scholarly journals BeadNet: deep learning-based bead detection and counting in low-resolution microscopy images

2020 ◽  
Vol 36 (17) ◽  
pp. 4668-4670
Author(s):  
Tim Scherr ◽  
Karolin Streule ◽  
Andreas Bartschat ◽  
Moritz Böhland ◽  
Johannes Stegmaier ◽  
...  
Keyword(s):  
Expert Knowledge ◽  
State Of The Art ◽  
Supplementary Information ◽  
Bacterial Invasion ◽  
Low Resolution ◽  
Image Labeling ◽  
Detection And Counting ◽  
Software Code ◽  
High Throughput Experiments ◽  
Microscopy Images

Abstract Motivation An automated counting of beads is required for many high-throughput experiments such as studying mimicked bacterial invasion processes. However, state-of-the-art algorithms under- or overestimate the number of beads in low-resolution images. In addition, expert knowledge is needed to adjust parameters. Results In combination with our image labeling tool, BeadNet enables biologists to easily annotate and process their data reducing the expertise required in many existing image analysis pipelines. BeadNet outperforms state-of-the-art-algorithms in terms of missing, added and total amount of beads. Availability and implementation BeadNet (software, code and dataset) is available at https://bitbucket.org/t_scherr/beadnet. The image labeling tool is available at https://bitbucket.org/abartschat/imagelabelingtool. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Evaluating recommender systems for AI-driven biomedical informatics

2020 ◽  
Author(s):  
William La Cava ◽  
Heather Williams ◽  
Weixuan Fu ◽  
Steve Vitale ◽  
Durga Srivatsan ◽  
...  
Keyword(s):  
Septic Shock ◽  
Recommender Systems ◽  
Data Science ◽  
Expert Knowledge ◽  
State Of The Art ◽  
Optimal Algorithm ◽  
Supplementary Information ◽  
Biomedical Data ◽  
Classification Problems ◽  
Systems Research

Abstract Motivation Many researchers with domain expertise are unable to easily apply machine learning (ML) to their bioinformatics data due to a lack of ML and/or coding expertise. Methods that have been proposed thus far to automate ML mostly require programming experience as well as expert knowledge to tune and apply the algorithms correctly. Here, we study a method of automating biomedical data science using a web-based AI platform to recommend model choices and conduct experiments. We have two goals in mind: first, to make it easy to construct sophisticated models of biomedical processes; and second, to provide a fully automated AI agent that can choose and conduct promising experiments for the user, based on the user’s experiments as well as prior knowledge. To validate this framework, we conduct an experiment on 165 classification problems, comparing to state-of-the-art, automated approaches. Finally, we use this tool to develop predictive models of septic shock in critical care patients. Results We find that matrix factorization-based recommendation systems outperform metalearning methods for automating ML. This result mirrors the results of earlier recommender systems research in other domains. The proposed AI is competitive with state-of-the-art automated ML methods in terms of choosing optimal algorithm configurations for datasets. In our application to prediction of septic shock, the AI-driven analysis produces a competent ML model (AUROC 0.85±0.02) that performs on par with state-of-the-art deep learning results for this task, with much less computational effort. Availability and implementation PennAI is available free of charge and open-source. It is distributed under the GNU public license (GPL) version 3. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Adaptive multiorientation resolution analysis of complex filamentous network images

2020 ◽  
Vol 36 (20) ◽  
pp. 5093-5103 ◽  
Author(s):  
Mark Kittisopikul ◽  
Amir Vahabikashi ◽  
Takeshi Shimi ◽  
Robert D Goldman ◽  
Khuloud Jaqaman
Keyword(s):  
State Of The Art ◽  
Spatial Localization ◽  
Fixed Number ◽  
Automated Image Analysis ◽  
Supplementary Information ◽  
Manual Segmentation ◽  
Arbitrary Geometry ◽  
Resolution Analysis ◽  
Single Orientation ◽  
Microscopy Images

