Humanize MLE Agents: Multi-Agent Session Alternation Beyond Single-Agent Limits

Machine learning engineering (MLE) tasks require long-horizon decision making over iterative solution debugging and refinement, under expensive and feedback-driven environment interactions. Developing and training a monolithic agent for such tasks is fundamentally challenging, as it must simultaneously manage extremely long and noisy contexts, explore vast solution spaces, and remain effective under limited model capacity and computational budgets. To address these challenges, we propose Matryoshka Agent, a unified hierarchical agent framework for complex long-horizon tasks. Matryoshka Agent decomposes agentic problem solving into a coordinated hierarchy of decision making and execution: a high-level Orchestrator maintains compact, long-horizon exploration states and issues strategic instructions, while lower-level Sub-Agents execute concrete solution attempts through direct environment interaction, mediated by standardized Tool interface. This design decouples strategic exploration from costly execution, substantially reducing the burden of long-context reasoning and enabling efficient iterative refinement. We further develop an efficient training paradigm for Matryoshka Agent. Experimental results on a broad range of MLE tasks with diverse model types and scales demonstrate that Matryoshka Agent is an effective and scalable paradigm for long-horizon MLE tasks and complex agentic problem solving. Notably, Matryoshka Agent enables Qwen3-4B-Instruct to reach Orchestrator performance comparable to o4-mini. Applying Matryoshka Agent to Qwen3-30B-Coder results in at most 36.7% relative performance gain.

Large language models (LLMs) are expanding from assisting scientific research and engineering to autonomously developing and improving AI systems, advancing AI for AI (AI4AI) as a pathway toward recursive self-improvement (RSI). Workflow-driven machine learning engineering (MLE) systems provide a practical path toward this pursuit through complex orchestration that manages long-horizon experimentation, while recent MLE systems adopt model-directed interaction, allowing models to autonomously organize experiments and adapt optimization strategies based on execution feedback. However, feedback from each experiment reflects several preceding decisions, and a long MLE run contains many such costly experiments. Training must therefore select useful supervision from long interaction trajectories and learn from intermediate outcomes. We propose a post-training method for autonomous long-horizon MLE optimization and apply it to train MLExpert, a 35B Mixture-of-Experts agentic model. We design the Kaggle-MLE Factory to construct executable tasks and an interaction harness for model-directed experimentation. Hierarchical agentic SFT transfers general tool-use and coding capabilities to MLE through outcome-guided supervision. Windowed Interaction RL (WIRL) treats the multi-turn decisions between successive experiment results as an execution window and assigns it a shared outcome-based reward. Asynchronous collection and policy correction support policy updates before the trajectory ends. On MLE-Bench Lite, MLExpert improves the average medal rate of the base model from 37.9% to 72.7%, achieving performance comparable to larger frontier models such as Kimi-K3 and GLM-5.3. Further experiments show that MLExpert improves performance on NatureBench Lite, agent scaffold optimization, and algorithm optimization, suggesting that the learned optimization capability generalizes to other tasks.

Recent autonomous machine learning engineering (MLE) agents have made significant progress on public leaderboards. Often motivated by progress stagnation over long-horizon cycles and limited Large Language Model (LLM) primitives, modern MLE agents are deployed on top of increasingly elaborate machinery: multi-agent orchestrators, dedicated retrieval subagents, and more. While such harnesses expand, the use of more primitive but improved coding agents - where LLMs have direct access to the execution environment through read, write, and bash primitives - has received little attention in the field. In this paper we find that, under an equal time budget and the same frontier LLM backbone, open-source state-of-the-art harnesses provide no advantages over a single session of a minimal-harness coding agent baseline, pointing to the backbone as the primary driver for performance. Via a series of large-scale systematic ablation studies, we argue that the machinery layers become redundant in the coding agent setting. We conclude that the effort spent elaborating hand-crafted harnesses around strong models yields poor returns for current MLE benchmarks.