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The majority of mammalian genomic transcripts do not directly code for proteins and it is currently believed that most of these are not under evolutionary constraint. However given the abundance non-coding RNA (ncRNA) and its strong…
The classical Sankoff algorithm for the simultaneous folding and alignment of homologous RNA sequences is highly influential, but it suffers from two major limitations in efficiency and modeling power. First, it takes $O(n^6)$ for two…
Efficient communication is central to both biological and artificial intelligence (AI) systems. In biological brains, the challenge of long-range communication across regions is addressed through sparse, spike-based signaling, minimizing…
Artificial neural networks (ANNs), particularly large language models (LLMs), demonstrate powerful inference capabilities but consume substantial energy. Conversely, spiking neural networks (SNNs) exhibit exceptional energy efficiency due…
This paper introduces a modular and scalable design optimization framework for the glider wing design process that enables faster early-phase design while ensuring aerodynamic stability. The pipeline starts with the generation of initial…
Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial…
Antibodies are versatile proteins that bind to pathogens like viruses and stimulate the adaptive immune system. The specificity of antibody binding is determined by complementarity-determining regions (CDRs) at the tips of these Y-shaped…
Large Language Models (LLMs) have demonstrated exceptional performance across diverse tasks, yet their training remains highly resource-intensive and susceptible to critical challenges such as training instability. A predominant source of…
In a distributed storage systems (DSS) with $k$ systematic nodes, robustness against node failure is commonly provided by storing redundancy in a number of other nodes and performing repair mechanism to reproduce the content of the failed…
Small regulatory RNAs (sRNAs) are short non-coding RNAs in bacteria capable of post-transcriptional regulation. sRNAs have recently gained attention as tools in basic and applied sciences for example to fine-tune genetic circuits or…
Round Robin (RR) Algorithm is considered as optimal in time shared environment because the static time is equally shared among the processes. If the time quantum taken is static then it undergoes degradation of the CPU performance and leads…
The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spurred unprecedented and concerted worldwide research to curtail and eradicate this pathogen. SARS-CoV-2 has four structural proteins:…
Proteins perform their biological functions through three-dimensional structures encoded by amino acid sequences, and ligand-binding protein co-design requires models that generate sequence-structure compatible proteins under explicit…
The performance of principal component analysis (PCA) suffers badly in the presence of outliers. This paper proposes two novel approaches for robust PCA based on semidefinite programming. The first method, maximum mean absolute deviation…
The standard genetic code is known to be much more efficient in minimizing adverse effects of misreading errors and one-point mutations in comparison with a random code having the same structure, i.e. the same number of codons coding for…
Background. The DURATIONS design has been recently proposed as a practical alternative to a standard two-arm non-inferiority design when the goal is to optimise some continuous aspect of treatment administration, e.g. duration or frequency,…
The stability of model proteins with designed sequences is assessed in terms of the number of sequences (obtained from the designed sequence through mutations), which fold into 5the ``native'' conformation. By a complete enumeration of the…
Peptide vaccines are growing in significance for fighting diverse diseases. Machine learning has improved the identification of peptides that can trigger immune responses, and the main challenge of peptide vaccine design now lies in…
The SARS-CoV-2 RNA pseudoknot is a promising target for antiviral intervention, as it regulates the efficiency of $-$1 programmed ribosomal frameshifting ($-$1 PRF), a mechanism that is essential for viral protein synthesis. The pseudoknot…
The rapid advancement of artificial intelligence (AI) has been marked by the large language models exhibiting human-like intelligence. However, these models also present unprecedented challenges to energy consumption and environmental…