Abstract Motivation Microscopy images of cytoskeletal, nucleoskeletal and other structures contain complex junctions of overlapping filaments with arbitrary geometry. Yet, state-of-the-art algorithms generally perform single orientation analysis to segment these structures, resulting in gaps near junctions, or assume particular junction geometries to detect them. Results We developed a fully automated image analysis approach to address the challenge of determining the number of orientations and their values at each point in space to detect both lines and their junctions. Our approach does not assume any fixed number of orientations or any particular geometry in the case of multiple coincident orientations. It is based on analytically resolving coincident orientations revealed by steerable ridge filtering in an adaptive manner that balances orientation resolution and spatial localization. Combining this multiorientation resolution information with a generalization of the concept of non-maximum suppression allowed us to then identify the centers of lines and their junctions in an image. We validated our approach using a wide array of synthetic junctions and by comparison to manual segmentation. We also applied it to light microscopy images of cytoskeletal and nucleoskeletal networks. Availability and implementation https://github.com/mkitti/AdaptiveResolutionOrientationSpace. Supplementary information Supplementary information is available at Bioinformatics online.

Survey of the State-of-the-Art Expert/Knowledge Based Systems in Civil Engineering.

1986 ◽  
Author(s):  
Simon S. Kim ◽  
Mary Lou Maher ◽  
Raymond E. Levitt ◽  
Martin F. Rooney ◽  
Thomas J. Siller
Keyword(s):  
Civil Engineering ◽  
Expert Knowledge ◽  
State Of The Art ◽  
The State ◽  
Knowledge Based Systems ◽  
Knowledge Based

scholarly journals CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes

2020 ◽  
Author(s):  
Matteo Chiara ◽  
Federico Zambelli ◽  
Marco Antonio Tangaro ◽  
Pietro Mandreoli ◽  
David S Horner ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Ad Hoc ◽  
State Of The Art ◽  
Supplementary Information ◽  
Genomic Sequences ◽  
Supplementary Data ◽  
Evolutionary Patterns ◽  
Genomic Variants ◽  
Art Methods ◽  
Available Resources

Abstract Summary While over 200 000 genomic sequences are currently available through dedicated repositories, ad hoc methods for the functional annotation of SARS-CoV-2 genomes do not harness all currently available resources for the annotation of functionally relevant genomic sites. Here, we present CorGAT, a novel tool for the functional annotation of SARS-CoV-2 genomic variants. By comparisons with other state of the art methods we demonstrate that, by providing a more comprehensive and rich annotation, our method can facilitate the identification of evolutionary patterns in the genome of SARS-CoV-2. Availabilityand implementation Galaxy   http://corgat.cloud.ba.infn.it/galaxy; software: https://github.com/matteo14c/CorGAT/tree/Revision_V1; docker: https://hub.docker.com/r/laniakeacloud/galaxy_corgat. Supplementary information Supplementary data are available at Bioinformatics online.

Vesseg: An Open-Source Tool for Deep Learning-Based Atherosclerotic Plaque Quantification in Histopathology Image

2021 ◽  
Author(s):  
J.M. Murray ◽  
P. Pfeffer ◽  
R. Seifert ◽  
A. Hermann ◽  
J. Handke ◽  
...  
Keyword(s):  
Deep Learning ◽  
Open Source ◽  
Atherosclerotic Plaque ◽  
State Of The Art ◽  
The Mean ◽  
Time Savings ◽  
Plaque Quantification ◽  
Atherosclerosis Research ◽  
Hematoxylin Eosin ◽  
Microscopy Images

Objective: Manual plaque segmentation in microscopy images is a time-consuming process in atherosclerosis research and potentially subject to unacceptable user-to-user variability and observer bias. We address this by releasing Vesseg a tool that includes state-of-the-art deep learning models for atherosclerotic plaque segmentation. Approach and Results: Vesseg is a containerized, extensible, open-source, and user-oriented tool. It includes 2 models, trained and tested on 1089 hematoxylin-eosin stained mouse model atherosclerotic brachiocephalic artery sections. The models were compared to 3 human raters. Vesseg can be accessed at https://vesseg .online or downloaded. The models show mean Soerensen-Dice scores of 0.91±0.15 for plaque and 0.97±0.08 for lumen pixels. The mean accuracy is 0.98±0.05. Vesseg is already in active use, generating time savings of >10 minutes per slide. Conclusions: Vesseg brings state-of-the-art deep learning methods to atherosclerosis research, providing drastic time savings, while allowing for continuous improvement of models and the underlying pipeline.

