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Reconstruction of family trees, or pedigree reconstruction, for a group of individuals is a fundamental problem in genetics. The problem is known to be NP-hard even for datasets known to only contain siblings. Some recent methods have been…

Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any…

This paper presents an improved LLM based model for Grammatical Error Detection (GED), which is a very challenging and equally important problem for many applications. The traditional approach to GED involved hand-designed features, but…

Consider a genetic locus carrying a strongly beneficial allele which has recently fixed in a large population. As strongly beneficial alleles fix quickly, sequence diversity at partially linked neutral loci is reduced. This phenomenon is…

Mendelian randomization uses genetic variants to make causal inferences about the effect of a risk factor on an outcome. With fine-mapped genetic data, there may be hundreds of genetic variants in a single gene region any of which could be…

We study the problem of eliminating recursion from monadic datalog programs on trees with an infinite set of labels. We show that the boundedness problem, i.e., determining whether a datalog program is equivalent to some nonrecursive one is…

Much of the on-going statistical analysis of DNA sequences is focused on the estimation of characteristics of coding and non-coding regions that would possibly allow discrimination of these regions. In the current approach, we concentrate…

We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…

Our goal is procedural text comprehension, namely tracking how the properties of entities (e.g., their location) change with time given a procedural text (e.g., a paragraph about photosynthesis, a recipe). This task is challenging as the…

Motivation: Modern genomics laboratories generate massive volumes of sequencing data, often resulting in significant storage costs. Genomics storage consists of duplicate files, temporary processing files, and redundant intermediate data.…

We present methods for inference about relationships between contributors to a DNA mixture and other individuals of known genotype: a basic example would be testing whether a contributor to a mixture is the father of a child of known…

Multithreshold Entropy Linear Classifier (MELC) is a density based model which searches for a linear projection maximizing the Cauchy-Schwarz Divergence of dataset kernel density estimation. Despite its good empirical results, one of its…

Data contamination is a known threat to the reliability of model evaluation. However, it remains underexplored in code large language models (LLMs), where contamination often goes beyond exact duplication. We present TRACER, a…

The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…

Valid estimation of a causal effect using instrumental variables requires that all of the instruments are independent of the outcome conditional on the risk factor of interest and any confounders. In Mendelian randomization studies with…

Diagnosing an inherited disease often requires identifying the pattern of inheritance in a patient's family. We represent family trees with genetic patterns of inheritance using hypergraphs and latent state space models to provide…

Causal-consistent reversible debugging allows one to explore concurrent computations back and forth in order to locate the source of an error. In this setting, backward steps can be chosen freely as long as they are "causal consistent",…

Evaluating consistency in large language models (LLMs) is crucial for ensuring reliability, particularly in complex, multi-step interactions between humans and LLMs. Traditional self-consistency methods often miss subtle semantic changes in…

Genealogy research is the study of family history using available resources such as historical records. Ancestry provides its customers with one of the world's largest online genealogical index with billions of records from a wide range of…