen und Herausforderungen0

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  1. Toward Building Science Discovery Machines

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  2. AI Descartes: Combining Data and Theory for Derivable Scientific Discovery

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  3. Rawls’s Original Position and Algorithmic Fairness

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  4. Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs

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  5. A WAY TO SUSTAINABLE CROP PRODUCTION THROUGH SCIENTIST−FARMER ENGAGEMENT

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  9. Automated Rational Design of Metal–Organic Polyhedra

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  10. Automation of yeast spot assays using an affordable liquid handling robot

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  12. Using natural language processing to find research topics in Living Machines conferences and their intersections with Bioinspiration & Biomimetics publications

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  13. SCICERO: A deep learning and NLP approach for generating scientific knowledge graphs in the computer science domain

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  14. On scientific understanding with artificial intelligence

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  15. Automation of yeast spot assays using an affordable liquid handling robot

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  16. Knowledge Engineering in Chemistry: From Expert Systems to Agents of Creation

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  17. What is missing in autonomous discovery: open challenges for the community

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  27. Lessons from shortcomings in machine learning for medical imaging

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  28. Preface

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  29. Quantifying the “cognitive extent” of science and how it has changed over time and across countries

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  30. The end of Moore’s Law? Innovation in computer systems continues at a high pace

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  31. Leveraging pre-trained language models for mining microbiome-disease relationships

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  32. Chemical Species Ontology for Data Integration and Knowledge Discovery

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  33. How do clinical researchers generate data-driven scientific hypotheses? Cognitive events using think-aloud protocol

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  34. Curiosity-driven AI for Science : Automated Discovery of Self-Organized Structures

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  35. Formalizing chemical physics using the Lean theorem prover

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  36. Hypotheses devised by AI could find ‘blind spots’ in research

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  37. Asking the right questions for mutagenicity prediction from BioMedical text

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  38. Data-driven hypothesis generation among inexperienced clinical researchers: A comparison of secondary data analyses with visualization (VIADS) and other tools

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  39. Data-Driven Hypothesis Generation in Clinical Research: What We Learned from a Human Subject Study?

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  40. Revisiting Self-Operating Mathematical Universe (SOMU) as a Theory for Artificial General Intelligence, AGI and G+ Consciousness

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  41. Using think-aloud protocol to identify cognitive events while generating data-driven scientific hypotheses by inexperienced clinical researchers.

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  42. A dynamic knowledge graph approach to distributed self-driving laboratories

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  43. Towards AI Research Agents in the Chemical Sciences

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  44. Hacking decarbonization with a community-operated CreatorSpace

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  45. CRISPR-Based Therapies: Revolutionizing Drug Development and Precision Medicine

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  46. Transforming research laboratories with connected digital twins

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  48. Artificial intelligence and illusions of understanding in scientific research

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  49. Replicating a High-Impact Scientific Publication Using Systems of Large Language Models

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  50. The automated lab of tomorrow

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