scholarly journals Deep Descriptive Clustering

2021 ◽  
Author(s):  
Hongjing Zhang ◽  
Ian Davidson
Keyword(s):  
Machine Learning ◽  
Linear Programming ◽  
Empirical Distribution ◽  
Representation Learning ◽  
Complex Data ◽  
High Quality ◽  
Symbolic Data ◽  
Public Data ◽  
Cluster Level ◽  
Modern Machine

Recent work on explainable clustering allows describing clusters when the features are interpretable. However, much modern machine learning focuses on complex data such as images, text, and graphs where deep learning is used but the raw features of data are not interpretable. This paper explores a novel setting for performing clustering on complex data while simultaneously generating explanations using interpretable tags. We propose deep descriptive clustering that performs sub-symbolic representation learning on complex data while generating explanations based on symbolic data. We form good clusters by maximizing the mutual information between empirical distribution on the inputs and the induced clustering labels for clustering objectives. We generate explanations by solving an integer linear programming that generates concise and orthogonal descriptions for each cluster. Finally, we allow the explanation to inform better clustering by proposing a novel pairwise loss with self-generated constraints to maximize the clustering and explanation module's consistency. Experimental results on public data demonstrate that our model outperforms competitive baselines in clustering performance while offering high-quality cluster-level explanations.

scholarly journals MACHINE LEARNING FOR SEA ICE MONITORING FROM SATELLITES

2019 ◽  
Vol XLII-2/W16 ◽  
pp. 83-89
Author(s):  
C. O. Dumitru ◽  
V. Andrei ◽  
G. Schwarz ◽  
M. Datcu
Keyword(s):  
Machine Learning ◽  
Sea Ice ◽  
Weather Conditions ◽  
Representation Learning ◽  
Image Understanding ◽  
Machine Learning Techniques ◽  
Polar Regions ◽  
Learning Approaches ◽  
Automated Processing ◽  
Modern Machine

<p><strong>Abstract.</strong> Today, radar imaging from space allows continuous and wide-area sea ice monitoring under nearly all weather conditions. To this end, we applied modern machine learning techniques to produce ice-describing semantic maps of the polar regions of the Earth. Time series of these maps can then be exploited for local and regional change maps of selected areas. What we expect, however, are fully-automated unsupervised routine classifications of sea ice regions that are needed for the rapid and reliable monitoring of shipping routes, drifting and disintegrating icebergs, snowfall and melting on ice, and other dynamic climate change indicators. Therefore, we designed and implemented an automated processing chain that analyses and interprets the specific ice-related content of high-resolution synthetic aperture radar (SAR) images. We trained this system with selected images covering various use cases allowing us to interpret these images with modern machine learning approaches. In the following, we describe a system comprising representation learning, variational inference, and auto-encoders. Test runs have already demonstrated its usefulness and stability that can pave the way towards future artificial intelligence systems extending, for instance, the current capabilities of traditional image analysis by including content-related image understanding.</p>

Big Data to Knowledge: Application of Machine Learning to Predictive Modeling of Therapeutic Response in Cancer.

2020 ◽  
Vol 21 ◽  
Author(s):  
Sukanya Panja ◽  
Sarra Rahem ◽  
Cassandra J. Chu ◽  
Antonina Mitrofanova
Keyword(s):  
Machine Learning ◽  
Missing Values ◽  
Therapeutic Response ◽  
Patient Data ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Complex Data ◽  
Human Machine Interaction ◽  
Data Repositories ◽  
Response Modeling

Background: In recent years, the availability of high throughput technologies, establishment of large molecular patient data repositories, and advancement in computing power and storage have allowed elucidation of complex mechanisms implicated in therapeutic response in cancer patients. The breadth and depth of such data, alongside experimental noise and missing values, requires a sophisticated human-machine interaction that would allow effective learning from complex data and accurate forecasting of future outcomes, ideally embedded in the core of machine learning design. Objective: In this review, we will discuss machine learning techniques utilized for modeling of treatment response in cancer, including Random Forests, support vector machines, neural networks, and linear and logistic regression. We will overview their mathematical foundations and discuss their limitations and alternative approaches all in light of their application to therapeutic response modeling in cancer. Conclusion: We hypothesize that the increase in the number of patient profiles and potential temporal monitoring of patient data will define even more complex techniques, such as deep learning and causal analysis, as central players in therapeutic response modeling.

