Related papers: Ococo: an online variant and consensus caller
We consider resequencing studies of associated loci and the problem of prioritizing sequence variants for functional follow-up. Working within the multivariate linear regression framework helps us to account for correlation across variants,…
Conformance checking (CC) techniques of the process mining field gauge the conformance of the sequence of events in a case with respect to a business process model, which simply put is an amalgam of certain behavioral relations or rules.…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
The detection of rare variants is important for understanding the genetic heterogeneity in mixed samples. Recently, next-generation sequencing (NGS) technologies have enabled the identification of single nucleotide variants (SNVs) in mixed…
Reservoir computing is a recently introduced, highly efficient bio-inspired approach for processing time dependent data. The basic scheme of reservoir computing consists of a non linear recurrent dynamical system coupled to a single input…
We present scalable parallel algorithms with sublinear per-processor communication volume and low latency for several fundamental problems related to finding the most relevant elements in a set, for various notions of relevance: We begin…
Among the genetic algorithms generally used for optimization problems in the recent decades, quantum-inspired variants are known for fast and high-fitness convergence and small resource requirement. Here the application to the patient…
Introducing variability while maintaining coherence is a core task in learning to generate utterances in conversation. Standard neural encoder-decoder models and their extensions using conditional variational autoencoder often result in…
The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed…
A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of set of species…
Multi-view clustering can explore consistent information from different views to guide clustering. Most existing works focus on pursuing shallow consistency in the feature space and integrating the information of multiple views into a…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
Inference-time scaling has emerged as a powerful way to improve large language model (LLM) performance by generating multiple candidate responses and selecting among them. However, existing work on dynamic allocation for test-time compute…
This paper presents Callico, a web-based open source platform designed to simplify the annotation process in document recognition projects. The move towards data-centric AI in machine learning and deep learning underscores the importance of…
Reasoning is a fundamental capability of Large Language Models. While prior research predominantly focuses on enhancing narrow skills like math or code generation, improving performance on many other reasoning tasks remains challenging due…
There are two major approaches for sequence labeling. One is the probabilistic gradient-based methods such as conditional random fields (CRF) and neural networks (e.g., RNN), which have high accuracy but drawbacks: slow training, and no…
Error-Correcting Output Codes (ECOCs) offer a principled approach for combining simple binary classifiers into multiclass classifiers. In this paper, we investigate the problem of designing optimal ECOCs to achieve both nominal and…
Random Indexing is a simple implementation of Random Projections with a wide range of applications. It can solve a variety of problems with good accuracy without introducing much complexity. Here we use it for identifying the language of…
Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical…