scholarly journals Machine learning-based real-time object locator/evaluator for cryo-EM data collection

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Koji Yonekura ◽  
Saori Maki-Yonekura ◽  
Hisashi Naitow ◽  
Tasuku Hamaguchi ◽  
Kiyofumi Takaba

AbstractIn cryo-electron microscopy (cryo-EM) data collection, locating a target object is error-prone. Here, we present a machine learning-based approach with a real-time object locator named yoneoLocr using YOLO, a well-known object detection system. Implementation shows its effectiveness in rapidly and precisely locating carbon holes in single particle cryo-EM and in locating crystals and evaluating electron diffraction (ED) patterns in automated cryo-electron crystallography (cryo-EX) data collection. The proposed approach will advance high-throughput and accurate data collection of images and diffraction patterns with minimal human operation.

2021 ◽  
Author(s):  
Koji Yonekura ◽  
Saori Maki-Yonekura ◽  
Hisashi Naitow ◽  
Tasuku Hamaguchi ◽  
Kiyofumi Takaba

In cryo-electron microscopy (cryo-EM) data collection, locating a target object is the most error-prone. Here, we present a machine learning-based approach with a real-time object locator named yoneoLocr using YOLO, a well-known object detection system. Implementation showed its effectiveness in rapidly and precisely locating carbon holes in single particle cryo-EM and for locating crystals and evaluating electron diffraction (ED) patterns in automated cryo-electron crystallography (cryo-EX) data collection.


Author(s):  
Marc J.C. de Jong ◽  
Wim M. Busing ◽  
Max T. Otten

Biological materials damage rapidly in the electron beam, limiting the amount of information that can be obtained in the transmission electron microscope. The discovery that observation at cryo temperatures strongly reduces beam damage (in addition to making it unnecessaiy to use chemical fixatives, dehydration agents and stains, which introduce artefacts) has given an important step forward to preserving the ‘live’ situation and makes it possible to study the relation between function, chemical composition and morphology.Among the many cryo-applications, the most challenging is perhaps the determination of the atomic structure. Henderson and co-workers were able to determine the structure of the purple membrane by electron crystallography, providing an understanding of the membrane's working as a proton pump. As far as understood at present, the main stumbling block in achieving high resolution appears to be a random movement of atoms or molecules in the specimen within a fraction of a second after exposure to the electron beam, which destroys the highest-resolution detail sought.


2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Suppawong Tuarob ◽  
Poom Wettayakorn ◽  
Ponpat Phetchai ◽  
Siripong Traivijitkhun ◽  
Sunghoon Lim ◽  
...  

AbstractThe explosion of online information with the recent advent of digital technology in information processing, information storing, information sharing, natural language processing, and text mining techniques has enabled stock investors to uncover market movement and volatility from heterogeneous content. For example, a typical stock market investor reads the news, explores market sentiment, and analyzes technical details in order to make a sound decision prior to purchasing or selling a particular company’s stock. However, capturing a dynamic stock market trend is challenging owing to high fluctuation and the non-stationary nature of the stock market. Although existing studies have attempted to enhance stock prediction, few have provided a complete decision-support system for investors to retrieve real-time data from multiple sources and extract insightful information for sound decision-making. To address the above challenge, we propose a unified solution for data collection, analysis, and visualization in real-time stock market prediction to retrieve and process relevant financial data from news articles, social media, and company technical information. We aim to provide not only useful information for stock investors but also meaningful visualization that enables investors to effectively interpret storyline events affecting stock prices. Specifically, we utilize an ensemble stacking of diversified machine-learning-based estimators and innovative contextual feature engineering to predict the next day’s stock prices. Experiment results show that our proposed stock forecasting method outperforms a traditional baseline with an average mean absolute percentage error of 0.93. Our findings confirm that leveraging an ensemble scheme of machine learning methods with contextual information improves stock prediction performance. Finally, our study could be further extended to a wide variety of innovative financial applications that seek to incorporate external insight from contextual information such as large-scale online news articles and social media data.


Science ◽  
2018 ◽  
Vol 361 (6405) ◽  
pp. 876-880 ◽  
Author(s):  
Yifan Cheng

Cryo–electron microscopy, or simply cryo-EM, refers mainly to three very different yet closely related techniques: electron crystallography, single-particle cryo-EM, and electron cryotomography. In the past few years, single-particle cryo-EM in particular has triggered a revolution in structural biology and has become a newly dominant discipline. This Review examines the fascinating story of its start and evolution over the past 40-plus years, delves into how and why the recent technological advances have been so groundbreaking, and briefly considers where the technique may be headed in the future.


2020 ◽  
Vol 3 (3) ◽  
Author(s):  
Kashish Bansal ◽  
Kashish Mittal ◽  
Gautam Ahuja ◽  
Ashima Singh ◽  
Sukhpal Singh Gill

2020 ◽  
Vol 24 (5) ◽  
pp. 709-722
Author(s):  
Kieran Woodward ◽  
Eiman Kanjo ◽  
Andreas Oikonomou ◽  
Alan Chamberlain

Abstract In recent years, machine learning has developed rapidly, enabling the development of applications with high levels of recognition accuracy relating to the use of speech and images. However, other types of data to which these models can be applied have not yet been explored as thoroughly. Labelling is an indispensable stage of data pre-processing that can be particularly challenging, especially when applied to single or multi-model real-time sensor data collection approaches. Currently, real-time sensor data labelling is an unwieldy process, with a limited range of tools available and poor performance characteristics, which can lead to the performance of the machine learning models being compromised. In this paper, we introduce new techniques for labelling at the point of collection coupled with a pilot study and a systematic performance comparison of two popular types of deep neural networks running on five custom built devices and a comparative mobile app (68.5–89% accuracy within-device GRU model, 92.8% highest LSTM model accuracy). These devices are designed to enable real-time labelling with various buttons, slide potentiometer and force sensors. This exploratory work illustrates several key features that inform the design of data collection tools that can help researchers select and apply appropriate labelling techniques to their work. We also identify common bottlenecks in each architecture and provide field tested guidelines to assist in building adaptive, high-performance edge solutions.


2021 ◽  
Author(s):  
Priyanka Gupta ◽  
Lokesh Yadav ◽  
Deepak Singh Tomar

The Internet of Things (IoT) connects billions of interconnected devices that can exchange information with each other with minimal user intervention. The goal of IoT to become accessible to anyone, anytime, and anywhere. IoT has engaged in multiple fields, including education, healthcare, businesses, and smart home. Security and privacy issues have been significant obstacles to the widespread adoption of IoT. IoT devices cannot be entirely secure from threats; detecting attacks in real-time is essential for securing devices. In the real-time communication domain and especially in IoT, security and protection are the major issues. The resource-constrained nature of IoT devices makes traditional security techniques difficult. In this paper, the research work carried out in IoT Intrusion Detection System is presented. The Machine learning methods are explored to provide an effective security solution for IoT Intrusion Detection systems. Then discussed the advantages and disadvantages of the selected methodology. Further, the datasets used in IoT security are also discussed. Finally, the examination of the open issues and directions for future trends are also provided.


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