Beneath the Diff: Diagnosing and Mitigating Algorithmic Mode Collapse in Code-Level Autonomous Research Loops

We study auto research as a closed empirical loop driven by external measurement. Each submitted trial carries a hypothesis, an executable code edit, an evaluator-owned outcome, and feedback that shapes the next proposal. The output is not a generated paper or a single model checkpoint, but an auditable trajectory of proposals, code diffs, experiments, scores, and failure labels. We instantiate this loop with specialist agents that partition recipe surfaces and share measured lineage across trials. The central empirical finding is that lineage feedback lets agents turn evaluator outcomes, including crashes, budget overruns, size failures, and accuracy-gate misses, into later program-level recipe edits rather than one-shot suggestions. Across 1,197 headline-run trials plus 600 Parameter Golf control trials after one-time setup and launch, humans did not choose proposals, edit recipes, override scores, or repair failed trials during the search. In the three headline runs, the same submitted-trial loop reduces Parameter Golf validation bpb by $0.81\%$, raises NanoChat-D12 CORE by $38.7\%$, and reduces CIFAR-10 Airbench96 wallclock by $4.59\%$, with each task measured by its own external evaluator and legality checks. The trace includes a strict architecture-domain audit of 157 headline-run submissions and program rewrites such as a NanoChat attention-kernel path change. Within this scope the loop autonomously writes code, submits experiments, absorbs feedback, applies and combines known techniques inside each environment, and improves public starting recipes.

Recursive self-training can degrade neural generative models when generated data is reused without fresh human data or external quality control. We study this risk in code LLMs, where AI-generated code can enter real repositories, later become training data, and create a repository-scale self-training loop. While software development traditionally interrupts this loop through pull-request review, tests, compilation, and human approval, AI coding tools now produce code faster than humans can review it, and code review itself is increasingly automated by AI systems. We therefore compare three recursive fine-tuning regimes: no review, Human-gate review using model-independent filters such as compilation and static quality checks, and AI-self-gate review using the code LLM's own signals such as perplexity and binary self-scoring. Across multiple code LLMs and benchmarks, no review collapses fastest, Human-gate filters slow but do not stop collapse, and AI-self-gate filters can look strong early but later lose their filtering effect. In the clearest case, the binary self-gate enters a rubber-stamp regime where acceptance scores rise while benchmark correctness falls. We explain this behavior by formulating review as gated distributional reweighting, proving that AI self-gating degenerates to ungated self-training under a self-confirming acceptance condition, and giving a spectral analysis of representation-level covariance concentration under recursive retraining. These results suggest that stable recursive code LLM training requires exogenous verification rather than model-coupled self-review.

Self-improvement can self-regress. In REINFORCE post-training for code, a model can quickly improve on its optimized metric and then collapse within the same training campaign. We study this in a controlled multi-seed testbed using Qwen-2.5-3B and Qwen-2.5-7B, trained on competitive-programming tasks with binary CodeGrader reward across 10 sequential 20-step campaigns. Across campaigns, pass@1 shows a robust rise-then-collapse pattern: it peaks within tens of gradient steps and then falls back, sometimes to near zero. This is not cross-task catastrophic forgetting, but within-task policy over-optimization on a fixed distribution; KL- and EWC-style constraints do not prevent it. We ask where the control loop should sit. We compare three levels: CARE, a between-campaign memory mechanism with a capability posterior, transfer gate, and regression-aware belief revision; ES, a within-campaign early-stop rule that rolls forward the peak checkpoint and sets the next budget to peak_step+3; and GRPO, which changes the RL update using group-relative reward normalization. The answer is regime-dependent. On Qwen-2.5-3B, where naive REINFORCE is fragile, CARE v2 nearly doubles end-of-chain pass@1 from 4.9% to 9.5%, with paired bootstrap 95% CI [+0.4,+8.9] and gains in 4/5 seeds. On Qwen-2.5-7B, CARE reaches parity with naive REINFORCE, 13.8% vs. 11.8%, while ES reaches 22.2% [14.1,28.0]. Out-of-the-box GRPO reaches 20.7% [15.7,25.1], nearly matching REINFORCE+ES. GRPO raises the floor but does not remove the cliff. Its 7B gain mainly comes from better between-campaign carryover, while the within-campaign peak-to-end gap remains about 17 points under both REINFORCE and GRPO. GRPO+ES gives mixed evidence: 2/3 seeds improve, but one final cliff lowers the mean to 17.0% [0.0,28.1]. A Gemma-3-4B pilot shows the same signature, suggesting the phenomenon is not limited to Qwen.