Junwoo Park, Minyoung Shin, Cheol Soon Lee +1cs.AI cs.LG
Large language models (LLMs) are widely applied across chemical tasks, such as molecular property prediction, which underpins drug discovery. Molecular LLMs represent a molecule through several modalities, notably a 1D SMILES sequence or a 2D molecular graph. Both encode molecular information implicitly, so the contribution of individual substructures remains opaque. Retrieval and augmentation methods add context, but from external sources. However, the cues chemists reason over are the internal substructures that drive a property up or down. We propose MR-MoL, a multi-granular rationale-guided molecular LLM that supplies this evidence directly. A fine-tuned GNN scores each substructure through masking, and the most influential ones are serialized as a ranked, direction-tagged rationale that the LLM reads alongside the SMILES sequence and molecular graph. The rationale spans three levels of granularity: Murcko scaffolds with their side chains, BRICS fragments, and functional groups. This is, to our knowledge, the first method to expose GNN-derived attributions to an LLM as evidence for property prediction. On eight MoleculeNet tasks, MR-MoL achieves the best overall results among generalist models and narrows the gap to specialist models tuned for each task. Five diagnostics further confirm that the model reads the rationale rather than merely benefiting from its presence. Its direction, rank, and substructure each shape the prediction, and its attributions reproduce known structure-property relationships.
Language models can generate plausible rationales for their predictions, but these explanations may not faithfully represent the model's internal reasoning. We propose verifier-coupled reasoning, a framework that inserts inline claims into reasoning traces and trains an auxiliary consistency head to predict programmatic verifier outputs from rationale-span hidden states. The central finding is a gap between decodability and faithfulness: consistency training reliably makes verifier information decodable from rationale representations, but decodability does not guarantee faithful generation. In LeanCheck (formal theorem proving), rationale-only and proof-only pooling achieve perfect directional separation under counterfactual conflict. In KataGo (Go engine), commentary spans encode 10-way win-rate buckets at 81% accuracy. Yet in a code setting, the model achieves 98.6% coupling while its generated explanations remain unfaithful: fluent prose with correct structured claims, but describing unrelated algorithms; a controlled pretrained-vs-from-scratch comparison shows the gap is not capacity-driven. Synthetic activation patching confirms causal influence (73-89% vs. 31% baseline), FEVER reveals that evidence-only pooling isolates genuine evidence sensitivity at the cost of raw accuracy, and per-claim analysis shows that consistency loss disproportionately benefits fine-grained claims over binary ones. These results establish that consistency losses are effective diagnostics and representation-shaping tools, but not sufficient conditions for faithful reasoning.
Retrieving external knowledge is essential for solving real-world tasks, yet it remains challenging when the relationship between a query and its relevant knowledge involves implicit and complex reasoning beyond surface-level semantic or lexical matching (e.g., mathematical problems relying on the same theorem or coding requiring deep reasoning). Existing approaches primarily rely on query-side reasoning (e.g., query rewriting), which introduces significant online latency and underutilizes the opportunity to perform reasoning over the knowledge corpus itself (i.e., index-side reasoning). In this paper, we propose RL-Index, an agentic indexing framework that formulates retrieval index reasoning as a reinforcement learning problem. Instead of performing reasoning at query time, RL-Index shifts reasoning to the indexing stage by augmenting documents with LLM-generated rationales that explicitly encode the latent query-knowledge relationship. To optimize the quality of these rationales, we employ Group Relative Policy Optimization (GRPO) and use retrieval similarity as a verifiable reward signal, enabling direct optimization of indexing decisions for retrieval effectiveness. Extensive experiments on the BRIGHT benchmark demonstrate that RL-Index consistently improves both retrieval and downstream question-answering performance, while significantly reducing online inference latency. Moreover, the learned rationale augmentation generalizes across diverse retrievers and generators, highlighting its robustness as a plug-and-play indexing strategy across different retrieval systems.
Automated L2 speech assessment can assign proficiency labels, but often lacks interpretability. We propose a rubric-guided SpeechLLM for multi-aspect, multi-granular assessment, trained with a hybrid objective combining supervised fine-tuning and Bounded Direct Preference Optimization. The model jointly predicts ordinal labels at the sentence-level (accuracy, fluency, prosody), word/phoneme-level accuracy, and generates a natural-language rationale in the same response. On SpeechOcean762, our approach matches or outperforms single-granularity models while remaining competitive with prior approaches. We analyze rationale reliability along two axes: self-consistency with model predictions and alignment with ground-truth labels, using sentiment consistency (plausibility) and mention-based agreement (faithfulness). Rationales are plausible at the sentence level, but faithfulness degrades at the word/phoneme level: references are sparse and weakly aligned with token-level labels.