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Formal models for gene assembly in ciliates have been developed, in particular the string pointer reduction system (SPRS) and the graph pointer reduction system (GPRS). The reduction graph is a valuable tool within the SPRS, revealing much…
The robustness of gaze and head pose estimation models is highly dependent on the amount of labeled data. Recently, generative modeling has shown excellent results in generating photo-realistic images, which can alleviate the need for…
Single-nucleotide-resolution chemical mapping for structured RNA is being rapidly advanced by new chemistries, faster readouts, and coupling to computational algorithms. Recent tests have shown that selective 2'-hydroxyl acylation by primer…
There is a growing interest in automated neural architecture search (NAS) methods. They are employed to routinely deliver high-quality neural network architectures for various challenging data sets and reduce the designer's effort. The NAS…
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…
N-terminal coding sequence (NCS) influences gene expression by impacting the translation initiation rate. The NCS optimization problem is to find an NCS that maximizes gene expression. The problem is important in genetic engineering.…
Semantic segmentation of blood vessels is an important task in medical image analysis, but its progress is often hindered by the scarcity of large annotated datasets and the poor generalization of models across different imaging modalities.…
We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e., DNA…
As the deployment of low carbon transportation technologies, specifically electric vehicles (EVs), is increasing, the concept of their eco-driving is gaining significant attention. Contrary to the eco-driving techniques used in conventional…
This paper introduces a novel multi-object tracking (MOT) method, dubbed GenTrack, whose main contributions include: a hybrid tracking approach employing both stochastic and deterministic manners to robustly handle unknown and time-varying…
The massive amount of genomic data appearing for SARS-CoV-2 since the beginning of the COVID-19 pandemic has challenged traditional methods for studying its dynamics. As a result, new methods such as Pangolin, which can scale to the…
Compiler pass auto-tuning is critical for enhancing software performance, yet finding the optimal pass sequence for a specific program is an NP-hard problem. Traditional, general-purpose optimization flags like -O3 and -Oz adopt a…
Based on the BioBricks standard, restriction synthesis is a novel catabolic iterative DNA synthesis method that utilizes endonucleases to synthesize a query sequence from a reference sequence. In this work, the reference sequence is built…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
There has been significant recent interest towards achieving highly efficient deep neural network architectures. A promising paradigm for achieving this is the concept of evolutionary deep intelligence, which attempts to mimic biological…
Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed…
Visually Rich Documents (VRDs), comprising elements such as charts, tables, and paragraphs, convey complex information across diverse domains. However, extracting key information from these documents remains labour-intensive, particularly…
Finding cancer driver genes has been a focal theme of cancer research and clinical studies. One of the recent approaches is based on network structural controllability that focuses on finding a control scheme and driver genes that can steer…
Integrative biomolecular modeling of RNA relies on structural refined collections and accurate experimental data that reflect binding and folding behavior. However, the prediction of such collections remains challenging due to the rugged…
Foundation models have advanced computer vision by enabling strong performance across diverse tasks through large-scale pretraining and supervised fine-tuning. However, they may underperform in domains with distribution shifts and scarce…