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Progress in digital pathology is hindered by high-resolution images and the prohibitive cost of exhaustive localized annotations. The commonly used paradigm to categorize pathology images is patch-based processing, which often incorporates…
The Segment Anything Model (SAM) has advanced interactive segmentation but is limited by the high computational cost on high-resolution images. This requires downsampling to meet GPU constraints, sacrificing the fine-grained details needed…
In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…
We propose a new method that employs transfer learning techniques to effectively correct sampling selection errors introduced by sparse annotations during supervised learning for automated tumor segmentation. The practicality of current…
Binary code is pervasive, and binary analysis is a key task in reverse engineering, malware classification, and vulnerability discovery. Unfortunately, while there exist large corpora of malicious binaries, obtaining high-quality corpora of…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
Decomposing a network flow into weighted paths has numerous applications. Some applications require any decomposition that is optimal w.r.t. some property such as number of paths, robustness, or length. Many bioinformatic applications…
Atomic-accuracy structure prediction of macromolecules is a long-sought goal of computational biophysics. Accurate modeling should be achievable by optimizing a physically realistic energy function but is presently precluded by incomplete…
In Proteomics, only the de novo peptide sequencing approach allows a partial amino acid sequence of a peptide to be found from a MS/MS spectrum. In this article a preliminary work is presented to discover a complete protein sequence from…
This paper presents STrEAM (SuperTrace Evaluation Automated for Matching), a Mathematica package that calculates all functional supertraces which arise when matching a generic UV model onto a relativistic Effective Field Theory (EFT) at one…
Accurate organ segmentation is essential for clinical tasks such as radiotherapy planning and disease monitoring. Recent foundation models like MedSAM achieve strong results using point or bounding-box prompts but still require manual…
Spatial transcriptomics (ST) technologies enable gene expression profiling with spatial resolution, offering unprecedented insights into tissue organization and disease heterogeneity. However, current analysis methods often struggle with…
The use of deep learning models in computational biology has increased massively in recent years, and it is expected to continue with the current advances in the fields such as Natural Language Processing. These models, although able to…
Motivation: Intimately tied to assembly quality is the complexity of the de Bruijn graph built by the assembler. Thus, there have been many paradigms developed to decrease the complexity of the de Bruijn graph. One obvious combinatorial…
Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation of DNA in chromatin of living tissue can…
The exponential growth of DNA sequencing data has outpaced traditional heuristic-based methods, which struggle to scale effectively. Efficient computational approaches are urgently needed to support large-scale similarity search, a…
WebAssembly enables near-native execution in web applications and is increasingly adopted for tasks that demand high performance and robust security. However, its assembly-like syntax, implicit stack machine, and low-level data types make…
Decomposing a flow on a Directed Acyclic Graph (DAG) into a weighted sum of a small number of paths is an essential task in operations research and bioinformatics. This problem, referred to as Sparse Flow Decomposition (SFD), has gained…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
Foundation models like the Segment Anything Model (SAM) excel in zero-shot segmentation for natural images but struggle with medical image segmentation due to differences in texture, contrast, and noise. Annotating medical images is costly…