Digging for the truth: the case for active annotation in evaluating the credibility of online medical information (Preprint)

2020 ◽  
Author(s):  
Mikołaj Morzy ◽  
Bartłomiej Balcerzak ◽  
Adam Wierzbicki ◽  
Adam Wierzbicki
Keyword(s):  
Machine Learning ◽  
Medical Information ◽  
Representation Learning ◽  
Training Dataset ◽  
Highly Qualified ◽  
Human In The Loop ◽  
Annotation Process ◽  
Comprehensive Framework ◽  
Online Sources ◽  
The Web

BACKGROUND With the rapidly accelerating spread of dissemination of false medical information on the Web, the task of establishing the credibility of online sources of medical information becomes a pressing necessity. The sheer number of websites offering questionable medical information presented as reliable and actionable suggestions with possibly harmful effects poses an additional requirement for potential solutions, as they have to scale to the size of the problem. Machine learning is one such solution which, when properly deployed, can be an effective tool in fighting medical disinformation on the Web. OBJECTIVE We present a comprehensive framework for designing and curating of machine learning training datasets for online medical information credibility assessment. We show how the annotation process should be constructed and what pitfalls should be avoided. Our main objective is to provide researchers from medical and computer science communities with guidelines on how to construct datasets for machine learning models for various areas of medical information wars. METHODS The key component of our approach is the active annotation process. We begin by outlining the annotation protocol for the curation of high-quality training dataset, which then can be augmented and rapidly extended by employing the human-in-the-loop paradigm to machine learning training. To circumvent the cold start problem of insufficient gold standard annotations, we propose a pre-processing pipeline consisting of representation learning, clustering, and re-ranking of sentences for the acceleration of the training process and the optimization of human resources involved in the annotation. RESULTS We collect over 10 000 annotations of sentences related to selected subjects (psychiatry, cholesterol, autism, antibiotics, vaccines, steroids, birth methods, food allergy testing) for less than $7 000 employing 9 highly qualified annotators (certified medical professionals) and we release this dataset to the general public. We develop an active annotation framework for more efficient annotation of non-credible medical statements. The results of the qualitative analysis support our claims of the efficacy of the presented method. CONCLUSIONS A set of very diverse incentives is driving the widespread dissemination of medical disinformation on the Web. An effective strategy of countering this spread is to use machine learning for automatically establishing the credibility of online medical information. This, however, requires a thoughtful design of the training pipeline. In this paper we present a comprehensive framework of active annotation. In addition, we publish a large curated dataset of medical statements labelled as credible, non-credible, or neutral.

scholarly journals Deep Transfer Learning Based Intrusion Detection System for Electric Vehicular Networks

Sensors ◽  
2021 ◽  
Vol 21 (14) ◽  
pp. 4736
Author(s):  
Sk. Tanzir Mehedi ◽  
Adnan Anwar ◽  
Ziaur Rahman ◽  
Kawsar Ahmed
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Intrusion Detection ◽  
Real Time ◽  
Transfer Learning ◽  
Security Requirements ◽  
Detection Accuracy ◽  
Area Network ◽  
Complex Data ◽  
Network Intrusion

