Inferring the phylogenetic relationships among a sample of organisms is a fundamental problem in modern biology. While distance-based hierarchical clustering algorithms achieved early success on this task, these have been supplanted by Bayesian and maximum likelihood search procedures based on complex models of molecular evolution. In this work we describe minimal neural network architectures that can approximate classic phylogenetic distance functions and the properties required to learn distances under a variety of molecular evolutionary models. In contrast to model-based inference (and recently proposed model-free convolutional and transformer networks), these architectures have a small computational footprint and are scalable to large numbers of taxa and molecular characters. The learned distance functions generalize well and, given an appropriate training dataset, achieve results comparable to state-of-the art inference methods.

Model merging allows combining the capabilities of existing models into a new one - post hoc, without additional training. This has made it increasingly popular thanks to its low cost and the availability of libraries that support merging on consumer GPUs. Recent work shows that pairing merging with evolutionary algorithms can boost performance, but no framework currently supports flexible experimentation with such strategies in language models. We introduce Mergenetic, an open-source library for evolutionary model merging. Mergenetic enables easy composition of merging methods and evolutionary algorithms while incorporating lightweight fitness estimators to reduce evaluation costs. We describe its design and demonstrate that Mergenetic produces competitive results across tasks and languages using modest hardware.

With the rapid advancement of large language models (LLMs), foundational models (FMs) have seen significant advancements. Healthcare is one of the most crucial application areas for these FMs, given the significant time and effort required for physicians to analyze large volumes of patient data. Recent efforts have focused on adapting multimodal FMs to the medical domain through techniques like instruction-tuning, leading to the development of medical foundation models (MFMs). However, these approaches typically require large amounts of training data to effectively adapt models to the medical field. Moreover, most existing models are trained on English datasets, limiting their practicality in non-English-speaking regions where healthcare professionals and patients are not always fluent in English. The need for translation introduces additional costs and inefficiencies. To address these challenges, we propose a \textbf{J}apanese \textbf{Radi}ology report generation model enhanced by \textbf{Evo}lutionary optimization of model merging (JRadiEvo). This is the first attempt to extend a non-medical vision-language foundation model to the medical domain through evolutionary optimization of model merging. We successfully created a model that generates accurate Japanese reports from X-ray images using only 50 translated samples from publicly available data. This model, developed with highly efficient use of limited data, outperformed leading models from recent research trained on much larger datasets. Additionally, with only 8 billion parameters, this relatively compact foundation model can be deployed locally within hospitals, making it a practical solution for environments where APIs and other external services cannot be used due to strict privacy and security requirements.

This paper aims to shed light on the evolutionary dynamics of diverse and social populations by introducing the rich expressiveness of generative models into the trait expression of social agent-based evolutionary models. Specifically, we focus on the evolution of personality traits in the context of a game-theoretic relationship as a situation in which inter-individual interests exert strong selection pressures. We construct an agent model in which linguistic descriptions of personality traits related to cooperative behavior are used as genes. The deterministic strategies extracted from Large Language Model (LLM) that make behavioral decisions based on these personality traits are used as behavioral traits. The population is evolved according to selection based on average payoff and mutation of genes by asking LLM to slightly modify the parent gene toward cooperative or selfish. Through preliminary experiments and analyses, we clarify that such a model can indeed exhibit the evolution of cooperative behavior based on the diverse and higher-order representation of personality traits. We also observed the repeated intrusion of cooperative and selfish personality traits through changes in the expression of personality traits, and found that the emerging words in the evolved gene well reflected the behavioral tendency of its personality in terms of their semantics.

We propose methods for the analysis of hierarchical clustering that fully use the multi-resolution structure provided by a dendrogram. Specifically, we propose a loss for choosing between clustering methods, a feature importance score and a graphical tool for visualizing the segmentation of features in a dendrogram. Current approaches to these tasks lead to loss of information since they require the user to generate a single partition of the instances by cutting the dendrogram at a specified level. Our proposed methods, instead, use the full structure of the dendrogram. The key insight behind the proposed methods is to view a dendrogram as a phylogeny. This analogy permits the assignment of a feature value to each internal node of a tree through an evolutionary model. Real and simulated datasets provide evidence that our proposed framework has desirable outcomes and gives more insights than state-of-art approaches. We provide an R package that implements our methods.

Accurate and efficient inference in evolutionary trees is a central problem in computational biology.While classical treatments have made unrealistic site independence assumptions, ignoring insertions and deletions, realistic approaches require tracking insertions and deletions along the phylogenetic tree--a challenging and unsolved computational problem. We propose a new ancestry resampling procedure for inference in evolutionary trees. We evaluate our method in two problem domains--multiple sequence alignment and reconstruction of ancestral sequences--and show substantial improvement over the current state of the art.