Related papers: Pep2Prob Benchmark: Predicting Fragment Ion Probab…
Determining the structure of a protein has been a decades-long open question. A protein's three-dimensional structure often poses nontrivial computation costs, when classical simulation algorithms are utilized. Advances in the transformer…
PET/CT imaging is the gold standard for tumor detection, offering high accuracy in identifying local and metastatic lesions. Radiologists often begin assessment with rotational Multi-Angle Maximum Intensity Projections (MIPs) from PET,…
Quantum-based molecular dynamics (QMD) is a highly accurate and transferable method for material science simulations. However, the time scales and system sizes accessible to QMD are typically limited to picoseconds and a few hundred atoms.…
One of the fundamental tasks in understanding genomics is the problem of predicting Transcription Factor Binding Sites (TFBSs). With more than hundreds of Transcription Factors (TFs) as labels, genomic-sequence based TFBS prediction is a…
Background: Brain tumor segmentation has a significant impact on the diagnosis and treatment of brain tumors. Accurate brain tumor segmentation remains challenging due to their irregular shapes, vague boundaries, and high variability.…
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…
Proteins constitute a large group of macromolecules with a multitude of functions for all living organisms. Proteins achieve this by adopting distinct three-dimensional structures encoded by the sequence of their constituent amino acids in…
Coronary heart disease (CHD) is a leading cause of death worldwide and contributes significantly to annual healthcare expenditures. To develop a non-invasive diagnostic approach, we designed a model based on a multilayer perceptron (MLP)…
The pancreatic disease taxonomy includes ten types of masses (tumors or cysts)[20,8]. Previous work focuses on developing segmentation or classification methods only for certain mass types. Differential diagnosis of all mass types is…
Image segmentation is a critical step in computational biomedical image analysis, typically evaluated using metrics like the Dice coefficient during training and validation. However, in clinical settings without manual annotations,…
Atom probe tomography (APT) is a valuable near-atomic scale imaging technique, which yields mass spectrographic data. Experimental correctness can often pivot on the identification of peaks within a dataset, this is a manual process where…
Periodic material or crystal property prediction using machine learning has grown popular in recent years as it provides a computationally efficient replacement for classical simulation methods. A crucial first step for any of these…
Mass spectrometry is a widely used method to study molecules and processes in medicine, life sciences, chemistry, catalysis, and industrial product quality control, among many other applications. One of the main features of some mass…
Malignant pleural mesothelioma (MPM) is the most common form of mesothelioma. To assess response to treatment, tumor measurements are acquired and evaluated based on a patient's longitudinal computed tomography (CT) scans. Tumor volume,…
Graph Neural Networks (GNNs) have achieved strong results in molecular property prediction, but polymers present distinct challenges: labeled datasets are scarce and small (typically in the order of hundreds of polymers) due to the need for…
Identification of nearly all proteins in a system using data-dependent acquisition (DDA) mass spectrometry has become routine for simple organisms, such as bacteria and yeast. Still, quantification of the identified proteins may be a…
Quantitative molecular imaging is central to treatment response assessment in oncology, yet clinical practice remains largely dominated by patient-level or limited target-lesion criteria that ignore inter-lesion heterogeneity. This…
Multicellular tumor spheroids (MCTS) are advanced cell culture systems for assessing the impact of combinatorial radio(chemo)therapy. They exhibit therapeutically relevant in-vivo-like characteristics from 3D cell-cell and cell-matrix…
While prefractionation has previously been shown to improve results in MS analysis, a novel combination provides an additional dimension of separation: protein fractionation by SDS-PAGE followed by IEF of tryptic peptides before separation…
Accurately assigning folds for divergent protein sequences is a major obstacle to structural studies and underlies the inverse protein folding problem. Herein, we outline our theories for fold-recognition in the "twilight-zone" of sequence…