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Comprehensive and confident identifications of metabolites and other chemicals in complex samples will revolutionize our understanding of the role these chemically diverse molecules play in biological systems. Despite recent advances,…
Numerous machine learning (ML) models employed in protein function and structure prediction depend on evolutionary information, which is captured through multiple-sequence alignments (MSA) or position-specific scoring matrices (PSSM) as…
Oral cancer is a significant global health burden, and early detection remains a critical clinical need. Electrical impedance spectroscopy (EIS) offers a promising non-invasive approach for real-time tissue characterization, but…
We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol…
An Intrusion Detection System (IDS) is a software that monitors a single or a network of computers for malicious activities (attacks) that are aimed at stealing or censoring information or corrupting network protocols. Most techniques used…
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…
Understanding and predicting the phase behavior of intrinsically disordered proteins (IDPs) is of significant interest due to their role in many biological processes. However, effectively characterizing phase behavior and its complex…
In groundwater contaminant remediation and risk assessment, it is important to identify parameters of the contaminant source and hydraulic conductivity field by solving an inverse problem. However, if the dimensionality of the inverse…
The use of gene microchips has enabled a rapid accumulation of gene-expression data. One of the major challenges of analyzing this data is the diversity, in both size and signal strength, of the various modules in the gene regulatory…
Identification of features is a critical task in microbiome studies that is complicated by the fact that microbial data are high dimensional and heterogeneous. Masked by the complexity of the data, the problem of separating signals from…
Antibiotic resistance presents a growing global health crisis, demanding new therapeutic strategies that target novel bacterial mechanisms. Recent advances in protein structure prediction and machine learning-driven molecule generation…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
Complex information extraction (IE) pipelines assembled by plumbing together off-the-shelf operators, specially customized operators, and operators re-used from other text processing pipelines are becoming an integral component of most text…
Intrusion Detection Systems (IDSs) have played a significant role in the detection and prevention of cyber-attacks in traditional computing systems. It is not surprising that this technology is now being applied to secure Internet of Things…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
Screening traditionally refers to the problem of detecting active inputs in the computer model. In this paper, we develop methodology that applies to screening, but the main focus is on detecting active inputs not in the computer model…
A recent technology breakthrough in spatial molecular profiling has enabled the comprehensive molecular characterizations of single cells while preserving spatial information. It provides new opportunities to delineate how cells from…
Intrusion detection systems (IDS) monitor system logs and network traffic to recognize malicious activities in computer networks. Evaluating and comparing IDSs with respect to their detection accuracies is thereby essential for their…
The constant growth in the number of malware - software or code fragment potentially harmful for computers and information networks - and the use of sophisticated evasion and obfuscation techniques have seriously hindered classic…
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…