What Do Evolutionary Coding Agents Evolve?

Recent work pairs LLMs with evolutionary search to iteratively generate, modify, and select code using task-specific feedback. These systems have produced strong results in mathematical discovery and algorithm design, yet a fundamental question remains: what do they actually evolve? Progress is typically summarized by the best score a run reaches under a task-specific evaluator, but that score can reflect several different mechanisms: new algorithmic structure, re-tuning an existing strategy, recombining ideas already in the model's internal knowledge, or overfitting to the evaluator. Distinguishing these mechanisms requires inspecting the search process itself, not only its final outcome. We introduce EvoTrace, a dataset of evolutionary coding traces spanning four evolutionary frameworks, reasoning and non-reasoning models, and 16 tasks across mathematics and algorithm design. To analyze these traces, we develop EvoReplay, a replay-based methodology that reconstructs the local search states behind high-scoring solutions and tests controlled interventions, including adjusting constants, removing program components and substituting models or prompting contexts. We annotate every code edit in EvoTrace with one of nine recurring edit types using an LLM-as-judge pipeline validated against blind human re-annotation. Across EvoTrace, most score gains come from a small subset of these edit types. We further find a deterministic cycling pattern: about 30% of code lines added during search are byte-identical re-introductions of previously-deleted lines, present throughout nearly every run. These results show that benchmark gains in evolutionary coding agents can arise from qualitatively different mechanisms, only some of which correspond to new algorithmic structure. EvoTrace enables more diagnostic evaluation of evolutionary coding agents beyond final benchmark scores.

When Does Sparsity Mitigate the Curse of Depth in LLMs

Recent work has demonstrated the curse of depth in large language models (LLMs), where later layers contribute less to learning and representation than earlier layers. Such under-utilization is linked to the accumulated growth of variance in Pre-Layer Normalization, which can push deep blocks toward near-identity behavior. In this paper, we demonstrate that, sparsity, beyond enabling efficiency, acts as a regulator of variance propagation and thereby improves depth utilization. Our investigation covers two sources of sparsity: (i) implicit sparsity, which emerges from training and data conditions, including weight sparsity induced by weight decay and attention sparsity induced by long context inputs; and (ii) explicit sparsity, which is enforced by architectural design, including key/value-sharing sparsity in Grouped-Query Attention and expert-activation sparsity in Mixtureof-Experts. Our claim is thoroughly supported by controlled depth-scaling experiments and targeted layer effectiveness interventions. Across settings, we observe a consistent relationship: sparsity improves layer utilization by reducing output variance and promoting functional differentiation. We eventually distill our findings into a practical rule-of-thumb recipe for training deptheffective LLMs, yielding a notable 4.6% accuracy improvement on downstream tasks. Our results reveal sparsity, arising naturally from standard design choices, as a key yet previously overlooked mechanism for effective depth scaling in LLMs. Code is available at https://github.com/pUmpKin-Co/SparsityAndCoD.

The Agentic Researcher: A Practical Guide to AI-Assisted Research in Mathematics and Machine Learning

AI tools and agents are reshaping how researchers work, from proving theorems to training neural networks. Yet for many, it remains unclear how these tools fit into everyday research practice. This paper is a practical guide to AI-assisted research in mathematics and machine learning: We discuss how researchers can use modern AI systems productively, where these systems help most, and what kinds of guardrails are needed to use them responsibly. It is organized into three parts: (I) a five-level taxonomy of AI integration, (II) an open-source framework that, through a set of methodological rules formulated as agent prompts, turns CLI coding agents (e.g., Claude Code, Codex CLI, OpenCode) into autonomous research assistants, and (III) case studies from deep learning and mathematics. The framework runs inside a sandboxed container, works with any frontier LLM through existing CLI agents, is simple enough to install and use within minutes, and scales from personal-laptop prototyping to multi-node, multi-GPU experimentation across compute clusters. In practice, our longest autonomous session ran for over 20 hours, dispatching independent experiments across multiple nodes without human intervention. We stress that our framework is not intended to replace the researcher in the loop, but to augment them. Our code is publicly available at https://github.com/ZIB-IOL/The-Agentic-Researcher.

Computational Algebra with Attention: Transformer Oracles for Border Basis Algorithms

Solving systems of polynomial equations, particularly those with finitely many solutions, is a crucial challenge across many scientific fields. Traditional methods like Gr\"obner and Border bases are fundamental but suffer from high computational costs, which have motivated recent Deep Learning approaches to improve efficiency, albeit at the expense of output correctness. In this work, we introduce the Oracle Border Basis Algorithm, the first Deep Learning approach that accelerates Border basis computation while maintaining output guarantees. To this end, we design and train a Transformer-based oracle that identifies and eliminates computationally expensive reduction steps, which we find to dominate the algorithm's runtime. By selectively invoking this oracle during critical phases of computation, we achieve substantial speedup factors of up to 3.5x compared to the base algorithm, without compromising the correctness of results. To generate the training data, we develop a sampling method and provide the first sampling theorem for border bases. We construct a tokenization and embedding scheme tailored to monomial-centered algebraic computations, resulting in a compact and expressive input representation, which reduces the number of tokens to encode an $n$-variate polynomial by a factor of $O(n)$. Our learning approach is data efficient, stable, and a practical enhancement to traditional computer algebra algorithms and symbolic computation.

Approximating Latent Manifolds in Neural Networks via Vanishing Ideals

Deep neural networks have reshaped modern machine learning by learning powerful latent representations that often align with the manifold hypothesis: high-dimensional data lie on lower-dimensional manifolds. In this paper, we establish a connection between manifold learning and computational algebra by demonstrating how vanishing ideals can characterize the latent manifolds of deep networks. To that end, we propose a new neural architecture that (i) truncates a pretrained network at an intermediate layer, (ii) approximates each class manifold via polynomial generators of the vanishing ideal, and (iii) transforms the resulting latent space into linearly separable features through a single polynomial layer. The resulting models have significantly fewer layers than their pretrained baselines, while maintaining comparable accuracy, achieving higher throughput, and utilizing fewer parameters. Furthermore, drawing on spectral complexity analysis, we derive sharper theoretical guarantees for generalization, showing that our approach can in principle offer tighter bounds than standard deep networks. Numerical experiments confirm the effectiveness and efficiency of the proposed approach.