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新论文 · v1arXiv:2611.04420

Verifier strength does not buy discovery quality: a pre-registered two-domain test of LLM-based automated research, with post-hoc evidence pointing to proposer-pool composition

Peter Chen, Ni Zhang, Siyuan Zhang

原文摘要

Automated research pipelines pair an LLM proposer with a verifier on an implicit bet: discovery quality rises with verification strength. Under a pre-registered protocol we test this bet in two real-data domains -- job-shop scheduling and vehicular edge offloading on Beijing T-Drive trajectories -- across 100 matched LLM/random pairs per domain and three verifier tiers. The manipulation binds -- a 429-case mutation battery shows scores rising across tiers -- yet the paired LLM-over-random advantage does not scale with it (A, one-sided p=0.1115; D, p=0.9994), and in D shrinks under the strict tier (margin contrast -0.040, p=0.0013). The two lower gates promote identical candidates in 100/100 and 99/100 pairs, so the strict order is untestable when they coincide. Constructively, LLM proposals carry a real paired advantage over random controls, but a post-hoc union-pool analysis shows the fastest path to better discovery is widening the pool, not tightening the gate: mixing the two pools adds +1.52 holdout-value units in domain A (one-sided Wilcoxon, n=100, p=0.0002) -- evidence that pool composition, not verification strength, is the lever. Criteria, ledgers and scripts are archived on Zenodo (DOI: 10.5281/zenodo.23308866).

cs.AI · cs.SE

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新论文 · v1arXiv:2611.04338

Patching the Protocol: A Taxonomy of Pre-Registration Repairs in LLM-Proposer Experiments

Peter Chen, Ni Zhang, Siyuan Zhang

原文摘要

Pre-registration is increasingly proposed as a trust mechanism for machine-learning research involving LLM-generated content, but its canonical form assumes a frozen protocol can be executed unchanged. Software-intensive studies violate this assumption: the protocol is partly implemented, and implementations carry defects. We report a three-case study of protocol repairs ("patches") from a program where an LLM proposes executable rules that a programmatic verifier gates, across production scheduling, incentive design, and task assignment. Each protocol required exactly one defect-repair patch: three events in total. None modified a numbered judgment criterion, its threshold, or the scoring rule, and none altered already collected data; two changed pre-registered design parameters before any data were collected, each with a recorded rationale. We propose a two-axis taxonomy of patches (defect class: environmental / feasibility / correctness, x timing: pre-data / post-data), introduce a verifiable non-impact claim for post-data repairs, and distill a nine-item checklist; all nine items were exercised by at least one patch event -- an observation of use, not a validation of sufficiency. The credibility of verifier-bound, LLM-proposer studies depends less on whether patches occur than on whether they are auditable.

cs.AI · cs.SE

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arXiv ↗PDF ↗
新论文 · v1arXiv:2611.02311

CytoWave: Perturbation-Centric Pretraining for Single-Cell Response Prediction

Yuwei Miao, Jingquan Yan, Hehuan Ma, Thao M. Dang, Lin Xu, Siyuan Zhang, Junzhou Huang

原文摘要

Predicting gene expression under perturbations from single-cell data is a fundamental task for modeling cellular responses, with applications in discovering gene function and designing therapeutics. However, existing methods often struggle to generalize across datasets due to differences in experimental protocols, biological contexts, and species. We present \textbf{CytoWave}, a perturbation-centric pretraining framework for single-cell genetic perturbation response prediction. We leverage large-scale cross-species perturbation datasets unified via orthology and train CytoWave in a two-stage manner. In the first stage, we learn reference control cell states via masked gene expression recovery on unperturbed cells. In the second stage, we pretrain the model to predict perturbed gene expression given control states and perturbation signals, together with a contrastive objective that aligns latent representations of perturbation responses with perturbation signals. We perform strict dataset-held-out evaluation across multiple condition combinations and case studies of pathway activity changes, demonstrating consistent and effective performance of CytoWave in predicting single-cell genetic perturbation responses.

cs.LG

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