scholarly journals Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

2019 ◽  
Vol 95 (9) ◽  
pp. 952-965 ◽  
Author(s):  
Juan C. Caicedo ◽  
Jonathan Roth ◽  
Allen Goodman ◽  
Tim Becker ◽  
Kyle W. Karhohs ◽  
...  
2018 ◽  
Author(s):  
Juan C. Caicedo ◽  
Jonathan Roth ◽  
Allen Goodman ◽  
Tim Becker ◽  
Kyle W Karhohs ◽  
...  

Identifying nuclei is often a critical first step in analyzing microscopy images of cells, and classical image processing algorithms are most commonly used for this task. Recent developments in deep learning can yield superior accuracy, but typical evaluation metrics for nucleus segmentation do not satisfactorily capture error modes that are relevant in cellular images. We present an evaluation framework to measure accuracy, types of errors, and computational efficiency; and use it to compare deep learning strategies and classical approaches. We publicly release a set of 23,165 manually annotated nuclei and source code to reproduce experiments and run the proposed evaluation methodology. Our evaluation framework shows that deep learning improves accuracy and can reduce the number of biologically relevant errors by half.


2021 ◽  
Vol 190 ◽  
pp. 116849
Author(s):  
Seyed Moein Rassoulinejad-Mousavi ◽  
Firas Al-Hindawi ◽  
Tejaswi Soori ◽  
Arif Rokoni ◽  
Hyunsoo Yoon ◽  
...  

Author(s):  
Yun Zhang ◽  
Ling Wang ◽  
Xinqiao Wang ◽  
Chengyun Zhang ◽  
Jiamin Ge ◽  
...  

An effective and rapid deep learning method to predict chemical reactions contributes to the research and development of organic chemistry and drug discovery.


2021 ◽  
Vol 241 ◽  
pp. 114315
Author(s):  
D. Manno ◽  
G. Cipriani ◽  
G. Ciulla ◽  
V. Di Dio ◽  
S. Guarino ◽  
...  

2022 ◽  
Vol 9 (2) ◽  
pp. 246-258
Author(s):  
Luca Butera ◽  
Alberto Ferrante ◽  
Mauro Jermini ◽  
Mauro Prevostini ◽  
Cesare Alippi

2022 ◽  
Vol 6 (1) ◽  
Author(s):  
Marco Rossi ◽  
Sofia Vallecorsa

AbstractIn this work, we investigate different machine learning-based strategies for denoising raw simulation data from the ProtoDUNE experiment. The ProtoDUNE detector is hosted by CERN and it aims to test and calibrate the technologies for DUNE, a forthcoming experiment in neutrino physics. The reconstruction workchain consists of converting digital detector signals into physical high-level quantities. We address the first step in reconstruction, namely raw data denoising, leveraging deep learning algorithms. We design two architectures based on graph neural networks, aiming to enhance the receptive field of basic convolutional neural networks. We benchmark this approach against traditional algorithms implemented by the DUNE collaboration. We test the capabilities of graph neural network hardware accelerator setups to speed up training and inference processes.


2021 ◽  
Vol 9 (2) ◽  
pp. 1051-1052
Author(s):  
K. Kavitha, Et. al.

Sentiments is the term of opinion or views about any topic expressed by the people through a source of communication. Nowadays social media is an effective platform for people to communicate and it generates huge amount of unstructured details every day. It is essential for any business organization in the current era to process and analyse the sentiments by using machine learning and Natural Language Processing (NLP) strategies. Even though in recent times the deep learning strategies are becoming more familiar due to higher capabilities of performance. This paper represents an empirical study of an application of deep learning techniques in Sentiment Analysis (SA) for sarcastic messages and their increasing scope in real time. Taxonomy of the sentiment analysis in recent times and their key terms are also been highlighted in the manuscript. The survey concludes the recent datasets considered, their key contributions and the performance of deep learning model applied with its primary purpose like sarcasm detection in order to describe the efficiency of deep learning frameworks in the domain of sentimental analysis.


2020 ◽  
Author(s):  
Nikhil Prakash ◽  
Andrea Manconi ◽  
Simon Loew

<p>Landslide hazard has always been a significant source of economic losses and fatalities in the mountainous regions. Knowledge of the spatial extent of the past and present landslide activity, compiled in the form of a landslide inventory map, is essential for effective risk management. High-resolution data acquired by Earth observation (EO) satellites are often used to map landslides by identifying morphological expressions that can be associated with past and/or recent deformation. This is a slow and difficult process as it requires extensive manual efforts. As a result, such maps are not readily available for all the landslide hazard affected regions. Fully automated methods are required to exploit the exponentially increasing amount of EO data available for landslide hazard assessments. In this context, conventional methods like pixel-based and object-based machine learning strategies have been studied extensively in the last decade. Recent advances in convolutional neural network (CNN), a type of deep-learning method, has outperformed other conventional learning methods in similar image interpretation tasks. In this work, we present a deep-learning based method for semantic segmentation of landslides from EO images. We present the results from a study area in the south of Portland in Oregon, USA. The landslide inventory for training and ground truth was extracted from the Statewide Landslide Information Database of Oregon (SLIDO). We were able to achieve a probability of detection (POD) greater than 0.70. This method can also be extended to be used for rapid mapping of landslides after a major triggering event (like earthquake or extreme metrological event) has occurred.</p><p>This work is done in the framework of European Commission's Horizon 2020 project "BETTER”. More information is available on the website https://www.ec-better.eu/.</p>


2021 ◽  
Author(s):  
Benjamin Schwarz ◽  
Korbinian Sager ◽  
Philippe Jousset ◽  
Gilda Currenti ◽  
Charlotte Krawczyk ◽  
...  

<p><span>Fiber-optic cables form an integral part of modern telecommunications infrastructure and are ubiquitous in particular in regions where dedicated seismic instrumentation is traditionally sparse or lacking entirely. Fiber-optic seismology promises to enable affordable and time-extended observations of earth and environmental processes at an unprecedented temporal and spatial resolution. The method’s unique potential for combined large-N and large-T observations implies intriguing opportunities but also significant challenges in terms of data storage, data handling and computation.</span></p><p><span>Our goal is to enable real-time data enhancement, rapid signal detection and wave field characterization without the need for time-demanding user interaction. We therefore combine coherent wave field analysis, an optics-inspired processing framework developed in controlled-source seismology, with state-of-the-art deep convolutional neural network (CNN) architectures commonly used in visual perception. While conventional deep learning strategies have to rely on manually labeled or purely synthetic training datasets, coherent wave field analysis labels field data based on physical principles and enables large-scale and purely data-driven training of the CNN models. The shear amount of data already recorded in various settings makes artificial data generation by numerical modeling superfluous – a task that is often constrained by incomplete knowledge of the embedding medium and an insufficient description of processes at or close to the surface, which are challenging to capture in integrated simulations.</span></p><p><span>Applications to extensive field datasets acquired with dark-fiber infrastructure at a geothermal field in SW Iceland and in a town at the flank of Mt Etna, Italy, reveal that the suggested framework generalizes well across different observational scales and environments, and sheds new light on the origin of a broad range of physically distinct wave fields that can be sensed with fiber-optic technology. Owing to the real-time applicability with affordable computing infrastructure, our analysis lends itself well to rapid on-the-fly data enhancement, wave field separation and compression strategies, thereby promising to have a positive impact on the full processing chain currently in use in fiber-optic seismology.</span></p>


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