arXiv:2606. 00555v1 Announce Type: new Abstract: Structure-based drug design increasingly employs LLM agents to iteratively refine ligands against a target pocket, yet a viable ligand must satisfy two often-conflicting objectives -- binding affinity and druggability -- which single optimization steps rarely improve together.
By Zaifei Yang, Weiyu Chen, Yaqing Wang, James Kwok
The paper introduces AgentDiff, a metric that quantifies how much LLM agents’ answers differ when inputs are altered by meaning‑bearing rewrites (paraphrases, synonym substitutions) versus presentation changes (reordering, formatting, distractors). Across 68 model–benchmark–scaffold combinations involving ten LLMs and over 1,500 questions, meaning‑bearing rewrites consistently produce a roughly 20‑percentage‑point higher inconsistency rate than presentation changes, a gap that persists across severity proxies and remains significant even outside the Qwen family. Trace analysis reveals that meaning‑bearing rewrites preserve the first action but reduce thought similarity from the second step onward, extending the divergence cascade—a phenomenon termed “stealth divergence.”
By Liyun Zhang, Jiayi Guo
Budgeted Quotient-Residual Guidance (QRG) is an inference-time correction that enables quotient-based lead‑optimization objectives—such as distances, contacts, and anchored substructures—to be actively used with frozen pocket‑conditioned molecular diffusion models without retraining. QRG lifts quotient covectors to metric‑horizontal ambient directions and delivers them through a trust budget set by the sampler’s step norm, providing a closed‑form sampler‑budget update and a product‑budget split for section and residual controls. Experiments on frozen TargetDiff backbones show that QRG improves ligand‑generation quality on fragment growing, scaffold hopping, and linker design while preserving novelty and diversity.
By Xinyu Wang, Jinbo Bi, Minghu Song
arXiv:2606. 17107v1 Announce Type: cross Abstract: Prefix caching reuses prefill only across an exactly shared prefix, so one changed field invalidates the entire downstream cache.
By Bojie Li
arXiv:2610.15738v1 Announce Type: new
Abstract: LLM optimization loops often show the proposer the candidates it has already tried and rejected, but leave it to the proposer to avoid them. We ask whe...
By Jianlin Chen, Wenhui Chen, Chi Man Vong
The study evaluates whether a portfolio of compact, semantically named descriptor blocks can match the performance of a 2048‑dimensional CheMeleon embedding in low‑data molecular assays. Using a fixed 11‑dimensional physicochemical base and greedily adding provenance‑screened blocks, the portfolio achieves a mean test AUC of 0.762 across nine ADME/Tox assays, comparable to CheMeleon’s 0.764 and better than Mordred’s 0.756. The results meet a predeclared pooled parity threshold but not all per‑assay thresholds, and further analysis confirms the competitiveness of the auditable representation while highlighting unresolved assay‑level differences.
By Yiqi Yao, Miquel Duran-Frigola