Unlocking LLM Creativity in Science through Analogical Reasoning
Authors: Andrew Shen, Shaul Druckmann, James Zou
Organizations: Stanford University
Abstract
Autonomous science promises to augment scientific discovery, particularly in complex fields like biomedicine. However, this requires AI systems that can consistently generate novel and diverse solutions to open-ended problems. We evaluate LLMs on the task of open-ended solution generation and quantify their tendency to mode collapse into low-diversity generations. To mitigate this mode collapse, we introduce analogical reasoning (AR) as a new approach to solution generation. AR generates analogies to cross-domain problems based on shared relational structure, then uses those analogies to search for novel solutions. Compared to baselines, AR discovers significantly more diverse generations (improving solution diversity metrics by 90-173%), generates novel solutions over 50% of the time (compared to as little as 1.6% for baselines), and produces high-quality analogies. To validate the real-world feasibility of AR, we implement AR-generated solutions across four biomedical problems, yielding consistent quantitative gains. AR-generated approaches achieve a nearly 13-fold improvement on distributional metrics for perturbation effect prediction, outperform all baselines on AUPRC when predicting cell-cell communication, infer brain region interactions with a high Spearman correlation (ρ=0.729) to published methods, and establish state-of-the-art performance on 2 datasets for oligonucleotide property prediction. The novel and diverse solutions produced by AR can be used to augment the search space of existing solution generation methods.
Generating multiple diverse and high-quality solutions is valuable for many applications, such as code-test generation and drug discovery. However, Large Language Models (LLMs) tend to converge on a single high-confidence solution during inference, limiting exploration of alternative valid solution paths. Existing test-time methods promote diversity through tree-like search and prune semantically similar branches using response-level semantic embeddings. However, we find that such embeddings are easily confounded by linguistic and stylistic similarities, making it difficult to distinguish genuinely distinct solution paths. To address this, we introduce Answer Probing, which probes the potential answer an LLM would reach from an intermediate reasoning path. We demonstrate that the hidden states of probed answers more effectively differentiate distinct solution paths than semantic embeddings, and the perplexity of probed answers serves as a practical proxy for reasoning correctness. Based on these findings, we propose Answer Probing-Guided Tree Search (APTS), which guides the tree search by the probed answers' hidden state similarity and perplexity. Experiments on three reasoning tasks across two LLMs show that APTS consistently enhances solution diversity, demonstrating its effectiveness and robustness.
Large Language Models (LLMs) have demonstrated remarkable potential for analogy making, a core cognitive capability that drives novelty and creativity. While prior research has extensively investigated the applications and underlying mechanisms of LLM-based analogy making, its output diversity remains largely unexplored, despite being essential for broadening cross-domain connections and fostering scientific innovation. In this work, we present a comprehensive evaluation of analogy diversity across ten state-of-the-art open- and closed-source LLMs. Our findings highlight a concerning issue of domain homogeneity, a prevalent tendency for LLMs to generate analogies from a narrow set of target domains, limiting both inter-query and intra-model diversity. Furthermore, our analysis reveals a fundamental trade-off in existing LLM diversity-enhancement methods: increasing output diversity often comes at the expense of output quality. Finally, our causal analysis of LLM information flow reveals substantial differences in the model-sensitive regions governing analogy diversity across LLMs, suggesting a potential mechanism for the observed diversity-quality trade-off. To our knowledge, this is among the first studies to systematically investigate output diversity in LLM-based analogy making.
Yuanhao Shen, Daniel Xavier de Sousa, Caio César Sifuentes Barcelos +2
Three paradigmatic forms of inference recur across scientific reasoning: deduction, induction, and causal abduction. Reliably evaluating LLMs on these in scientific settings is currently out of reach: scientific benchmarks built on human annotations are costly and lack mechanistic ground truth, while synthetic logical-reasoning benchmarks do not resemble real scientific documents. We introduce SciR, a benchmark that combines multi-paradigm reasoning with controllable scientific rendering, anchored on three paradigmatic scientific problems. Tasks are generated from formal objects (deduction tree, inductive rule hypothesis, causal graph) to guarantee verifiable answers, then rendered into multi-document scientific discourse via per-track domain-tuned genres. The construction lets us independently vary two difficulty axes: how hard it is to extract the key information needed for inference, and how hard the principled inference itself is. We test six models. Both axes hurt every model, and their effects compound. The rendering even hurts neurosymbolic pipelines, which hand inference to a verified solver. The two axes yield a per-model extraction-vs-inference profile: for instance, reasoning models like deepseek-r1 mostly surpass non-reasoning instruct models on the inference axis. To our knowledge, SciR is the first multi-paradigm scientific-reasoning benchmark with parametric control on both extraction and inference difficulty.