Related papers: SSCU: an R/Bioconductor package for analyzing sele…
We introduce a variant of Multicut Decomposition Algorithms (MuDA), called CuSMuDA (Cut Selection for Multicut Decomposition Algorithms), for solving multistage stochastic linear programs that incorporates a class of cut selection…
Spatial transcriptomics (ST) provides essential spatial context by mapping gene expression within tissue, enabling detailed study of cellular heterogeneity and tissue organization. However, aligning ST data with histology images poses…
In [1], we have explored the theoretical aspects of feature selection and evolutionary algorithms. In this chapter, we focus on optimization algorithms for enhancing data analytic process, i.e., we propose to explore applications of…
Large-scale ad hoc analytics of genomic data is popular using the R-programming language supported by 671 software packages provided by Bioconductor. More recently, analytical jobs are benefitting from on-demand computing and storage, their…
A well-constructed classification model highly depends on input feature subsets from a dataset, which may contain redundant, irrelevant, or noisy features. This challenge can be worse while dealing with medical datasets. The main aim of…
We introduce KodCode, a synthetic dataset that addresses the persistent challenge of acquiring high-quality, verifiable training data across diverse difficulties and domains for training Large Language Models for coding. Existing…
We investigate a family of $(\mu+\lambda)$ Genetic Algorithms (GAs) which creates offspring either from mutation or by recombining two randomly chosen parents. By scaling the crossover probability, we can thus interpolate from a fully…
Self-attention networks (SANs) with selective mechanism has produced substantial improvements in various NLP tasks by concentrating on a subset of input words. However, the underlying reasons for their strong performance have not been well…
This paper proposes the Symbolic-Stochastic Chase Decoding Algorithm (S-SCA) for the Reed-Solomon (RS) and BCH codes. By efficient usage of void space between constellation points for $q$-ary modulations and using soft information at the…
ExpressInHost (https://gitlab.com/a.raguin/expressinhost) is a GTK/C++ based user friendly graphical interface that allows tuning the codon sequence of an mRNA for recombinant protein expression in a host microorganism. Heterologous gene…
Measuring natural selection on genomic elements involved in the cis-regulation of gene expression -- such as transcriptional enhancers and promoters -- is critical for understanding the evolution of genomes, yet it remains a major…
Evaluation metrics are crucial in the field of code synthesis. Commonly used code evaluation metrics canbe classified into three types: match-based, semantic-based, and execution-based. Among them, the execution-basedPass@k metric…
The primary step in search of the gene prediction is an identification of the coding region from genomic DNA sequence. Gene structure in the case of a eukaryotic organism is composed of promoter, intron, start codon, exons, stop codon, etc.…
The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. Some argue that the specific form of the code with its twenty amino-acids might be a 'frozen accident' because of the overwhelming effects of any…
This study introduces an innovative crossover operator named Particle Swarm Optimization-inspired Crossover (PSOX), which is specifically developed for real-coded genetic algorithms. Departing from conventional crossover approaches that…
The genetic code markup is the assignment of stop codons. The standard genetic code markup ensures the maximum possible stability of genetic information with respect to two fault classes: frameshift and nonsense mutations. There are only…
Independence screening is a variable selection method that uses a ranking criterion to select significant variables, particularly for statistical models with nonpolynomial dimensionality or "large p, small n" paradigms when p can be as…
Despite Retrieval-Augmented Generation improving code completion, traditional retrieval methods struggle with information redundancy and a lack of diversity within limited context windows. To solve this, we propose a resource-optimized…
COVID-19 has affected the world tremendously. It is critical that biological experiments and clinical designs are informed by computational approaches for time- and cost-effective solutions. Comparative analyses particularly can play a key…
Many constraint satisfaction and optimisation problems can be solved effectively by encoding them as instances of the Boolean Satisfiability problem (SAT). However, even the simplest types of constraints have many encodings in the…