Related papers: ProSt: computing, storing and visualizing attribut…
In recent years, the sequencing, assembling and annotation of prokaryotic genomes has become increasingly easy and cheap. Thus it becomes increasingly feasible and interesting to perform comparative genomics analyses of new genomes to those…
Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary information, but they are unable to explicitly acquire protein functions, which is the end goal of…
ProFIT is an extension of Standard Prolog with Features, Inheritance and Templates. ProFIT allows the programmer or grammar developer to declare an inheritance hierarchy, features and templates. Sorted feature terms can be used in ProFIT…
The genome-scale metabolic model with protein constraint (PC-model) has been increasingly popular for microbial metabolic simulations. We present PROSO Toolbox, a unified and simple-to-use PC-model toolbox that takes any high-quality…
In this work, we propose the novel Prototypical Graph Regression Self-explainable Trees (ProGReST) model, which combines prototype learning, soft decision trees, and Graph Neural Networks. In contrast to other works, our model can be used…
Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have…
Shaped by natural selection and other evolutionary forces, an organism's evolutionary history is reflected through its genome sequence, content of functional elements and organization. Consequently, organisms connected through phylogeny,…
Motivation: High-throughput sequencing (HTS) enables population-scale genomics but generates massive datasets, creating bottlenecks in storage, transfer, and analysis. FASTQ, the standard format for over two decades, stores one byte per…
The number of available genomes of prokaryotic organisms is rapidly growing enabling comparative genomics studies. The comparison of genomes of organisms with a common phenotype, habitat or phylogeny often shows that these genomes share…
Proust is a small Racket program offering rudimentary interactive assistance in the development of verified proofs for propositional and predicate logic. It is constructed in stages, some of which are done by students before using it to…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
The semantics and the recursive execution model of Prolog make it very natural to express language interpreters in form of AST (Abstract Syntax Tree) interpreters where the execution follows the tree representation of a program. An…
The recent super-exponential growth in the amount of sequencing data generated worldwide has put techniques for compressed storage into the focus. Most available solutions, however, are strictly tied to specific bioinformatics formats,…
Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data…
The research community continues to seek increasingly more advanced synthetic data generators to reliably evaluate the strengths and limitations of machine learning methods. This work aims to increase the availability of datasets…
We present CREST (Compact Retrieval-Based Speculative Decoding), a redesign of REST that allows it to be effectively "compacted". REST is a drafting technique for speculative decoding based on retrieving exact n-gram matches of the most…
We present a new probing dataset named PROST: Physical Reasoning about Objects Through Space and Time. This dataset contains 18,736 multiple-choice questions made from 14 manually curated templates, covering 10 physical reasoning concepts.…
We introduce a compressed representation of sets of sets that exploits how much they differ from each other. Our representation supports access, membership, predecessor and successor queries on the sets within logarithmic time. In addition,…
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…
The development of the Parallel ROOT Facility, PROOF, enables a physicist to analyze and understand much larger data sets on a shorter time scale. It makes use of the inherent parallelism in event data and implements an architecture that…