arXiv subjects

Daniel Burkhardt

Publications and source records attributed to Daniel Burkhardt.

4 recordsLinked to original sources

arXiv2026

The Red Queen G\"odel Machine: Co-Evolving Agents and Their Evaluators

Self-improving agents are state-of-the-art (SOTA) on agentic coding benchmarks and have recently been extended to general domains. However, their search methods generally assume a stationary evaluation criterion: a fixed verifier, benchmark, or labeled dataset that remains valid as the agent improves. This ignores a central feature of evolution: species adapt as their environments change with them. We aim to bring the same principle to recursive self-improvement, making evaluation part of the improvement loop and opening search to evolving evaluators, adversarial objectives, and dynamic utilities that may surpass static benchmarks. We introduce the Red Queen Godel Machine (RQGM), an evolutionary framework for recursive self-improvement under non-stationary utilities. The RQGM makes this possible through controlled utility evolution: search is organized into epochs with a fixed within-epoch evaluation criterion, while the utility can be updated at epoch boundaries, so self-improvement guarantees hold per epoch as the objective evolves across them. We begin by showing that even on verifiable coding tasks, the RQGM improves test pass rate over the prior SOTA by adding a complementary agent-as-a-judge code-review signal. This signal is cheaper and the RQGM uses 1.35x-1.72x fewer tokens. We then turn to scientific paper writing and reviewing, and Olympiad-level proof writing and grading, where the RQGM improves performance over prior self-improving agents: co-evolved writers reach 1.78x-1.86x higher acceptance rates under a diverse agent-as-a-judge panel, while co-evolved graders reach 9% higher ground-truth accuracy. In paper reviewing, the strongest baseline reviewer over-accepts AI-generated papers at up to 1.91x the human rate. The RQGM corrects this by introducing an adversarial objective that discovers reviewers equally stringent on AI and human work.

cs.LG↗

arXiv2025

Overcoming Knowledge Discrepancies: Structuring Reasoning Threads through Knowledge Balancing in Interactive Scenarios

Reasoning in interactive problem solving scenarios requires models to construct reasoning threads that reflect user understanding and align with structured domain knowledge. However, current reasoning models often lack explicit semantic hierarchies, user-domain knowledge alignment, and principled mechanisms to prune reasoning threads for effectiveness. These limitations result in lengthy generic output that does not guide users through goal-oriented reasoning steps. To address this, we propose a prototype-inspired, two-phases Reasoning-Threads-Evaluation (ReT-Eval) framework, drawing inspiration from human-like reasoning strategies that emphasize structured knowledge reuse. In the first phase, semantically relevant knowledge structures are extracted from a sparse domain knowledge graph using a graph neural network and enriched with intrinsic large language model knowledge to resolve knowledge discrepancies. In the second phase, these threads are evaluated and pruned using a reward-guided strategy aimed at maintaining semantic coherence to generate effective reasoning threads. Experiments and expert evaluations show that ReT-Eval enhances user understanding and outperforms state-of-the-art reasoning models.

cs.AI↗

arXiv2025

Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop

Artificial intelligence holds immense promise for transforming biology, yet a lack of standardized, cross domain, benchmarks undermines our ability to build robust, trustworthy models. Here, we present insights from a recent workshop that convened machine learning and computational biology experts across imaging, transcriptomics, proteomics, and genomics to tackle this gap. We identify major technical and systemic bottlenecks such as data heterogeneity and noise, reproducibility challenges, biases, and the fragmented ecosystem of publicly available resources and propose a set of recommendations for building benchmarking frameworks that can efficiently compare ML models of biological systems across tasks and data modalities. By promoting high quality data curation, standardized tooling, comprehensive evaluation metrics, and open, collaborative platforms, we aim to accelerate the development of robust benchmarks for AI driven Virtual Cells. These benchmarks are crucial for ensuring rigor, reproducibility, and biological relevance, and will ultimately advance the field toward integrated models that drive new discoveries, therapeutic insights, and a deeper understanding of cellular systems.

cs.LG↗

arXiv2019

Finding Archetypal Spaces Using Neural Networks

Archetypal analysis is a data decomposition method that describes each observation in a dataset as a convex combination of "pure types" or archetypes. These archetypes represent extrema of a data space in which there is a trade-off between features, such as in biology where different combinations of traits provide optimal fitness for different environments. Existing methods for archetypal analysis work well when a linear relationship exists between the feature space and the archetypal space. However, such methods are not applicable to systems where the feature space is generated non-linearly from the combination of archetypes, such as in biological systems or image transformations. Here, we propose a reformulation of the problem such that the goal is to learn a non-linear transformation of the data into a latent archetypal space. To solve this problem, we introduce Archetypal Analysis network (AAnet), which is a deep neural network framework for learning and generating from a latent archetypal representation of data. We demonstrate state-of-the-art recovery of ground-truth archetypes in non-linear data domains, show AAnet can generate from data geometry rather than from data density, and use AAnet to identify biologically meaningful archetypes in single-cell gene expression data.

cs.LG↗