Related papers: ProCaliper: functional and structural analysis, vi…
We introduce a new model of proteins, which extends and enhances the traditional graphical representation by associating a combinatorial object called a fatgraph to any protein based upon its intrinsic geometry. Fatgraphs can easily be…
cityseer-api is a Python package consisting of computational tools for fine-grained street-network and land-use analysis, helpful in assessing the morphological precursors to vibrant neighbourhoods. It is underpinned by network-based…
Existing profilers for scripting languages (a.k.a. "glue" languages) like Python suffer from numerous problems that drastically limit their usefulness. They impose order-of-magnitude overheads, report information at too coarse a…
Motivation: The rapid growth of biological data has intensified the need for transparent, reproducible, and well-documented computational workflows. The ability to clearly connect the steps of a workflow in the code with their description…
This paper proposes Scalene, a profiler specialized for Python. Scalene combines a suite of innovations to precisely and simultaneously profile CPU, memory, and GPU usage, all with low overhead. Scalene's CPU and memory profilers help…
Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and…
PlayMolecule Viewer is a web-based data visualization toolkit designed to streamline the exploration of data resulting from structural bioinformatics or computer-aided drug design efforts. By harnessing state-of-the-art web technologies…
Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand…
Proteins encode diverse functions within complex three-dimensional structures, yet most deep learning representations remain highly entangled, obscuring the biophysical signals that underlie function. Here we introduce ProtDiS, a…
We present the v1.0.1 release of DFormPy, the first Python library providing an interactive visualisation of differential forms. DFormPy is also capable of exterior algebra and vector calculus, building on the capabilities of NumPy and…
DisCoPy (Distributional Compositional Python) is an open source toolbox for computing with string diagrams and functors. In particular, the diagram data structure allows to encode various kinds of quantum processes, with functors for…
As supercomputers continue to grow in scale and capabilities, it is becoming increasingly difficult to isolate processor and system level causes of performance degradation. Over the last several years, a significant number of performance…
We present a software framework for statistical data analysis, called HistFitter, that has been used extensively by the ATLAS Collaboration to analyze big datasets originating from proton-proton collisions at the Large Hadron Collider at…
Multi-human parsing is an image segmentation task necessitating both instance-level and fine-grained category-level information. However, prior research has typically processed these two types of information through separate branches and…
We present gradiend, an open-source Python package that operationalizes the GRADIEND method for learning feature directions from factual-counterfactual MLM and CLM gradients in language models. The package provides a unified workflow for…
Current protein forcefields like the ones seen in CHARMM or Xplor-NIH have many terms that include bonded and non-bonded terms. Yet the forcefields do not take into account the use of hydrogen bonds which are important for secondary…
Background:Prediction of protein three-dimensional structures from amino acid sequences is a long-standing goal in computational/molecular biology. The successful discrimination of protein folds would help to improve the accuracy of protein…
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…
Change captioning generates descriptions that explicitly describe the differences between two visually similar images. Existing methods operate on static image pairs, thus ignoring the rich temporal dynamics of the change procedure, which…
Despite many advances in computational modeling of protein structures, these methods have not been widely utilized by experimental structural biologists. Two major obstacles are preventing the transition from a purely-experimental to a…