An Interaction Language Model: Mechanism Discovery from Statistical Patterns of Physical Interactions

Abstract

Interactions among building blocks in physical, chemical, and biological systems follow structured patterns interpretable as a learnable language: just as language models learn which words tend to follow others, one can learn which physical phenomena follow others and under what conditions. We introduce an Interaction Language Model (ILM): a framework that treats interaction as a statistically structured, learnable language for design-to-function reasoning across fields. By learning statistical dependencies and ordering among components, ILMs infer interaction pathways, identify missing steps, and predict the next likely interaction. We demonstrate it through two complementary components, PhenoLink and PhenoSeq, applied to molecular diffusion, a ubiquitous mechanism for energy and particle transport. PhenoLink is a directed graph of interactions among diffusion-based events extracted from publications, where each edge aggregates paragraph-level evidence and carries a transition probability interpreted as an information cost. PhenoSeq complements this with a sequence model that proposes missing mechanistic steps under endpoint constraints. Together they form a generate-then-verify pipeline returning every explanation with a reproducible, per-step, corpus-grounded audit trail. Across four held-out suites of 172 queries, the pipeline matches a zero-shot Claude Opus 4.7 baseline on in-distribution accuracy, yet unlike the baseline, which fabricates a chain for every impossible query, it refuses up to 93.5% of transitions in corpus evidence by construction. ILM thus delivers what zero-shot generation structurally cannot: deterministic refusal of evidence-absent queries and auditable, per-step support. The framework extends to natural and engineered systems where function emerges from sequential and conditional interactions among molecules, cells, devices, or other components.