Reasoning or Just Prompting? Probing the Mechanism of Latent Chemical Reasoning

Large language models offer a promising foundation for chemical reasoning, bringing together chemical knowledge and multistep problem solving. Chemical intuition can provide an initial sense of plausible outcomes before the details of a solution are fully worked out. Inspired by how such expectations complement explicit analysis, we study how continuous latent thoughts can be trained to anticipate informative aspects of future solutions without verbalizing every intermediate step. We introduce Latent JEPA, a framework that combines autoregressive learning with joint-embedding prediction of one or more future views. For chemical reasoning, we develop textual and molecular prediction objectives that connect latent thoughts to both subsequent reasoning and molecular outcomes. Experiments on ChemCoTBench show gains in molecular optimization and on several editing and reaction metrics. Representation analyses show that future prediction makes latent thoughts more informative about molecular outcomes and strengthens their correspondence with chemical structure. These findings support abstract future prediction as a learning principle for connecting continuous latent reasoning with scientific outcomes.

Chemical reasoning language models are expected to derive molecular answers through faithful chain-of-thought (CoT). However, across four reasoning model families and twelve chemistry tasks, hallucination is widespread and largely decoupled from answer correctness: correct answers often coexist with fabricated structural claims absent from the relevant molecules. Yet this does not make the reasoning trace computationally irrelevant. Attribution analyses suggest a shared scratchpad function expressed in model-specific forms: Chem-R and ether-0 rely on fragmented SMILES drafts, whereas ChemDFM-R emphasizes scaffold, positional, and naming cues. Notably, perturbing Chem-R's SMILES sketches degrades generation, showing that structural drafts can be causally load-bearing even when verbal structural claims are largely inert. Together, these results show that chemical CoT is neither a faithful explanation nor merely a post-hoc rationalization, but a hallucination-prone molecular scratchpad. This finding cautions against treating CoT as direct evidence of faithful reasoning and motivates process-level supervision beyond answer-only evaluation.

Latent chain-of-thought replaces written reasoning steps with continuous hidden states, giving models additional steps to compute before answering. It remains unclear what computation these steps actually perform. High task accuracy and decodable intermediate answers do not establish that a model uses its latent chain to reach an answer. We study this question across twenty-one model-task configurations covering three training recipes, three reasoning tasks, and two backbones. We combine chain deletion and content replacement with probes and trajectory analysis to test whether the chain affects the answer, what it encodes, and how its states change. On logical tasks, COCONUT often carries an answer that is already readable before the chain begins. Its states settle early, and deleting the chain leaves predictions almost unchanged. Per-step supervision produces an ordered layout of reasoning steps and can make the model depend on the chain. Yet even an ordered chain can act as a placeholder, with deletion hurting performance while content replacement leaves answers unchanged. On arithmetic tasks, all tested recipes show dependence on chain content. These results show why readable latent states alone are insufficient evidence of reasoning. We introduce a taxonomy that separates what a chain represents from how the model uses it. Seen this way, earlier reports no longer compete: placeholder tokens, collapsed superposition and step-dependent causal roles are each consistent with a different kind of chain, each obtained on a different task, training recipe or measurement. Once a study says which property it tested, whether the model uses the chain, what the chain holds, or how its state moves, claims about latent reasoning can be compared.