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Gene expression prediction, which predicts mRNA expression levels from DNA sequences, presents significant challenges. Previous works often focus on extending input sequence length to locate distal enhancers, which may influence target…
The development of foundation vision models has pushed the general visual recognition to a high level, but cannot well address the fine-grained recognition in specialized domain such as invasive species classification. Identifying and…
A reinforcement learning-enhanced genetic algorithm (RLGA) is proposed for wind farm layout optimization (WFLO) problems. While genetic algorithms (GAs) are among the most effective and accessible methods for WFLO, their performance and…
Transposed elements (TEs) are mobile genetic sequences. During the evolution of eukaryotes TEs were inserted into active protein-coding genes, affecting gene structure, expression and splicing patterns, and protein sequences. Genomic…
Polygenic risk scores and other genomic analyses require large individual-level genotype datasets, yet strict data access restrictions impede sharing. Synthetic genotype generation offers a privacy-preserving alternative, but most existing…
Next-generation sequencing technologies have enhanced the scope of Internet-of-Things (IoT) to include genomics for personalized medicine through the increased availability of an abundance of genome data collected from heterogeneous sources…
Solving inverse problems is central to geosciences and remote sensing. Radiative transfer models (RTMs) represent mathematically the physical laws which govern the phenomena in remote sensing applications (forward models). The numerical…
Abstract Recent advances in immunology and synthetic biology have accelerated the development of deep generative methods for DNA sequence design. Two dominant approaches in this field are AutoRegressive (AR) models and Diffusion Models…
We inject a random value into the evaluation of highly evolved deep integer GP trees 9743720 times and find 99.7percent Suggesting crossover and mutation's impact are dissipated and seldom propagate outside the program. Indeed only errors…
Positive selection drives the emergence of adaptive mutations in Mycobacterium tuberculosis, shaping drug resistance, transmissibility, and virulence. Phylogenetic trees capture evolutionary relationships among isolates and provide a…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
Estimating population-level prevalence and transmission dynamics of wildlife pathogens can be challenging, partly because surveillance data is sparse, detection-driven, and unevenly sequenced. Using highly pathogenic avian influenza A/H5…
Multi-trait genome-wide association studies (GWAS) use multi-variate statistical methods to identify associations between genetic variants and multiple correlated traits simultaneously, and have higher statistical power than independent…
Introducing noise in the training of machine learning systems is a powerful way to protect individual privacy via differential privacy guarantees, but comes at a cost to utility. This work looks at whether the inherent randomness of…
With the recent advent of high-throughput genotyping techniques, genetic data for genome-wide association studies (GWAS) have become increasingly available, which entails the development of efficient and effective statistical approaches.…
Coarse-grained simulations are often employed to study the translocation of DNA through a nanopore. The majority of these studies investigate the translocation process in a relatively generic sense and do not endeavour to match any…
When conducting inter-species regression analyses, the phylogenetic relationships between the individual species need to be taken into account. In this paper, a procedure for conducting such analyses is proposed, which only requires the use…
Identifying gene splicing is a core and significant task confronted in modern collaboration between artificial intelligence and bioinformatics. Past decades have witnessed great efforts on this concern, such as the bio-plausible splicing…
Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…
Post-genomic research deals with challenging problems in screening genomes of organisms for particular functions or potential for being the targets of genetic engineering for desirable biological features. 'Phenotyping' of wild type and…