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Federated learning (FL) is a privacy-preserving machine learning method that has been proposed to allow training of models using data from many different clients, without these clients having to transfer all their data to a central server.…
One of the basic questions of phylogenomics is how gene function evolves, whether among species or inside gene families. In this chapter, we provide a brief overview of the problems associated with defining gene function in a manner which…
Feature Transformation (FT) is a core data-centric AI task that improves feature space quality to advance downstream predictive performance. However, discovering effective transformations remains challenging due to the large space of…
The relationship between the quality of a string, as judged by a human reader, and its probability, $p(\boldsymbol{y})$ under a language model undergirds the development of better language models. For example, many popular algorithms for…
We investigate labeling schemes supporting adjacency, ancestry, sibling, and connectivity queries in forests. In the course of more than 20 years, the existence of $\log n + O(\log \log)$ labeling schemes supporting each of these functions…
In this paper we examine the usefulness of two classes of algorithms Distance Methods, Discrete Character Methods (Felsenstein and Felsenstein 2003) widely used in genetics, for predicting the family relationships among a set of related…
The study of spoken languages comprises phonology, morphology, and grammar. The languages can be classified as root languages, inflectional languages, and stem languages. In addition, languages continually change over time and space by…
Gene expression in cells is stochastic, yet differentiation is robust. We propose a mechanism in which frustrated genes with weakly stable intermediate expression undergo noise-driven switching between basins of attraction, followed by…
Convergent evolution provides powerful evidence for natural selection, yet its molecular basis is typically sought in protein-coding amino acid substitutions. Whether adaptive pressures can drive the convergent evolution of synonymous codon…
The long-range dependencies among the tokens, which originate from hierarchical structures, are a defining hallmark of human language. However, whether similar dependencies exist within the sequential vocalization of non-human animals…
Large Language Models (LLMs) are widely deployed in real-world applications, yet little is known about their training dynamics at the token level. Evaluation typically relies on aggregated training loss, measured at the batch level, which…
Federated Learning (FL) enables collaborative model training across decentralized devices while preserving data privacy. However, traditional FL suffers from communication overhead, system heterogeneity, and straggler effects. Asynchronous…
Lateral gene transfer (LGT) is a common mechanism of non-vertical evolution where genetic material is transferred between two more or less distantly related organisms. It is particularly common in bacteria where it contributes to adaptive…
We consider a federated learning (FL) system consisting of multiple clients and a server, where the clients aim to collaboratively learn a common decision model from their distributed data. Unlike the conventional FL framework that assumes…
Protein language models (pLMs) pre-trained on vast protein sequence databases excel at various downstream tasks but often lack the structural knowledge essential for some biological applications. To address this, we introduce a method to…
Given the rapidly evolving landscape of linguistic prevalence, whereby a majority of the world's existing languages are dying out in favor of the adoption of a comparatively fewer set of languages, the factors behind this phenomenon has…
Is it possible to develop a `physics of language' which can explain the spatial, temporal and social patterns we see, and which can predict future change like we forecast the weather? Such a theory is likely to involve ideas from…
It is proposed that the theory of dynamical systems offers appropriate tools to model many phonological aspects of both speech production and perception. A dynamic account of speech rhythm is shown to be useful for description of both…
Multi-type birth-death processes underlie approaches for inferring evolutionary dynamics from phylogenetic trees across biological scales, ranging from deep-time species macroevolution to rapid viral evolution and somatic cellular…
Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models…