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Beyond Current Boundaries: Integrating Deep Learning and AlphaFold for Enhanced Protein Structure Prediction from Low-Resolution Cryo-EM Maps

arXiv.org Artificial Intelligence

Constructing atomic models from cryo-electron microscopy (cryo-EM) maps is a crucial yet intricate task in structural biology. While advancements in deep learning, such as convolutional neural networks (CNNs) and graph neural networks (GNNs), have spurred the development of sophisticated map-to-model tools like DeepTracer and ModelAngelo, their efficacy notably diminishes with low-resolution maps beyond 4 {\AA}. To address this shortfall, our research introduces DeepTracer-LowResEnhance, an innovative framework that synergizes a deep learning-enhanced map refinement technique with the power of AlphaFold. This methodology is designed to markedly improve the construction of models from low-resolution cryo-EM maps. DeepTracer-LowResEnhance was rigorously tested on a set of 37 protein cryo-EM maps, with resolutions ranging between 2.5 to 8.4 {\AA}, including 22 maps with resolutions lower than 4 {\AA}. The outcomes were compelling, demonstrating that 95.5\% of the low-resolution maps exhibited a significant uptick in the count of total predicted residues. This denotes a pronounced improvement in atomic model building for low-resolution maps. Additionally, a comparative analysis alongside Phenix's auto-sharpening functionality delineates DeepTracer-LowResEnhance's superior capability in rendering more detailed and precise atomic models, thereby pushing the boundaries of current computational structural biology methodologies.


Caring Without Sharing: A Federated Learning Crowdsensing Framework for Diversifying Representation of Cities

arXiv.org Artificial Intelligence

Mobile Crowdsensing has become main stream paradigm for researchers to collect behavioral data from citizens in large scales. This valuable data can be leveraged to create centralized repositories that can be used to train advanced Artificial Intelligent (AI) models for various services that benefit society in all aspects. Although decades of research has explored the viability of Mobile Crowdsensing in terms of incentives and many attempts have been made to reduce the participation barriers, the overshadowing privacy concerns regarding sharing personal data still remain. Recently a new pathway has emerged to enable to shift MCS paradigm towards a more privacy-preserving collaborative learning, namely Federated Learning. In this paper, we posit a first of its kind framework for this emerging paradigm. We demonstrate the functionalities of our framework through a case study of diversifying two vision algorithms through to learn the representation of ordinary sidewalk obstacles as part of enhancing visually impaired navigation.


Artificial Intelligence Advances for De Novo Molecular Structure Modeling in Cryo-EM

arXiv.org Artificial Intelligence

Cryo-electron microscopy (cryo-EM) has become a major experimental technology to determine the structures of large protein complexes and molecular assemblies, as evidenced by the 2017 Nobel Prize. Although cryo-EM has been drastically improved to generate high-resolution three-dimensional (3D) maps that contain detailed structural information about macromolecules, the computational methods for using the data to automatically build structure models are lagging far behind. Traditional cryo-EM model building approach is template-based homology modeling. Manual de novo modeling is very time-consuming when no template model could be found in the database. In recent years, de novo cryo-EM modeling using machine learning (ML) and deep learning (DL) has ranked among the top-performing methods in macromolecular structure modeling. Deep-learning-based de novo cryo-EM modeling is an important application of artificial intelligence, with impressive results and great potential for the next generation of molecular biomedicine. Accordingly, we systematically review the representative ML/DL-based de novo cryo-EM modeling methods. And their significances are discussed from both practical and methodological viewpoints. We also briefly describe the background of cryo-EM data processing workflow. Overall, this review provides an introductory guide to modern research on artificial intelligence (AI) for de novo molecular structure modeling and future directions in this emerging field.


Can Intelligent Hyperparameter Selection Improve Resistance to Adversarial Examples?

arXiv.org Machine Learning

Convolutional Neural Networks and Deep Learning classification systems in general have been shown to be vulnerable to attack by specially crafted data samples that appear to belong to one class but are instead classified as another, commonly known as adversarial examples. A variety of attack strategies have been proposed to craft these samples; however, there is no standard model that is used to compare the success of each type of attack. Furthermore, there is no literature currently available that evaluates how common hyperparameters and optimization strategies may impact a model's ability to resist these samples. This research bridges that lack of awareness and provides a means for the selection of training and model parameters in future research on evasion attacks against convolutional neural networks. The findings of this work indicate that the selection of model hyperparameters does impact the ability of a model to resist attack, although they alone cannot prevent the existence of adversarial examples.


SAP data management startup Winshuttle snapped up by Symphony Technology Group

ZDNet

Winshuttle, a startup focused on SAP-based automaton and data management in the enterprise, has been acquired by private equity firm Symphony Technology Group (STG). STG, which holds roughly $2 billion in assets, says the acquisition will assist the startup in moving from a high-potential technology vendor to a "definitive market leader" in the robotic process automation and data management space. The financial details of the acquisition were not disclosed. Bothell, Washington.-based Winshuttle specializes in solutions for the enterprise related to SAP and data management workflows. The company says that these services can assist in speeding product launches and financial accounting processes, finance, maintenance, data migration projects, and the supply chain.


EagleView Accelerates Machine Learning Development with Acquisition of OmniEarth

#artificialintelligence

Leading provider of aerial imagery and data analytics expands data extraction capabilities for local government, insurance and infrastructure sectors. Bothell, WA (April 26, 2017) – EagleView, the leading provider of aerial imagery and data analytics for government and commercial industries, is proud to announce the acquisition of OmniEarth, developer of machine learning technologies and decision-making tools for the water resource management, energy and insurance markets. With this acquisition, EagleView gains OmniEarth's machine learning capabilities, resulting in higher accuracy and precision of existing automated datasets. OmniEarth's ability to extract data from geospatial imagery will enhance EagleView's property reports and Pictometry imagery classification of land areas such as impervious surfaces or irrigated farmland. It will also better identify roof shape and condition, tree overhang, decks, pools and other notable property features.