Related papers: BGT: efficient and flexible genotype query across …
Efficient information retrieval (IR) from building information models (BIMs) poses significant challenges due to the necessity for deep BIM knowledge or extensive engineering efforts for automation. We introduce BIM-GPT, a prompt-based…
In this vignette, we introduce the UPG package for efficient Bayesian inference in probit, logit, multinomial logit and binomial logit models. UPG offers a convenient estimation framework for balanced and imbalanced data settings where…
Gaussian Boson Sampling (GBS) is a quantum computing concept based on drawing samples from a multimode nonclassical Gaussian state using photon-number resolving detectors. It was initially posed as a near-term approach aiming to achieve…
A widely used approach for extracting information from gene expression data employ the construction of a gene co-expression network and the subsequent application of algorithms that discover network structure. In particular, a common goal…
We present GLB, a programming model and an associated implementation that can handle a wide range of irregular paral- lel programming problems running over large-scale distributed systems. GLB is applicable both to problems that are easily…
Metagenomics offers a way to analyze biotopes at the genomic level and to reach functional and taxonomical conclusions. The bio-analyzes of large metagenomic projects face critical limitations: complex metagenomes cannot be assembled and…
Learning ensembles by bagging can substantially improve the generalization performance of low-bias, high-variance estimators, including those evolved by Genetic Programming (GP). To be efficient, modern GP algorithms for evolving (bagging)…
Property-based testing (PBT) relies on generators for random test cases, often constructed using embedded domain specific languages, which provide expressive combinators for building and composing generators. The effectiveness of PBT…
In this work, we propose a new deep learning model for Genomic Prediction (GP), which involves correlating genotypic data with phenotypic. The genotypes are typically fed as a sequence of characters to the 1D-Convolution Neural Network…
Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. Findings The first version appeared online twelve years ago and has been maintained and further developed ever since,…
We propose the use of conversational GPT models for easy and quick few-shot text classification in the financial domain using the Banking77 dataset. Our approach involves in-context learning with GPT-3.5 and GPT-4, which minimizes the…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
In this paper, we introduce the first diffusion model designed to generate complete synthetic human genotypes, which, by standard protocols, one can straightforwardly expand into full-length, DNA-level genomes. The synthetic genotypes mimic…
We propose a novel group testing method, termed semi-quantitative group testing, motivated by a class of problems arising in genome screening experiments. Semi-quantitative group testing (SQGT) is a (possibly) non-binary pooling scheme that…
Skeleton Ground Truth (GT) is critical to the success of supervised skeleton extraction methods, especially with the popularity of deep learning techniques. Furthermore, we see skeleton GTs used not only for training skeleton detectors with…
Generative pre-trained transformer (GPT) models have revolutionized the field of natural language processing (NLP) with remarkable performance in various tasks and also extend their power to multimodal domains. Despite their success, large…
Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of…
Beyond identifying genetic variants, we introduce a set of Boolean relations that allows for a comprehensive classification of the relations for every pair of variants by taking all minimal alignments into account. We present an efficient…
Bayesian adaptive clinical trials offer a flexible and efficient alternative to traditional fixed-design trials, but their implementation is often hindered by the complexity of Bayesian computations and the need for advanced statistical…