Large language models (LLMs) can propose vaccine adjuvant designs with plausible mechanistic rationales, but such outputs often lack grounding in established immunological knowledge. We present SAVANT, a neuro-symbolic framework for LLM-based adjuvant design that combines two-stage constrained generation with literature-grounded verification. SAVANT first generates a natural-language design rationale, then renders it into an ontology-constrained domain-specific language (DSL) using logic masks and finite-state control. To reason under fragmented evidence and incomplete first-principles rules, SAVANT verifies generated designs against literature-derived symbolic evidence through minimal sub-theorem proof. In expert-aligned evaluation, SAVANT shows greater stability in stage-level rank alignment than the strongest LLM-judge baselines, while achieving the strongest alignment for immune-effect support and mechanistic reasoning. SAVANT provides graded, interpretable assessments that distinguish supported mechanisms, under-supported hypotheses, and knowledge gaps for hypothesis-driven experimentation. Data and code will be released at https://github.com/banjiuyufen/SAVANT.

Large reasoning models (LRMs) show strong capabilities in complex reasoning, yet their marginal gains on evidence-dependent factual questions are limited. We find this limitation is partially attributable to a reasoning–answer hit gap, where the model identifies the correct facts during reasoning but fails to incorporate them into the final response, thereby reducing factual fidelity. To address this issue, we propose MR-ALIGN, a Meta-Reasoning informed alignment framework that enhances factuality without relying on external verifiers. MR-ALIGN quantifies state-transition probabilities along the model’s thinking process and constructs a transition-aware implicit reward that reinforces beneficial reasoning patterns while suppressing defective ones at the atomic thinking segments. This re-weighting reshapes token-level signals into probability-aware segment scores, encouraging coherent reasoning trajectories that are more conducive to factual correctness. Empirical evaluations across four factual QA datasets and one long-form factuality benchmark show that MR-ALIGN consistently improves accuracy and truthfulness while reducing misleading reasoning. These results highlight that aligning the reasoning process itself, rather than merely the outputs, is pivotal for advancing factuality in LRMs.