scholarly journals DeepMAsED: evaluating the quality of metagenomic assemblies

2020 ◽  
Vol 36 (10) ◽  
pp. 3011-3017 ◽  
Author(s):  
Olga Mineeva ◽  
Mateo Rojas-Carulla ◽  
Ruth E Ley ◽  
Bernhard Schölkopf ◽  
Nicholas D Youngblut
Keyword(s):  
Large Scale ◽  
State Of The Art ◽  
Ground Truth ◽  
Supplementary Information ◽  
Learning Approach ◽  
Wide Range ◽  
Metagenome Assembly ◽  
Model Training ◽  
Reference Genomes

Abstract Motivation Methodological advances in metagenome assembly are rapidly increasing in the number of published metagenome assemblies. However, identifying misassemblies is challenging due to a lack of closely related reference genomes that can act as pseudo ground truth. Existing reference-free methods are no longer maintained, can make strong assumptions that may not hold across a diversity of research projects, and have not been validated on large-scale metagenome assemblies. Results We present DeepMAsED, a deep learning approach for identifying misassembled contigs without the need for reference genomes. Moreover, we provide an in silico pipeline for generating large-scale, realistic metagenome assemblies for comprehensive model training and testing. DeepMAsED accuracy substantially exceeds the state-of-the-art when applied to large and complex metagenome assemblies. Our model estimates a 1% contig misassembly rate in two recent large-scale metagenome assembly publications. Conclusions DeepMAsED accurately identifies misassemblies in metagenome-assembled contigs from a broad diversity of bacteria and archaea without the need for reference genomes or strong modeling assumptions. Running DeepMAsED is straight-forward, as well as is model re-training with our dataset generation pipeline. Therefore, DeepMAsED is a flexible misassembly classifier that can be applied to a wide range of metagenome assembly projects. Availability and implementation DeepMAsED is available from GitHub at https://github.com/leylabmpi/DeepMAsED. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Analyze COVID-19 CT images based on evolutionary algorithm with dynamic searching space

2021 ◽  
Author(s):  
Yunhong Gong ◽  
Yanan Sun ◽  
Dezhong Peng ◽  
Peng Chen ◽  
Zhongtai Yan ◽  
...  
Keyword(s):  
Common Sense ◽  
Expert Knowledge ◽  
State Of The Art ◽  
Data Set ◽  
The Past ◽  
Computed Tomography Images ◽  
Intensive Use ◽  
Hospital Resources ◽  
The Common ◽  
Ct Data

AbstractThe COVID-19 pandemic has caused a global alarm. With the advances in artificial intelligence, the COVID-19 testing capabilities have been greatly expanded, and hospital resources are significantly alleviated. Over the past years, computer vision researches have focused on convolutional neural networks (CNNs), which can significantly improve image analysis ability. However, CNN architectures are usually manually designed with rich expertise that is scarce in practice. Evolutionary algorithms (EAs) can automatically search for the proper CNN architectures and voluntarily optimize the related hyperparameters. The networks searched by EAs can be used to effectively process COVID-19 computed tomography images without expert knowledge and manual setup. In this paper, we propose a novel EA-based algorithm with a dynamic searching space to design the optimal CNN architectures for diagnosing COVID-19 before the pathogenic test. The experiments are performed on the COVID-CT data set against a series of state-of-the-art CNN models. The experiments demonstrate that the architecture searched by the proposed EA-based algorithm achieves the best performance yet without any preprocessing operations. Furthermore, we found through experimentation that the intensive use of batch normalization may deteriorate the performance. This contrasts with the common sense approach of manually designing CNN architectures and will help the related experts in handcrafting CNN models to achieve the best performance without any preprocessing operations

scholarly journals A Soft-YoloV4 for High-Performance Head Detection and Counting

