On the Robustness of AlphaFold: A COVID-19 Case Study
University of Central Florida（中佛罗里达大学）；University of Texas at San Antonio（德克萨斯大学圣安东尼奥分校）；Air Force Research Laboratory（空军研究实验室）；Argonne National Laboratory（阿贡国家实验室）；SRI International（SRI国际）；Defense Advanced Research Projects Agency（国防高级研究计划局）
Ismail Alkhouri, Sumit Jha, Andre Beckus, George Atia, Alvaro Velasquez, Rickard Ewetz, Arvind Ramanathan, Susmit Jha
备注：
arXiv admin note: text overlap with arXiv:2109.04460
Protein folding neural networks (PFNNs) such as AlphaFold predict remarkably accurate structures of proteins compared to other approaches. However, the robustness of such networks has heretofore not been explored. This is particularly relevant given the broad social implications of such technologies and the fact that biologically small perturbations in the protein sequence do not generally lead to drastic changes in the protein structure. In this paper, we demonstrate that AlphaFold does not exhibit such robustness despite its high accuracy. This raises the challenge of detecting and quantifying the extent to which these predicted protein structures can be trusted. To measure the robustness of the predicted structures, we utilize (i) the root-mean-square deviation (RMSD) and (ii) the Global Distance Test (GDT) similarity measure between the predicted structure of the original sequence and the structure of its adversarially perturbed version. We prove that the problem of minimally perturbing protein sequences to fool protein folding neural networks is NP-complete. Based on the well-established BLOSUM62 sequence alignment scoring matrix, we generate adversarial protein sequences and show that the RMSD between the predicted protein structure and the structure of the original sequence are very large when the adversarial changes are bounded by (i) 20 units in the BLOSUM62 distance, and (ii) five residues (out of hundreds or thousands of residues) in the given protein sequence. In our experimental evaluation, we consider 111 COVID-19 proteins in the Universal Protein resource (UniProt), a central resource for protein data managed by the European Bioinformatics Institute, Swiss Institute of Bioinformatics, and the US Protein Information Resource. These result in an overall GDT similarity test score average of around 34%, demonstrating a substantial drop in the performance of AlphaFold.
AF2-Mutation: Adversarial Sequence Mutations against AlphaFold2 on Protein Tertiary Structure Prediction
Shanghai AI Laboratory（上海人工智能实验室）；Research Institute of Intelligent Complex Systems, Fudan University（复旦大学智能复杂系统研究院）；Institute of Metabolism and integrative biology, Fudan University（复旦大学代谢与整合生物学研究所）；Zelixir Biotech（泽里瑟生物科技公司）；WAVES, Ghent University（根特大学WAVES机构）
Diagnosis of COVID-19 at point of care is vital to the containment of the global pandemic. Point of care ultrasound (POCUS) provides rapid imagery of lungs to detect COVID-19 in patients in a repeatable and cost effective way. Previous work has used public datasets of POCUS videos to train an AI model for diagnosis that obtains high sensitivity. Due to the high stakes application we propose the use of robust and explainable techniques. We demonstrate experimentally that robust models have more stable predictions and offer improved interpretability. A framework of contrastive explanations based…
Georgia State University（佐治亚州立大学）；IBM T. J. Watson Research Center（IBM托马斯·J·沃森研究中心）
The rapid spread of the COVID-19 pandemic has resulted in an unprecedented amount of sequence data of the SARS-CoV-2 genome -- millions of sequences and counting. This amount of data, while being orders of magnitude beyond the capacity of traditional approaches to understanding the diversity, dynamics, and evolution of viruses is nonetheless a rich resource for machine learning (ML) approaches as alternatives for extracting such important information from these data. It is of hence utmost importance to design a framework for testing and benchmarking the robustness of these ML models. This pape…
University of Texas at San Antonio（得克萨斯大学圣安东尼奥分校）；Argonne National Laboratory（阿贡国家实验室）；University of Central Florida（中佛罗里达大学）；Air Force Research Laboratory（空军研究实验室）；SRI International（斯坦福国际研究院）
