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X-ray ptychography imaging at synchrotron facilities like the Advanced Photon Source (APS) involves controlling instrument hardwares to collect a set of diffraction patterns from overlapping coherent illumination spots on extended samples,…

The genetic code is connection between 64 codons, which are building blocks of the genes, and 20 amino acids, which are building blocks of the proteins. In addition to coding amino acids, a few codons code stop signal, which is at the end…

This paper presents our computational methodology using Genetic Algorithms (GA) for exploring the nature of RNA editing. These models are constructed using several genetic editing characteristics that are gleaned from the RNA editing system…

In recent years the computing landscape has seen an in- creasing shift towards specialized accelerators. Field pro- grammable gate arrays (FPGAs) are particularly promising as they offer significant performance and energy improvements…

Advances in genome sequencing technologies generate massive amounts of sequence data that are increasingly analyzed and shared through public repositories. On-demand infrastructure services on cloud computing platforms enable the processing…

Construction of synthetic genetic networks requires the assembly of DNA fragments encoding functional biological parts in a defined order. Yet this may become a time-consuming procedure. To address this technical bottleneck, we have created…

Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…

This paper introduces Multi-population Ensemble Genetic Programming (MEGP), a computational intelligence framework that integrates cooperative coevolution and the multiview learning paradigm to address classification challenges in…

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…

Artificial intelligence is reshaping scientific discovery, yet its use in materials research remains limited by fragmented computational ecosystems, reproducibility challenges, and dependence on commercial large language models (LLMs). Here…

Genetic Algorithms (GAs) are powerful metaheuristic techniques mostly used in many real-world applications. The sequential execution of GAs requires considerable computational power both in time and resources. Nevertheless, GAs are…

Reconfigurable computing refers to the use of processors, such as Field Programmable Gate Arrays (FPGAs), that can be modified at the hardware level to take on different processing tasks. A reconfigurable computing platform describes the…

PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of…

With the demand for machine learning increasing, so does the demand for tools which make it easier to use. Automated machine learning (AutoML) tools have been developed to address this need, such as the Tree-Based Pipeline Optimization Tool…

In recent years, heterogeneous computing has emerged as the vital way to increase computers? performance and energy efficiency by combining diverse hardware devices, such as Graphics Processing Units (GPUs) and Field Programmable Gate…

This paper consists of three parts. The first part provides a unified programming model for heterogeneous computing with CPU and accelerator (like GPU, FPGA, Google TPU, Atos QPU, and more) technologies. To some extent, this new programming…

A recent trend is to leverage machine learning models to improve the evolutionary design and optimization process. We propose a novel transformer-based mutation operator for Cartesian genetic programming (CGP) for the automated design of…

Epitopes are short antigenic peptide sequences which are recognized by antibodies or immune cell receptors. These are central to the development of immunotherapies, vaccines, and diagnostics. However, the rational design of synthetic…

Software documentation is an essential but labor intensive task that often requires a dedicated team of developers to ensure coverage and accuracy. Good documentation will help shorten the development cycle and improve the overall team…

This paper presents an investigation of the capabilities of Generative Pre-trained Transformers (GPTs) to auto-generate graphical process models from multi-modal (i.e., text- and image-based) inputs. More precisely, we first introduce a…