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Anti-analysis techniques, particularly packing, challenge malware analysts, making packer identification fundamental. Existing packer identifiers have significant limitations: signature-based methods lack flexibility and struggle against…
Motivation: With the rapid expansion of large-scale biological datasets, DNA and protein sequence alignments have become essential for comparative genomics and proteomics. These alignments facilitate the exploration of sequence similarity…
Composed Image Retrieval (CIR) aims to retrieve target images from a gallery based on a reference image and modification text as a combined query. Recent approaches focus on balancing global information from two modalities and encode the…
The fast evolution of generative models has heightened the demand for reliable detection of AI-generated images. To tackle this challenge, we introduce FUSE, a hybrid system that combines spectral features extracted through Fast Fourier…
PepSIRF is a command-line, module-based open-source software package that facilitates the analysis of data from highly-multiplexed serology assays (e.g., PepSeq or PhIP-Seq). It has nine separate modules in its current release (v1.5.0):…
Embedding image features into a binary Hamming space can improve both the speed and accuracy of large-scale query-by-example image retrieval systems. Supervised hashing aims to map the original features to compact binary codes in a manner…
To detect large-variance code clones (i.e. clones with relatively more differences) in large-scale code repositories is difficult because most current tools can only detect almost identical or very similar clones. It will make promotion and…
In large software ecosystems, semantically related code changes, such as alternative solutions or overlapping modifications are often discovered only days after submission, leading to duplicated effort and delayed reviews. We present…
Image alignment tasks require accurate pixel correspondences, which are usually recovered by matching local feature descriptors. Such descriptors are often derived using supervised learning on existing datasets with ground truth…
In just the last decade, a multitude of bio-technologies and software pipelines have emerged to revolutionize genomics. To further their central goal, they aim to accelerate and improve the quality of de novo whole-genome assembly starting…
In recent years, the distinctive advancement of handling huge data promotes the evolution of ubiquitous computing and analysis technologies. With the constantly upward system burden and computational complexity, adaptive coding has been a…
Cross-lingual document alignment aims to identify pairs of documents in two distinct languages that are of comparable content or translations of each other. In this paper, we exploit the signals embedded in URLs to label web documents at…
Alignment of structural RNAs is an important problem with a wide range of applications. Since function is often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information…
SweepFinder is a popular program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and…
Pansharpening fuses a high-resolution panchromatic (PAN) image with a low-resolution multispectral (LRMS) image to produce a high-resolution multispectral (HRMS) image. A key difficulty is that jointly processing PAN and MS features often…
Duplicate marking is a critical preprocessing step in gene sequence analysis to flag redundant reads arising from polymerase chain reaction(PCR) amplification and sequencing artifacts. Although Picard MarkDuplicates is widely recognized as…
Existing state-of-the-art feature matchers capture long-range dependencies with Transformers but are hindered by high spatial complexity, leading to demanding training and highlatency inference. Striking a better balance between performance…
Recent advances in digital pathology have led to the need for Histopathology Image Retrieval (HIR) systems that search through databases of biopsy images to find similar cases to a given query image. These HIR systems allow pathologists to…
Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a…
Calculating the similarities between a pair of genomic sequences is one of the most fundamental computational steps in genomic analysis. This step -- called sequence alignment -- is the computational bottleneck because: (1) it is…