Mathematics ◽  
2021 ◽  
Vol 9 (23) ◽  
pp. 3096
Author(s):  
Zhen Zhang ◽  
Shihao Xia ◽  
Yuxing Cai ◽  
Cuimei Yang ◽  
Shaoning Zeng
Keyword(s):  
High Performance ◽  
Detection Rate ◽  
Detection Method ◽  
State Of The Art ◽  
Counting Method ◽  
People Counting ◽  
Detection Model ◽  
Detection And Counting ◽  
Head Detection ◽  
Ap Value

Blockage of pedestrians will cause inaccurate people counting, and people’s heads are easily blocked by each other in crowded occasions. To reduce missed detections as much as possible and improve the capability of the detection model, this paper proposes a new people counting method, named Soft-YoloV4, by attenuating the score of adjacent detection frames to prevent the occurrence of missed detection. The proposed Soft-YoloV4 improves the accuracy of people counting and reduces the incorrect elimination of the detection frames when heads are blocked by each other. Compared with the state-of-the-art YoloV4, the AP value of the proposed head detection method is increased from 88.52 to 90.54%. The Soft-YoloV4 model has much higher robustness and a lower missed detection rate for head detection, and therefore it dramatically improves the accuracy of people counting.

scholarly journals Beyond Intra-modality: A Survey of Heterogeneous Person Re-identification

2020 ◽  
Author(s):  
Zheng Wang ◽  
Zhixiang Wang ◽  
Yinqiang Zheng ◽  
Yang Wu ◽  
Wenjun Zeng ◽  
...  
Keyword(s):  
Video Analysis ◽  
State Of The Art ◽  
Future Research ◽  
Low Resolution ◽  
Research Directions ◽  
Comprehensive Review ◽  
Practical Applications ◽  
Future Research Directions

An efficient and effective person re-identification (ReID) system relieves the users from painful and boring video watching and accelerates the process of video analysis. Recently, with the explosive demands of practical applications, a lot of research efforts have been dedicated to heterogeneous person re-identification (Hetero-ReID). In this paper, we provide a comprehensive review of state-of-the-art Hetero-ReID methods that address the challenge of inter-modality discrepancies. According to the application scenario, we classify the methods into four categories --- low-resolution, infrared, sketch, and text. We begin with an introduction of ReID, and make a comparison between Homogeneous ReID (Homo-ReID) and Hetero-ReID tasks. Then, we describe and compare existing datasets for performing evaluations, and survey the models that have been widely employed in Hetero-ReID. We also summarize and compare the representative approaches from two perspectives, i.e., the application scenario and the learning pipeline. We conclude by a discussion of some future research directions. Follow-up updates are available at https://github.com/lightChaserX/Awesome-Hetero-reID

scholarly journals Colour deconvolution: stain unmixing in histological imaging

2020 ◽  
Author(s):  
Gabriel Landini ◽  
Giovanni Martinelli ◽  
Filippo Piccinini
Keyword(s):  
Source Code ◽  
Supplementary Information ◽  
Optical Absorbance ◽  
Matlab Program ◽  
Colour Distribution ◽  
Program Function ◽  
Histological Images ◽  
New Applications ◽  
Microscopy Images ◽  
Imagej Plugin

Abstract Motivation Microscopy images of stained cells and tissues play a central role in most biomedical experiments and routine histopathology. Storing colour histological images digitally opens the possibility to process numerically colour distribution and intensity to extract quantitative data. Among those numerical procedures are colour deconvolution, which enable decomposing an RGB image into channels representing the optical absorbance and transmittance of the dyes when their RGB representation is known. Consequently, a range of new applications become possible for morphological and histochemical segmentation, automated marker localization and image enhancement. Availability and implementation Colour deconvolution is presented here in two open-source forms: a MATLAB program/function and an ImageJ plugin written in Java. Both versions run in Windows, Macintosh and UNIX-based systems under the respective platforms. Source code and further documentation are available at: https://blog.bham.ac.uk/intellimic/g-landini-software/colour-deconvolution-2/. Supplementary information Supplementary data are available at Bioinformatics online.

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