Search arXivSearch

arXiv · 2609.05450

SureRoute: Toward a Hallucination-Free Self-Improving Platform for Retrosynthesis

Abstract

AI models, including large language models, are increasingly integrated into scientific discovery workflows, yet they remain prone to hallucination. In experimental sciences, such errors translate directly into failed wet-lab validations and wasted resources; in self-improving agentic systems, confident errors risk being reinforced rather than corrected. Retrosynthesis provides a representative example of this failure mode: existing models can generate chemically plausible routes, but cannot reliably determine which routes are experimentally feasible. We define \textbf{Chemical Hallucination} as a route that appears valid yet fails under competing reactive sites, unresolved selectivity, or missing mechanistic support, a failure largely invisible to the Recall@$K$ metric. We introduce \textbf{SureRoute}, a chemical verifier-anchored retrosynthesis platform that suppresses Chemical Hallucination. SureRoute combines a multi-model ensemble, data asset retrieval, and \textbf{ChemHarness}, an executable chemical intuition engine for route verification and reliability-first ranking. On a benchmark of 350 real-world industrial targets, SureRoute reaches 74.3\% recall@1, 2.2--3.5$\times$ that of seven single-step models and three frontier LLMs, while cutting top-1 Chemical Hallucination to 4.6\%, a 4--6$\times$ reduction relative to frontier LLMs. As a model-agnostic reranker, ChemHarness drives detectable hallucination toward near-zero across arbitrary backbone candidates. SureRoute shows that reliable scientific AI requires not only strong generation, but executable verification.

Explore related subjects

Keep this discovery

BibTeXRIS

Jieli Zhou, Naiwu Chen, Longzhang Liu, Peiyu Zhang. 2026-08-04. SureRoute: Toward a Hallucination-Free Self-Improving Platform for Retrosynthesis. https://arxiv.org/abs/2609.05450

Cite the original work for its findings. Save a collection to share your selection of sources.

Discover connections

Connections use source metadata and explicit phrase matches, not verified experimental comparisons.

KEEP EXPLORING

Related papers

mRNA Design and Optimization with Deep Knowledge-Infused Approach

The mRNA optimization is essential for mRNA vaccines, therapies, and industrial protein production. Based on current explorations, an ideal optimization approach should simultaneously (i) prevent unintended amino-acid changes, (ii) optimize multiple, biologically relevant objectives, and (iii) retain computational efficiency. However, existing methods are forced to trade off between these perspectives, forming an "impossible triangle." We present RNop, a knowledge-infused Transformer that integrates mechanism-aligned losses to address this problem. By encoding biological prior knowledge in losses, RNop makes knowledge infusion explicit and controllable across optimization focus. Trained on over 6 million sequences, in silico analyses show RNop resolves the "impossible triangle" of mRNA optimization with absolute sequence fidelity, significantly improved biological metrics, and high throughput. In in vitro validation, it can deliver up to 2.28-fold expression gain. Ablation studies reveal how each prior contributes to targeted improvements, yielding mechanism-level interpretability. RNop represents a shift in mRNA optimization methodology: by infusing explicit and interpretable knowledge, the "black-box" mRNA design can be transformed into a predictable, explainable engineering problem. RNop is designed as an extensible platform: additional biological priors can be incorporated as modular, mechanism-aligned loss functions, enabling future development and adaptation to related sequence design problems.

q-bio.QM

Agentic BAIM-LLM Evaluation (ABLE): Benchmarking LLM Use of Protein Design Tools

We introduce ABLE, a benchmark for evaluating LLM agents' ability to use biological AI models (BAIMs), such as ProteinMPNN and AlphaFold3, in dual-use protein design workflows. ABLE assesses agent performance through a set of tasks spanning structure retrieval, sequence generation, and design validation. We evaluate 15 frontier models and find that seven refuse all tasks, while the remaining models exhibit substantial performance differences. Claude Sonnet 4 and Gemini 3 Pro achieve the highest scores across information retrieval, tool selection, and tool use. We further compare model performance on a subset of tasks against an expert human baseline. Our results suggest that current LLMs can substantially lower barriers to protein design, but remain inconsistent in planning, strategy generation, and integrating biological knowledge with tool use.

cs.AI

OmniBioTwin: A System-of-Twinned-Systems Framework for Health Digital Twins

Health digital twins (HDTs) promise patient-specific modeling and decision support but current approaches remain structurally fragmented: monolithic models that address a single organ or task lack cross-scale fidelity, while system-level twins lack generalizable architectural frameworks. We propose OmniBioTwin, a System-of-Twinned-Systems (SoTS) framework that organizes HDTs as modular computational entities coupled through explicit interaction operators within a multi-layer network architecture. The framework comprises seven coordinated layers - spanning data integration, autonomous twin modeling, cross-scale coupling, temporal synchronization, and human-in-the-loop decision support. We demonstrate OmniBioTwin by instantiating a multiscale twin for glucagon-like peptide-1 (GLP-1) signaling pathways in Alzheimer's disease, illustrating how molecular, cellular, and organ-level twins can be composed and coupled within a unified system.

q-bio.QM