An Inception Inspired Deep Network to Analyse Fundus Images. (arXiv:1911.08715v1 [eess.IV])

A fundus image usually contains the optic disc, pathologies and other structures in addition to vessels to be segmented. This study proposes a deep network for vessel segmentation, whose architecture is inspired by inception modules. The network contains three sub-networks, each with a different filter size, which are connected in the last layer of the…

Fast and Flexible Image Blind Denoising via Competition of Experts. (arXiv:1911.08724v1 [cs.CV])

Fast and flexible processing are two essential requirements for a number of practical applications of image denoising. Current state-of-the-art methods, however, still require either high computational cost or limited scopes of the target. We introduce an efficient ensemble network trained via a competition of expert networks, as an application for image blind denoising. We realize…

Pan-Cancer Diagnostic Consensus Through Searching Archival Histopathology Images Using Artificial Intelligence. (arXiv:1911.08736v1 [eess.IV])

The emergence of digital pathology has opened new horizons for histopathology and cytology. Artificial-intelligence algorithms are able to operate on digitized slides to assist pathologists with diagnostic tasks. Whereas machine learning involving classification and segmentation methods have obvious benefits for image analysis in pathology, image search represents a fundamental shift in computational pathology. Matching the…

CAT: CRF-based ASR Toolkit. (arXiv:1911.08747v1 [cs.LG])

In this paper, we present a new open source toolkit for automatic speech recognition (ASR), named CAT (CRF-based ASR Toolkit). A key feature of CAT is discriminative training in the framework of conditional random field (CRF), particularly with connectionist temporal classification (CTC) inspired state topology. CAT contains a full-fledged implementation of CTC-CRF and provides a…

Yottixel — An Image Search Engine for Large Archives of Histopathology Whole Slide Images. (arXiv:1911.08748v1 [eess.IV])

With the emergence of digital pathology, searching for similar images in large archives has gained considerable attention. Image retrieval can provide pathologists with unprecedented access to the evidence embodied in already diagnosed and treated cases from the past. This paper proposes a search engine specialized for digital pathology, called Yottixel, a portmanteau for “one yotta…

PDBMine: A Reformulation of the Protein Data Bank to Facilitate Structural Data Mining. (arXiv:1911.08614v1 [cs.DB])

Large scale initiatives such as the Human Genome Project, Structural Genomics, and individual research teams have provided large deposits of genomic and proteomic data. The transfer of data to knowledge has become one of the existing challenges, which is a consequence of capturing data in databases that are optimally designed for archiving and not mining.…

A genomic dominion with regulatory dependencies on human-specific single-nucleotide changes in Modern Humans. (arXiv:1911.08646v1 [q-bio.GN])

Gene set enrichment analyses of 8,405 genes linked with 35,074 human-specific (hs) regulatory single-nucleotide changes (SNCs) revealed the staggering breadth of significant associations with morphological structures, physiological processes, and pathological conditions of Modern Humans. Significant enrichment traits include more than 1,000 anatomically-distinct regions of the adult human brain, many different types of human cells and…

DomainScope: A disease network based on protein domain connections. (arXiv:1911.08676v1 [q-bio.GN])

Protein domains are highly conserved functional units of proteins. Because they carry functionally significant information, the majority of the coding disease variants are located on domains. Additionally, domains are specific units of the proteins that can be targeted for drug delivery purposes. Here, using information about variants sites associated with diseases, a disease network was…

Motility and Phototaxis of $Gonium$, the Simplest Differentiated Colonial Alga. (arXiv:1911.08837v1 [cond-mat.soft])

Green algae of the $Volvocine$ lineage, spanning from unicellular $Chlamydomonas$ to vastly larger $Volvox$, are models for the study of the evolution of multicellularity, flagellar dynamics, and developmental processes. Phototactic steering in these organisms occurs without a central nervous system, driven solely by the response of individual cells. All such algae spin about a body-fixed…

Model-based simulation of maintenance therapy of childhood acute lymphoblastic leukemia. (arXiv:1911.08929v1 [q-bio.QM])

Acute lymphoblastic leukemia is the most common malignancy in childhood. Successful treatment requires initial high-intensity chemotherapy, followed by low-intensity oral maintenance therapy with oral 6-mercaptopurine (6MP) and methotrexate (MTX) until 2-3 years after disease onset. However, intra- and interindividual variability in the pharmacokinetics (PK) and pharmacodynamics (PD) of 6MP and MTX make it challenging to…