Related papers: Agptools: a utility suite for editing genome assem…
Predicting the effect of mutations in proteins is one of the most critical challenges in protein engineering; by knowing the effect a substitution of one (or several) residues in the protein's sequence has on its overall properties, could…
Motivation: Despite significant advances in Third-Generation Sequencing (TGS) technologies, Next-Generation Sequencing (NGS) technologies remain dominant in the current sequencing market. This is due to the lower error rates and richer…
Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over ten years ago and did not incorporate the latest advances in…
Nowadays, application of Service Oriented Architecture is increasing rapidly; especially since introduction of distributed electronic services on the web. SOA software has a modular manner and works as a collaboration of independent…
To increase performance and efficiency, systems use FPGAs as reconfigurable accelerators. A key challenge in designing these systems is partitioning computation between processors and an FPGA. An appropriate division of labor may be…
Genetic programming is an evolutionary approach known for its performance in program synthesis. However, it is not yet mature enough for a practical use in real-world software development, since usually many training cases are required to…
Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…
Formal models for gene assembly in ciliates have been developed, in particular the string pointer reduction system (SPRS) and the graph pointer reduction system (GPRS). The reduction graph is a valuable tool within the SPRS, revealing much…
Accompaniment arrangement is a difficult music generation task involving intertwined constraints of melody, harmony, texture, and music structure. Existing models are not yet able to capture all these constraints effectively, especially for…
Automatic generation of medical reports from X-ray images can assist radiologists to perform the time-consuming and yet important reporting task. Yet, achieving clinically accurate generated reports remains challenging. Modeling the…
Hardware accelerators, in particular accelerators for tensor processing, have many potential application domains. However, they currently lack the software infrastructure to support the majority of domains outside of deep learning.…
Aggregation functions are widely used in answer set programming for representing and reasoning on knowledge involving sets of objects collectively. Current implementations simplify the structure of programs in order to optimize the overall…
We introduce Genome-Factory, the first integrated Python library for tuning, deploying, and interpreting genomic foundation models. Our core contribution is to simplify and unify the workflow for genomic model development: data collection,…
GPTIPS is a free, open source MATLAB based software platform for symbolic data mining (SDM). It uses a multigene variant of the biologically inspired machine learning method of genetic programming (MGGP) as the engine that drives the…
We introduce TurboGP, a Genetic Programming (GP) library fully written in Python and specifically designed for machine learning tasks. TurboGP implements modern features not available in other GP implementations, such as island and cellular…
The computational problem of inferring the full haplotype of a cell starting from read sequencing data is known as haplotype assembly, and consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the…
Lattice surgery is a leading approach for implementing fault-tolerant logical operations in surface code quantum computing, but compiling efficient lattice surgery layouts remains challenging. Existing compilers are largely circuit-centric…
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…
Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…
We present assembly-theory, a Rust package for computing assembly indices of covalently bonded molecular structures. This is a key complexity measure of assembly theory, a recent theoretical framework quantifying selection across diverse…