Related papers: PASS: De novo assembler for short peptide sequence…
A novel technique based on machine learning is introduced to reconstruct the decays of highly Lorentz-boosted particles. Using an end-to-end deep learning strategy, the technique bypasses existing rule-based particle reconstruction methods…
Beam emission spectroscopy (BES) is a powerful plasma diagnostic method especially suited for the measurement of plasma density and its fluctuations. As such, synthetic BES codes are regularly used to aid the design or utilization of these…
Peptide sequencing from mass spectrometry data is a key step in proteome research. Especially de novo sequencing, the identification of a peptide from its spectrum alone, is still a challenge even for state-of-the-art algorithmic…
Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…
Image Phase Alignment Super-Sampling (ImPASS) is a computational imaging algorithm for converting a sequence of displaced low-resolution images into a single high-resolution image. The method consists of a unique combination of Phase…
Probabilistic amplitude shaping (PAS) is on track to become the de facto coded modulation standard for communication systems aiming to operate close to channel capacity at high transmission rates. The essential component of PAS that breeds…
A common approach to the de novo molecular generation problem from mass spectra involves a two-stage pipeline: (1) encoding mass spectra into molecular fingerprints, followed by (2) decoding these fingerprints into molecular structures. In…
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…
Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10kbp in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long…
Motivation: Proteomic mass spectrometry analysis is becoming routine in clinical diagnostics, for example to monitor cancer biomarkers using blood samples. However, differential proteomics and identification of peaks relevant for class…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based…
Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have…
Molecular dynamics (MD) simulation is widely used to study protein conformations and dynamics. However, conventional simulation suffers from being trapped in some local energy minima that are hard to escape. Thus, most computational time is…
Sequential Monte Carlo (SMC) samplers are powerful tools for Bayesian inference but suffer from high computational costs due to their reliance on large particle ensembles for accurate estimates. We introduce persistent sampling (PS), an…
Generating peptides with desired properties is crucial for drug discovery and biotechnology. Traditional sequence-based and structure-based methods often require extensive datasets, which limits their effectiveness. In this study, we…
Mixture interpretation is a central challenge in forensic science, where evidence often contains contributions from multiple sources. In the context of DNA analysis, biological samples recovered from crime scenes may include genetic…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
Collection of massive well-annotated samples is effective in improving object detection performance but is extremely laborious and costly. Instead of data collection and annotation, the recently proposed Cut-Paste methods [12, 15] show the…
The detection of genomic structural variation (SV) has advanced tremendously in recent years due to progress in high-throughput sequencing technologies. Novel sequence insertions, insertions without similarity to a human reference genome,…