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Predicting protein-protein interactions from sequences is an important goal of computational biology. Various sources of information can be used to this end. Starting from the sequences of two interacting protein families, one can use…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Large language models (LLMs) achieve strong average performance yet remain unreliable at the instance level, with frequent hallucinations, brittle failures, and poorly calibrated confidence. We study reliability through the lens of…
Hybrid human-ML systems increasingly make consequential decisions in a wide range of domains. These systems are often introduced with the expectation that the combined human-ML system will achieve complementary performance, that is, the…
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to…
Provenance is information about the origin, derivation, ownership, or history of an object. It has recently been studied extensively in scientific databases and other settings due to its importance in helping scientists judge data validity,…
Microbes can affect processes from food production to human health. Such microbes are not isolated, but rather interact with each other and establish connections with their living environments. Understanding these interactions is essential…
In natural language processing, word-sense disambiguation (WSD) is an open problem concerned with identifying the correct sense of words in a particular context. To address this problem, we introduce a novel knowledge-based WSD system. We…
In this paper we identify several serious problems that arise in the use of syntactic data from the SSWL database for the purpose of computational phylogenetic reconstruction. We show that the most naive approach fails to produce reliable…
Prior work has shown that two NLP evaluation experiments that report results for the same quality criterion name (e.g. Fluency) do not necessarily evaluate the same aspect of quality, and the comparability implied by the name can be…
The Semantic Web standardizes concept meaning for humans and machines, enabling machine-operable content and consistent interpretation that improves advanced analytics. Reusing ontologies speeds development and enforces consistency, yet…
Evolutionary computation has long promised to deliver both high-performance optimization tools as well as rigorous scientific simulations of Darwinian evolution. However, modern algorithms frequently abandon evolutionary fidelity for…
As a key natural language processing (NLP) task, word sense disambiguation (WSD) evaluates how well NLP models can understand the lexical semantics of words under specific contexts. Benefited from the large-scale annotation, current WSD…
Prompts are the interface for eliciting the capabilities of large language models (LLMs). Understanding their structure and components is critical for analyzing LLM behavior and optimizing performance. However, the field lacks a…
Many optimization problems in science and engineering are highly nonlinear, and thus require sophisticated optimization techniques to solve. Traditional techniques such as gradient-based algorithms are mostly local search methods, and often…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
People can categorize the same entity at multiple taxonomic levels, such as basic (bear), superordinate (animal), and subordinate (grizzly bear). While prior research has focused on basic-level categories, this study is the first attempt to…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
This paper presents a novel framework for inferring timed temporal logic properties from data. The dataset comprises pairs of finite-time system traces and corresponding labels, denoting whether the traces demonstrate specific desired…
Researchers and managers model ecological communities to infer the biotic and abiotic variables that shape species' ranges, habitat use, and co-occurrence which, in turn, are used to support management decisions and test ecological…