Related papers: ProtoFold Neighborhood Inspector
In recent years, work has gone into developing deep interpretable methods for image classification that clearly attributes a model's output to specific features of the data. One such of these methods is the Prototypical Part Network…
The Protein Secondary Structure Visualizer ProS2Vi is a novel Python-based visualization tool designed to enhance the analysis and accessibility of protein secondary structures calculated and identified by the Dictionary of Secondary…
We report a 3D structure-based method of predicting protein-protein interaction partners. It involves screening for pairs of tetrahedra representing interacting amino acids at the interface of the protein-protein complex, with one…
Fourier ptychography (FP) is a newly developed computational imaging approach that achieves both high resolution and wide field of view by stitching a series of low-resolution images captured under angle-varied illumination. So far, many…
Brain-Computer Interfaces (BCIs) based on P300 event-related potentials offer promising applications in health, education, and assistive technologies. However, challenges related to inter- and intra-subject variability and the…
Background: The detection of perineural invasion (PNI) by carcinoma in prostate biopsies has been shown to be associated with poor prognosis. The assessment and quantification of PNI is; however, labor intensive. In the study we aimed to…
The local structure of a protein strongly impacts its function and interactions with other molecules. Therefore, a concise, informative representation of a local protein environment is essential for modeling and designing proteins and…
Penalized transformation models (PTMs) are a semiparametric location-scale regression family that estimate a response's conditional distribution directly from the data, and model the location and scale through structured additive…
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the…
Accurate localization of proteins from fluorescence microscopy images is challenging due to the inter-class similarities and intra-class disparities introducing grave concerns in addressing multi-class classification problems. Conventional…
We introduce a new nearest-prototype classifier, the prototype vector machine (PVM). It arises from a combinatorial optimization problem which we cast as a variant of the set cover problem. We propose two algorithms for approximating its…
Prototypical part neural networks (ProtoPartNNs), namely PROTOPNET and its derivatives, are an intrinsically interpretable approach to machine learning. Their prototype learning scheme enables intuitive explanations of the form, this…
In this paper we address the problem of protein classification starting from a multi-view 2D representation of proteins. From each 3D protein structure, a large set of 2D projections is generated using the protein visualization software…
Residue-residue interactions that fold a protein into a unique three-dimensional structure and make it play a specific function impose structural and functional constraints on each residue site. Selective constraints on residue sites are…
Predicting protein structure from the amino acid sequence has been a challenge with theoretical and practical significance in biophysics. Despite the recent progresses elicited by improved residue-residue contact prediction, contact-based…
Recent advances in distance-based protein folding have led to a paradigm shift in protein structure prediction. Through sufficiently precise estimation of the inter-residue distance matrix for a protein sequence, it is now feasible to…
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…
Thyroid nodule classification using ultrasound imaging is essential for early diagnosis and clinical decision-making; however, despite promising performance on in-distribution data, existing deep learning methods often exhibit limited…
Poisoning input views of 3D reconstruction systems has been recently studied. However, we identify that existing studies simply backpropagate adversarial gradients through the 3D reconstruction pipeline as a whole, without uncovering the…
Reflective and textureless surfaces remain a challenge in multi-view 3D reconstruction. Both camera pose calibration and shape reconstruction often fail due to insufficient or unreliable cross-view visual features. To address these issues,…