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This work focuses on effectively generating diverse solutions for satisfiability modulo theories (SMT) formulas, targeting the theories of bit-vectors, arrays, and uninterpreted functions, which is a critical task in software and hardware…
Classification tasks in NLP are typically addressed by selecting a pre-trained language model (PLM) from a model hub, and fine-tuning it for the task at hand. However, given the very large number of PLMs that are currently available, a…
Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call…
Applying deep learning to malware detection has drawn great attention due to its notable performance. With the increasing prevalence of cyberattacks targeting IoT devices, there is a parallel rise in the development of malware across…
Recognizing already explored places (a.k.a. place recognition) is a fundamental task in Simultaneous Localization and Mapping (SLAM) to enable robot relocalization and loop closure detection. In topological SLAM the recognition takes place…
Acquiring plausible pathways on high-dimensional structural distributions is beneficial in several domains. For example, in the drug discovery field, a protein conformational pathway, i.e. a highly probable sequence of protein structural…
Identifying the underlying models in a set of data points contaminated by noise and outliers, leads to a highly complex multi-model fitting problem. This problem can be posed as a clustering problem by the projection of higher order…
Long reads produced by third-generation sequencing technologies are used to construct an assembly (i.e., the subject's genome), which is further used in downstream genome analysis. Unfortunately, long reads have high sequencing error rates…
Sampling useful three-dimensional molecular structures along with their most favorable conformations is a key challenge in drug discovery. Current state-of-the-art 3D de-novo design flow matching or diffusion-based models are limited to…
Summary: With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment…
Downsampling and path planning are essential in robotics and autonomous systems, as they enhance computational efficiency and enable effective navigation in complex environments. However, current downsampling methods often fail to preserve…
Genome-wide eQTL mapping explores the relationship between gene expression values and DNA variants to understand genetic causes of human disease. Due to the large number of genes and DNA variants that need to be assessed simultaneously,…
Comprehensive discovery of structural variation (SV) in human genomes from DNA sequencing requires the integration of multiple alignment signals including read-pair, split-read and read-depth. However, owing to inherent technical…
Small-angle X-ray and neutron scattering experiments are used in many fields of the life sciences and condensed matter research to obtain answers to questions about the shape and size of nano-sized structures, typically in the range of 1 to…
We present a pipeline for unbiased and robust multimodal registration of neuroimaging modalities with minimal pre-processing. While typical multimodal studies need to use multiple independent processing pipelines, with diverse options and…
Cheap high-throughput DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food…
DNA sequence classification requires not only high predictive accuracy but also the ability to uncover latent site interactions, combinatorial regulation, and epistasis-like higher-order dependencies. Although the standard Transformer…
Spectroscopy is a central pillar of materials characterization, providing useful information on properties like structure, composition, or excited state dynamics of a system. However, many spectroscopic techniques present challenges in…
Next generation sequencing technology rapidly produces massive volume of data and quality control of this sequencing data is essential to any genomic analysis. Here we present MEEPTOOLS, which is a collection of open-source tools based on…
The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which…