GEMOT: Towards Mechanistic World Models for Biology

LLMs and World Models, Part 1

How do Large Language Models Make Sense of Their “Worlds”?

Artificial intelligences and human scientists exhibit...

We investigate the effectiveness of artificial intelligences (AI)-specifically large language models (LLMs)-relative to human scientists at high-level cognitive tasks in social science such as...

Higher-Order Knowledge Representations for Agentic Scientific Reasoning

Scientific inquiry requires systems-level reasoning that integrates heterogeneous experimental data, cross-domain knowledge, and mechanistic evidence into coherent explanations. While Large Language Models (LLMs) offer inferential capabilities, they often depend on retrieval-augmented contexts that lack structural depth. Traditional Knowledge Graphs (KGs) attempt to bridge this gap, yet their pairwise constraints fail to capture the irreducible higher-order interactions that govern emergent physical behavior. To address this, we introduce a methodology for constructing hypergraph-based knowledge representations that faithfully encode multi-entity relationships. Applied to a corpus of ≈\approx 1,100 manuscripts on biocomposite scaffolds, our framework constructs a global hypergraph of 161,172 nodes and 320,201 hyperedges, revealing a scale-free topology (power law exponent ≈\approx 1.23) organized around highly connected conceptual hubs. This representation prevents the combinatorial explosion typical of pairwise expansions and explicitly preserves the co-occurrence context of scientific formulations. We further demonstrate that equipping agentic systems with hypergraph traversal tools, specifically using node-intersection constraints, enables them to bridge semantically distant concepts. By exploiting these higher-order pathways, the system successfully generates grounded mechanistic hypotheses for novel composite materials, such as linking cerium oxide to PCL scaffolds via chitosan intermediates. This work establishes a “teacherless” agentic reasoning system where hypergraph topology acts as a verifiable guardrail, accelerating scientific discovery by uncovering relationships obscured by traditional graph methods.

The unintended consequences of large language models as a labor-augmenting technology in science

As a labor-augmenting technology, large language models (LLMs) have the potential to accelerate scientific activity across the research pipeline. But even if LLMs perform on par with human experts at selected tasks, their use will bring unintended consequences as they alter the balance of frictions and inducements that steer the allocation of research effort across projects. Here we develop a simple mathematical model to illustrate. In fields where LLMs are useful primarily as tools for discovering promising projects, researchers will become more selective about what they publish; where they facilitate the process of publishing existing data, researchers will become less selective. By allowing scientists to work more quickly, LLMs raise the opportunity cost of researcher time, creating incentives to refine papers less thoroughly before moving on. Enticing as it is to imagine that, by saving us time on mundane tasks, LLMs will provide us with more time to think deeply and develop projects completely, our results temper such hopes.

The unintended consequences of large language models as a labor-augmenting technology in science

As a labor-augmenting technology, large language models (LLMs) have the potential to accelerate scientific activity across the research pipeline. But even if LLMs perform on par with human experts at selected tasks, their use will bring unintended consequences as they alter the balance of frictions and inducements that steer the allocation of research effort across projects. Here we develop a simple mathematical model to illustrate. In fields where LLMs are useful primarily as tools for discovering promising projects, researchers will become more selective about what they publish; where they facilitate the process of publishing existing data, researchers will become less selective. By allowing scientists to work more quickly, LLMs raise the opportunity cost of researcher time, creating incentives to refine papers less thoroughly before moving on. Enticing as it is to imagine that, by saving us time on mundane tasks, LLMs will provide us with more time to think deeply and develop projects completely, our results temper such hopes.

Augmenting Research Ideation with Data: An Empirical Investigation...

Recent advancements in large language models (LLMs) demonstrate strong potential for generating novel research ideas, yet such ideas often struggle with feasibility and effectiveness. In this...

Beyond Model Collapse: Scaling Up with Synthesized Data Requires...

Large Language Models (LLM) are increasingly trained on data generated by other LLM, either because generated text and images become part of the pre-training corpus, or because synthetized data is...

The lost art of mathematical modelling

We provide a critique of mathematical biology in light of rapid developments in modern machine learning. We argue that out of the three modelling activities – (1) formulating models; (2) analysing models; and (3) fitting or comparing models to data – inherent to mathematical biology, researchers currently focus too much on activity (2) at the cost of (1). This trend, we propose, can be reversed by realising that any given biological phenomenon can be modelled in an infinite number of different ways, through the adoption of a pluralistic approach, where we view a system from multiple, different points of view. We explain this pluralistic approach using fish locomotion as a case study and illustrate some of the pitfalls – universalism, creating models of models, etc. – that hinder mathematical biology. We then ask how we might rediscover a lost art: that of creative mathematical modelling.

Bending the Curve: How AI is Transforming Scientific Discovery

Discover how researchers use LLMs and specialized AI models like AlphaFold as complementary tools to accelerate innovation and expand the scientific frontier.

Hypothesis generation and updating in large language models

Large language models (LLMs) increasingly help people solve problems, from debugging code to repairing machinery. This process requires generating plausible hypotheses from partial descriptions,...

Large language models are not the problem

If a Large Language Model (LLM) can replicate your scientific contribution, the problem is not the LLM. What does it say about our field that so much of the anxiety about AI comes down to the fear that a machine could do what we do? Perhaps it says we should be doing something better.

Critiques of World Models

Specifically, a World Model (WM) is a generative model that simulates the possibilities in diverse scenarios (e.g., physical world, mental world, social world, and evolutionary world). Operationally, a WM takes previous world state s𝑠sitalic_s and action a𝑎aitalic_a, and predicts or simulates the next world state s′superscript𝑠′s^{\prime}italic_s start_POSTSUPERSCRIPT ′ end_POSTSUPERSCRIPT through a transformation function, such as a conditional probability distribution:

Agentic Laboratories of the Future: Towards World Models for Scientific Discovery

Scientific discovery is fundamentally a problem-solving process involving distributed intelligence. Human intuition, computational reasoning, and experimental execution are distributed across people, instruments, and software systems, limiting the speed and scale of discovery. Although automation, high-throughput experimentation, foundation models, and cloud infrastructure have accelerated individual stages of the scientific workflow, they have not unified the discovery process. We hypothesize that the next generation of laboratories will be agentic: environments in which scientists, AI systems, and robotic platforms operate as collaborative discovery partners, with humans contributing the parts of discovery that remain hardest to make explicit: asking the right questions and holding provisional mechanistic models of how a system works. The key missing layer is an agentic harnessing layer that continuously integrates hypothesis, literature-derived evidence, experimental data, uncertainty, and experimental state into a shared “laboratory world model”—a dynamic representation of the scientific system and its evolving context. By maintaining and updating this lab world model, the agentic harnessing layer enables coordinated decision-making, adaptive planning, and increasingly autonomous scientific workflows across humans and machines. A central challenge is that much of the scientific research process remains inaccessible to machines, including tacit knowledge, human observations, adaptive decision-making, and evolving experimental context. Advances in multimodal AI and immersive interfaces may help bridge this gap, allowing humans, agents, and robotic systems to collaborate seamlessly in scientific discovery rather than simply automating isolated tasks. Agentic laboratories could provide a new architecture for science, integrating human, artificial, and physical intelligence into a unified discovery system.

Large language model

A large language model (LLM) is a neural network trained on a vast amount of text for natural language processing tasks, especially language generation. LLMs can typically generate, summarize, translate, and analyze text in many contexts, and are a foundational technology behind modern chatbots.[1] Biased or inaccurate training data can make an LLM's output less reliable.[2]