Deep neural networks such as AlphaFold and RoseTTAFold predict remarkably accurate structures of proteins compared to other algorithmic approaches. It is known that biologically small perturbations in the protein sequence do not lead to drastic changes in the protein structure. In this paper, we demonstrate that RoseTTAFold does not exhibit such a robustness despite its high accuracy, and biologically small perturbations for some input sequences result in radically different predicted protein structures. This raises the challenge of detecting when these predicted protein structures cannot be t…
Multi-Dataset Multi-Task Learning for COVID-19 Prognosis
Unit of Computer Systems \& Bioinformatics, Department of Engineering, Università Campus Bio-Medico di Roma, Rome, Italy College of Computer Science；Software Engineering, Shenzhen University, Shenzhen, China Department of Electrical Engineering, City University of Hong Kong, Hong Kong, China
Hangzhou Dianzi University（杭州电子科技大学）；Communication University of Zhejiang（浙江传媒学院）；University of North Carolina at Chapel Hill（北卡罗来纳大学教堂山分校）；Shanghai Jiao Tong University（上海交通大学）
Coronavirus disease 2019 (COVID-19) is one of the most destructive pandemic after millennium, forcing the world to tackle a health crisis. Automated lung infections classification using chest X-ray (CXR) images could strengthen diagnostic capability when handling COVID-19. However, classifying COVID-19 from pneumonia cases using CXR image is a difficult task because of shared spatial characteristics, high feature variation and contrast diversity between cases. Moreover, massive data collection is impractical for a newly emerged disease, which limited the performance of data thirsty deep learni…
Common compartmental modeling for COVID-19 is based on a priori knowledge and numerous assumptions. Additionally, they do not systematically incorporate asymptomatic cases. Our study aimed at providing a framework for data-driven approaches, by leveraging the strengths of the grey-box system theory or grey-box identification, known for its robustness in problem solving under partial, incomplete, or uncertain data. Empirical data on confirmed cases and deaths, extracted from an open source repository were used to develop the SEAIRD compartment model. Adjustments were made to fit current knowled…
Tsinghua University（清华大学）；Shanghai United Imaging Intelligence Co., Ltd.（上海联影智能科技有限公司）；Ruijin Hospital, Shanghai Jiao Tong University School of Medicine（上海交通大学医学院附属瑞金医院）；Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology（华中科技大学同济医学院附属同济医院）；China-Japan Union Hospital of Jilin University（吉林大学中日联谊医院）；Hangzhou First People’s Hospital, Zhejiang University School of Medicine（浙江大学医学院附属杭州市第一人民医院）；Shanghai Public Health Clinical Center, Fudan University（复旦大学附属上海市公共卫生临床中心）
The coronavirus disease, named COVID-19, has become the largest global public health crisis since it started in early 2020. CT imaging has been used as a complementary tool to assist early screening, especially for the rapid identification of COVID-19 cases from community acquired pneumonia (CAP) cases. The main challenge in early screening is how to model the confusing cases in the COVID-19 and CAP groups, with very similar clinical manifestations and imaging features. To tackle this challenge, we propose an Uncertainty Vertex-weighted Hypergraph Learning (UVHL) method to identify COVID-19 fr…
Under the epidemic of the novel coronavirus disease 2019 (COVID-19), chest X-ray computed tomography imaging is being used for effectively screening COVID-19 patients. The development of computer-aided systems based on deep neural networks (DNNs) has been advanced, to rapidly and accurately detect COVID-19 cases, because the need for expert radiologists, who are limited in number, forms a bottleneck for the screening. However, so far, the vulnerability of DNN-based systems has been poorly evaluated, although DNNs are vulnerable to a single perturbation, called universal adversarial perturbatio…
