Discovery under Hypothesis Redundancy: A Geometric Theory of Discovery Bottlenecks

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.

Open-ended scientific discovery with large language models (LLMs) increasingly operates as a long-horizon loop of hypothesis search and verification, where a reward signal guides which hypotheses to test next. A notable recent example is AutoDiscovery, which uses "Bayesian surprise" - the belief shift an LLM undergoes after observing evidence for a hypothesis - as both a discovery metric and a reward for search. We first observe that AutoDiscovery treats surprisal as a static quantity, while surprisal in human reasoning is non-stationary - it is defined relative to beliefs that evolve with experience, a prerequisite for continual scientific discovery. We address this mismatch with evidence-informed LLM beliefs: priors updated with evidence from previous hypotheses to compute non-stationary surprisal for new hypotheses. We compare in-context belief-updating mechanisms and find that embedding-based retrieval-augmented generation over prior discoveries best anticipates eventual posteriors, identifying 37.5% of static surprisals as spurious. We then modify search to avoid these spurious rewards and prioritize hypotheses that remain surprising under non-stationary beliefs. Concretely, we introduce two complementary changes to the original search procedure: belief-update filtering and diversity maximization. Across five discovery domains, our method increases accumulated non-stationary surprisal by 30.62% on average compared to the original search procedure, demonstrating that continual scientific discovery with LLMs requires not only better belief measurement but also search procedures that avoid redundancy and encourage diversity.

Scientific discovery is fundamentally an optimization problem, defined by a vast "state space" of theories and experiments, and an evaluation criterion based on quality, novelty, and validity. Large language models (LLMs) have enabled automated exploration of this space, but we argue that simultaneous modification of the evaluation criteria is equally important. Here, we propose formalizing research as meta-optimization, where the optimization objective itself is also being optimized. Our key contribution is "consensus objective aggregation," where LLM-generated objective functions are combined via correlation-weighted voting, yielding a stable, self-correcting evaluation criterion that evolves as understanding deepens. We apply this framework to algorithm discovery for 3-SAT problems based on digital MemComputing machines, reducing the baseline scaling with problem size $N$ from $\sim N^{2.51}$ to $\sim N^{1.33}$ and delivering a $\sim 67\times$ speedup on the largest instances tested. As a problem-agnostic framework, we hope this approach will considerably aid scientific discovery.