DN-Hypo-Pipeline: An AI-Driven Workflow for Generating Hypotheses using Large Language Models and Scientific Explanations
Authors: Lei Lin, Ronghao Wang, Chunbao Zhou, Jue Wang, Yangang Wang
Abstract
Modern artificial intelligence excels at prediction but cannot explain. From large language models to AI-for-science systems, today's machines answer what by recombining patterns already present in the human literature, yet they cannot reason out why a phenomenon must arise from underlying principles even though explanation, not prediction, lies at the heart of scientific discovery. Here we ask whether the structure of scientific explanation can be operationalized to guide how a machine generates hypotheses. We introduce DN-Hypo-Pipeline, a hypothesis-generation framework that adopts a layered, explanation-theoretic scaffold: Hempel's deductive-nomological (DN) model supplies the output form and deductive validity of a hypothesis, Salmon's causal-process account supplies an organizing constraint on where to search for the governing laws, and Armstrong's view of laws as relations between universals supplies the bridge from a phenomenon's constituent processes to the laws that may be associated with it. Rather than searching the space of what has been written, the framework searches the space of what principles govern a phenomenon: given an explanandum, it abstracts the universals instantiated in the phenomenon's formation process, retrieves the laws relating those universals, and deductively reconstructs a new, testable explanation. Evaluated in data-science modeling and judged by both LLMs and human experts, hypotheses generated through this principled reasoning significantly outperform those from direct prompting. Crucially, we translated the two highest-scoring hypotheses into novel algorithms one that reduces the Transformer's theoretical complexity with only minimal performance loss, and another that achieves competitive accuracy with substantially fewer parameters.
Modern Machine Learning (ML) and Artificial Intelligence (AI) models, especially large language models (LLMs), are increasingly used to generate scientific hypotheses and mechanistic explanations from observational data. This position paper argues that in the high-dimensional proxy regimes where modern ML excels, mechanistic learning is generically underdetermined: many incompatible mechanisms induce essentially the same observational relationships on the support of the data, so predictive success and coherent explanations are insufficient evidence of mechanism discovery. This underdetermination becomes uniquely hazardous with large language models (LLMs), which tend to collapse large equivalence classes of explanations into a single fluent narrative. This paper proposes concrete standards for ``mechanistic ML,'' and argues these norms are necessary if LLM-centered workflows are to support science rather than merely simulate it.
Large language models (LLMs) are on the rise for accelerating scientific discovery, most recently in advanced tasks such as generating valid scientific hypotheses. Yet in many discovery settings, the goal is not to identify a single best hypothesis since validation can be noisy and expensive, and scientists benefit from a set of high-quality alternative hypotheses that hedge against downstream uncertainty for the best solutions. Nevertheless, commonly used evolutionary search recipes tend to prioritize optimization over exploration in hypothesis generation, and the resulting selection pressure during the search process leads to diversity collapse. Motivated by these limitations, we formulate hypothesis search as a sampling problem, where the objective is to efficiently produce diverse, high-quality hypotheses under a fixed validation budget. Building on this perspective, we propose \ours, an evolutionary framework inspired by the classical parallel tempering algorithm that searches hypotheses at multiple temperature levels and enables principled information exchange across temperatures to improve exploration without disrupting convergence. Across domains including molecular discovery, equation discovery, and algorithm discovery, our approach consistently improves both hypothesis quality and diversity under the same validation budget, and produces candidates that remain robust under more expensive downstream computational validations.
Large language models (LLMs) show remarkable potential in scientific hypothesis discovery. However, existing approaches face two critical limitations: they treat divergent exploratory search and convergent fine-grained refinement as isolated tasks, and they operate autonomously with little to no human guidance. We present MOOSE-Copilot, the first unified framework to bridge this abstraction gap through a formalized human-AI interaction (HAII) protocol. Our system empowers scientists to steer the generative process via three explicit signals: initial blueprints, inter-stage routing, and intra-stage feedback. Using an oracle-simulated evaluation in which an LLM provides idealized expert signals, we show that injecting these structured signals significantly outperforms purely autonomous baselines, characterizing the gains achievable under high-quality guidance. Furthermore, we build a web-based interface that turns the framework into a no-code workflow: researchers pose a question, watch the hypothesis search unfold as an interactive tree, and steer it by selecting hypotheses, routing between stages, and injecting feedback-no command-line agents required. This makes end-to-end hypothesis discovery directly accessible to interdisciplinary researchers.