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Traditional linguistic theories have largely regard language as a formal system composed of rigid rules. However, their failures in processing real language, the recent successes in statistical natural language processing, and the findings…
We present TreeClone, a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution. Similar to most current methods, we consider data from next-generation sequencing of tumor…
Existing work implementing comparative reconstruction of ancestral languages (proto-languages) has usually required full supervision. However, historical reconstruction models are only of practical value if they can be trained with a…
Recent advances in large language models (LLMs) have made significant progress across multiple biomedical tasks, including biomedical question answering, lay-language summarization of the biomedical literature, and clinical note…
Competency Questions (CQs) are a form of ontology functional requirements expressed as natural language questions. Inspecting CQs together with the axioms in an ontology provides critical insights into the intended scope and applicability…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
Source-tract decomposition (or glottal flow estimation) is one of the basic problems of speech processing. For this, several techniques have been proposed in the literature. However studies comparing different approaches are almost…
Lexical resemblances among a group of languages indicate that the languages could be genetically related, i.e., they could have descended from a common ancestral language. However, such resemblances can arise by chance and, hence, need not…
To fully exploit the potential of computational phylogenetic methods for cognate data one needs to leverage specific (complex) models an machine learning-based techniques. However, both approaches require datasets that are substantially…
Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…
Preserving a speaker's voice identity while generating speech in a different language remains a fundamental challenge in spoken language technology, particularly in specialized domains such as scientific communication. In this paper, we…
Recent advances in neural network-based generative modeling have reignited the hopes in having computer systems capable of seamlessly conversing with humans and able to understand natural language. Neural architectures have been employed to…
This work suggests fundamentally rethinking the current practice of pruning large language models (LLMs). The way it is done is by divide and conquer: split the model into submodels, sequentially prune them, and reconstruct predictions of…
In phase retrieval and similar inverse problems, the stability of solutions across different noise levels is crucial for applications. One approach to promote it is using signal priors in a form of a generative model as a regularization, at…
Using Phylogenetic Algebraic Geometry, we analyze computationally the phylogenetic tree of subfamilies of the Indo-European language family, using data of syntactic structures. The two main sources of syntactic data are the SSWL database…
A key problem in the description of language structure is to explain its contradictory properties of specificity and generality, the contrasting poles of formulaic prescription and generative productivity. I argue that this is possible if…
In this paper we suggest how the mathematical concept of hyperstructures may be a useful tool in the study of the higher, hierachical structure of languages.
Hypothesis generation is a fundamental step in scientific discovery, yet it is increasingly challenged by information overload and disciplinary fragmentation. Recent advances in Large Language Models (LLMs) have sparked growing interest in…