The issue of COVID-19, increasing with a massive mortality rate. This led to the WHO declaring it as a pandemic. In this situation, it is crucial to perform efficient and fast diagnosis. The reverse transcript polymerase chain reaction (RTPCR) test is conducted to detect the presence of SARS-CoV-2. This test is time-consuming and instead chest CT (or Chest X-ray) can be used for a fast and accurate diagnosis. Automated diagnosis is considered to be important as it reduces human effort and provides accurate and low-cost tests. The contributions of our research are three-fold. First, it is aimed…
JP Morgan Chase（摩根大通）；University of Cambridge（剑桥大学）
Chest Computational Tomography (CT) scans present low cost, speed and objectivity for COVID-19 diagnosis and deep learning methods have shown great promise in assisting the analysis and interpretation of these images. Most hospitals or countries can train their own models using in-house data, however empirical evidence shows that those models perform poorly when tested on new unseen cases, surfacing the need for coordinated global collaboration. Due to privacy regulations, medical data sharing between hospitals and nations is extremely difficult. We propose a GAN-augmented federated learning m…
University of Texas Health Science Center at Houston（德克萨斯大学休斯顿健康科学中心）；McGovern Medical School of The University of Texas Health Science Center at Houston（德克萨斯大学休斯顿健康科学中心麦戈文医学院）
We propose a robust in-time predictor for in-hospital COVID-19 patient's probability of requiring mechanical ventilation. A challenge in the risk prediction for COVID-19 patients lies in the great variability and irregular sampling of patient's vitals and labs observed in the clinical setting. Existing methods have strong limitations in handling time-dependent features' complex dynamics, either oversimplifying temporal data with summary statistics that lose information or over-engineering features that lead to less robust outcomes. We propose a novel in-time risk trajectory predictive model to…
Concordia University（康考迪亚大学）；McGill University（麦吉尔大学）；Tehran University of Medical Sciences（德黑兰医科大学）；University of Montreal（蒙特利尔大学）；University of Toronto（多伦多大学）
The objective of this study is to develop a robust deep learning-based framework to distinguish COVID-19, Community-Acquired Pneumonia (CAP), and Normal cases based on chest CT scans acquired in different imaging centers using various protocols, and radiation doses. We showed that while our proposed model is trained on a relatively small dataset acquired from only one imaging center using a specific scanning protocol, the model performs well on heterogeneous test sets obtained by multiple scanners using different technical parameters. We also showed that the model can be updated via an unsuper…
Faculty of Computers and Artificial Intelligence, Cairo University（开罗大学计算机与人工智能学院）；MISR Higher Institute for Engineering and Technology（米斯尔高等工程技术学院）；Scientific Research Group in Egypt (SRGE)（埃及科学研究团队）
The COVID-19 coronavirus is one of the devastating viruses according to the world health organization. This novel virus leads to pneumonia, which is an infection that inflames the lungs' air sacs of a human. One of the methods to detect those inflames is by using x-rays for the chest. In this paper, a pneumonia chest x-ray detection based on generative adversarial networks (GAN) with a fine-tuned deep transfer learning for a limited dataset will be presented. The use of GAN positively affects the proposed model robustness and made it immune to the overfitting problem and helps in generating mo…
PepHarmony: A Multi-View Contrastive Learning Framework for Integrated Sequence and Structure-Based Peptide Encoding
Jilin University（吉林大学）；Syneron Technology；Beijing Life Science Academy（北京生命科学学院）；the University of Hong Kong（香港大学）；King Abdullah University of Science and Technology（阿卜杜拉国王科技大学）
Improving deep neural network generalization and robustness to background bias via layer-wise relevance propagation optimization
Alma Mater Studiorum - University of Bologna（博洛尼亚大学）；Center for Biomolecular Nanotechnologies, Istituto Italiano di Tecnologia（意大利技术研究院生物分子纳米技术中心）；School of Medical Sciences, University of Campinas (UNICAMP)（坎皮纳斯大学（UNICAMP）医学院）；Istituto Italiano di Tecnologia（意大利技术研究院）
