arXiv Machine Learning

TRON: Transferring Naturally Evolved Network Architectures into Neuroevolution

TRON (TRansfer Of Natural networks) is a neuroevolution framework that uses experimentally characterized protein‑protein interaction (PPI) networks as architectural priors instead of random topologies. By combining classical evolutionary operators with neuroevolution techniques such as speciation and species quarantine, TRON improves the preservation of functional organization during mutation and recombination. Evaluations on six benchmark datasets show that TRON achieves the best predictive performance on all classification tasks and most regression tasks, with lower variability across runs, indicating greater robustness and convergence stability at the cost of higher computational effort.

arXiv AI
Oct 2

Multi-Behavioral Evolved Substrates Through Neuromodulation and Activation Selection

The paper investigates whether artificial evolution can replicate biological neuromodulation and diverse neuron types in indirectly encoded substrates. Experiments show that neuromodulation alone cannot overcome a 75% performance ceiling on parity tasks, but combining neuromodulation with per‑task activation function selection allows a single evolving genotype to achieve 100% success across five tasks. This demonstrates that both neuromodulation and evolvable computational primitives are necessary for multi‑behavioral open‑ended evolution.

By Romain Claret, Michael O'Neill, Paul Cotofrei, Kilian Stoffel
arXiv AI
Oct 2

Per-Node Activation Function Evolution in Indirectly Encoded Substrates: Solvability, Limits, and Emergent Diversity

The paper demonstrates that using a single activation function across all nodes in artificial neural networks imposes hard limits on evolutionary search, particularly for sparse evolved substrates. By evolving per-node activation functions from an 18-function palette, the authors show that oscillatory functions can solve parity problems at all tested scales, while monotonic functions fail beyond the simplest case. The study reveals that the choice of activation functions, beyond topology and weights, critically influences what evolutionary search can achieve, and that heterogeneous assignments discovered via indirect encoding are unlikely to be selected manually.

By Romain Claret, Michael O'Neill, Paul Cotofrei, Kilian Stoffel
arXiv Machine Learning
Sep 25

EvoTreeNAD: Genealogy-Guided Evolution for LLM-Driven Neural Architecture Discovery

EvoTreeNAD is a genealogy‑guided evolutionary algorithm that autonomously discovers neural architectures without a predefined seed or search space. Starting from an empty root, it builds a persistent genealogy where each node represents a complete architecture; top‑percentile values from nodes and descendants steer lineage selection. The method combines an Idea Agent that proposes variants and a Code Agent that implements them, with theoretical analysis showing stationary variation regimes and empirical results demonstrating superior performance on CIFAR‑10/100 and MedMNIST‑v2 tasks.

By Lishan Yu, Derek Jiu, Qizhen Lan, Xiaoqian Jiang
arXiv AI
Oct 12

Meta-Reflective Evolution Effectively Improves Production AI Systems

Meta-Reflective Evolution Effectively Improves Production AI Systems describes CoCoEvolve, an evolutionary optimizer that uses meta-reflection to retrieve evidence from the entire evolutionary history and probe live systems before proposing mutations. The approach is applied to data agents, LLM-powered data pipelines, and data engineering workflows, achieving state‑of‑the‑art results on DABStep, multiple LLM pipeline workloads, and data-eng-bench. Ablation studies confirm that each component of CoCoEvolve contributes to its performance gains.

By Seung Won Wilson Yoo, Chang Zeng, Aditi Somayajula, Sahithi Ankireddy, Rohan Kosalge, Avishree Khare, John Mitchell, Aditya G. Parameswaran, Rajhans Samdani, Anupam Datta
arXiv AI
Sep 2

Flawed in Nature, Perfect through Evolution

arXiv:2609.00129v1 Announce Type: cross Abstract: The performance of artificial intelligence (AI) and machine learning (ML) models degrades when the problem they were trained on drifts. This is a nea...

By J. M. Diederik Kruijssen (Allora Foundation)
arXiv AI
Jun 9

AMix-1: A Pathway to Test-Time Scalable Protein Foundation Model

arXiv:2507. 08920v4 Announce Type: replace-cross Abstract: We introduce AMix-1, a powerful protein foundation model built on Bayesian Flow Networks and empowered by a systematic training methodology, encompassing pretraining scaling laws, emergent capability analysis, in-context learning mechanism, and test-time scaling algorithm.

By Changze Lv, Jiang Zhou, Siyu Long, Lihao Wang, Jiangtao Feng, Dongyu Xue, Yu Pei, Hao Wang, Zherui Zhang, Yuchen Cai, Zhiqiang Gao, Ziyuan Ma, Jiakai Hu, Chaochen Gao, Jingjing Gong, Yuxuan Song, Shuyi Zhang, Xiaoqing Zheng, Deyi Xiong, Lei Bai, Wanli Ouyang, Ya-Qin Zhang, Wei-Ying Ma, Bowen Zhou, Hao Zhou