Daily Papers

Publishers and funders increasingly ask authors to disclose how AI tools contributed to a piece of research. In computational work the repository is where an author or an auditor would look for the answer, and we ask what it can actually supply. We audit two single-investigator repositories by the same author in the same field, each carrying a different class of agent residue: a prescriptive trace of standing rule files and a narrative trace of a running agent scratchpad, in repositories of 466 and 103 commits. The two are legible in opposite ways. 85.6% of the lines ever committed to the prescriptive trace are visible at the current revision, and a standing rule states a conclusion and discards the episode behind it; the narrative trace records episodes and shows 21.8%. Counted by revision the gap is far smaller: 15 of the prescriptive trace's 41 revisions leave no visible line, against 18 of the narrative trace's 41. The Co-Authored-By trailer, the field an automated audit reads, is one of three AI trailer keys Project A carries and covers 66 of the 121 commits carrying any. In Project B it has low sensitivity against an explicit within-repository proxy: 39 commits revise a file maintained to hold an agent's working notes and 1 (2.6%) carries the trailer. Project A's repository-level rate is unstable in time too, stepping from 2.7% to 17.7% across a boundary we did not specify in advance. Repository channels disagree, and neither rate can be read as an involvement rate; we do not isolate the cause, and say so. We give a field-by-field account of which provenance claims such traces support, which they cannot, and which they answer confidently and wrongly, construct an auditable evidence ledger, and derive the requirements this places on any system meant to record research provenance as it happens.

A persistent challenge in machine learning for scientific applications is jointly achieving prediction and understanding. Statistical models excel on structured data but operate as black boxes, while existing interpretability methods are largely inspective: they answer "which features matter?" but do not articulate how features interact or refine explanations iteratively alongside human understanding. Asking an LLM to predict the target directly forces it to search the entire output space; we instead anchor predictions with a base model and ask the LLM the narrower question of what that model is missing. We introduce Multi-Agent Residual In-Context Learning (MARICL), an agentic framework in which LLM agents analyze where a base-model fails, hypothesize missing structure from high-residual examples provided in context, and produce explicit correction terms refined through multi-turn textual gradient optimization. Across nine benchmarks spanning scientific, biomedical, socioeconomic, and synthetic settings, MARICL improves consistently over its base model on all datasets. To test whether these corrections reflect real structure or batch-specific noise, we freeze formulas learned on one experimental batch of the Cell-Free Protein dataset and apply them (with no retraining and no further LLM calls) to held-out batches. Within the same reagent protocol, the frozen formulas improve predictions in over 92% of cases; across a different protocol, they fail systematically. The success boundary aligns with the biochemistry, not the batch count; direct evidence of mechanistic generalization.

As agent systems become more widely used, multiple agent sessions increasingly run alongside pre-existing user tasks in the same environment, sharing resources with limited capacity or mutually exclusive states. This creates a safety risk: when granted sufficient privileges, an agent may resolve a resource conflict by terminating or otherwise disrupting an existing task rather than reporting it. In this work, we identify and formalize this failure mode, which we term destructive resource preemption: obtaining the resources required for a requested task by terminating, overwriting, evicting, or degrading an incumbent task. To systematically study this risk, we introduce ClashBench, an executable benchmark comprising 268 validated conflict cases across 55 resource types, and evaluate 17 models through Codex, Claude Code, and OpenCode. We observe destructive preemption in 44.5% of trajectories, where the agent completes the requested task while causing the incumbent task to fail its health check. We also show that prompt-based safeguards are insufficient: an instruction to avoid affecting existing tasks reduces but does not eliminate preemption, while an instruction explicitly authorizing the agent to stop local processes increases it. More concerningly, in 31.9% of successful destructive-preemption cases, the final response mentions neither the resource conflict nor the action taken to resolve it, raising concerns about possible concealment. These findings establish destructive resource preemption as a broad safety risk in privileged agent systems and motivate stronger privilege controls, task isolation, and conflict-aware safeguards.