The Controller Area Network (CAN) bus works as an important protocol in the real-time In-Vehicle Network (IVN) systems for its simple, suitable, and robust architecture. The risk of IVN devices has still been insecure and vulnerable due to the complex data-intensive architectures which greatly increase the accessibility to unauthorized networks and the possibility of various types of cyberattacks. Therefore, the detection of cyberattacks in IVN devices has become a growing interest. With the rapid development of IVNs and evolving threat types, the traditional machine learning-based IDS has to update to cope with the security requirements of the current environment. Nowadays, the progression of deep learning, deep transfer learning, and its impactful outcome in several areas has guided as an effective solution for network intrusion detection. This manuscript proposes a deep transfer learning-based IDS model for IVN along with improved performance in comparison to several other existing models. The unique contributions include effective attribute selection which is best suited to identify malicious CAN messages and accurately detect the normal and abnormal activities, designing a deep transfer learning-based LeNet model, and evaluating considering real-world data. To this end, an extensive experimental performance evaluation has been conducted. The architecture along with empirical analyses shows that the proposed IDS greatly improves the detection accuracy over the mainstream machine learning, deep learning, and benchmark deep transfer learning models and has demonstrated better performance for real-time IVN security.

scholarly journals Graph Learning for Combinatorial Optimization: A Survey of State-of-the-Art

2021 ◽  
Author(s):  
Yun Peng ◽  
Byron Choi ◽  
Jianliang Xu
Keyword(s):  
Machine Learning ◽  
Combinatorial Optimization ◽  
Graph Embedding ◽  
Partial Solution ◽  
Complex Data ◽  
Learning Methods ◽  
Graph Learning ◽  
Second Stage ◽  
End To End ◽  
Embedding Methods

AbstractGraphs have been widely used to represent complex data in many applications, such as e-commerce, social networks, and bioinformatics. Efficient and effective analysis of graph data is important for graph-based applications. However, most graph analysis tasks are combinatorial optimization (CO) problems, which are NP-hard. Recent studies have focused a lot on the potential of using machine learning (ML) to solve graph-based CO problems. Most recent methods follow the two-stage framework. The first stage is graph representation learning, which embeds the graphs into low-dimension vectors. The second stage uses machine learning to solve the CO problems using the embeddings of the graphs learned in the first stage. The works for the first stage can be classified into two categories, graph embedding methods and end-to-end learning methods. For graph embedding methods, the learning of the the embeddings of the graphs has its own objective, which may not rely on the CO problems to be solved. The CO problems are solved by independent downstream tasks. For end-to-end learning methods, the learning of the embeddings of the graphs does not have its own objective and is an intermediate step of the learning procedure of solving the CO problems. The works for the second stage can also be classified into two categories, non-autoregressive methods and autoregressive methods. Non-autoregressive methods predict a solution for a CO problem in one shot. A non-autoregressive method predicts a matrix that denotes the probability of each node/edge being a part of a solution of the CO problem. The solution can be computed from the matrix using search heuristics such as beam search. Autoregressive methods iteratively extend a partial solution step by step. At each step, an autoregressive method predicts a node/edge conditioned to current partial solution, which is used to its extension. In this survey, we provide a thorough overview of recent studies of the graph learning-based CO methods. The survey ends with several remarks on future research directions.

scholarly journals Fabrication of High-Quality Thin Solid-State Electrolyte Films Assisted by Machine Learning

2021 ◽  
pp. 1639-1648
Author(s):  
Yu-Ting Chen ◽  
Marc Duquesnoy ◽  
Darren H. S. Tan ◽  
Jean-Marie Doux ◽  
Hedi Yang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Solid State ◽  
High Quality ◽  
Solid State Electrolyte

scholarly journals Prediction of Sugar Content in Port Wine Vintage Grapes Using Machine Learning and Hyperspectral Imaging

Processes ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 1241
Author(s):  
Véronique Gomes ◽  
Marco S. Reis ◽  
Francisco Rovira-Más ◽  
Ana Mendes-Ferreira ◽  
Pedro Melo-Pinto
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Hyperspectral Imaging ◽  
Sugar Content ◽  
Hyperspectral Data ◽  
Machine Learning Algorithms ◽  
Port Wine ◽  
Monitoring And Control ◽  
High Quality ◽  
Harvesting Stage

The high quality of Port wine is the result of a sequence of winemaking operations, such as harvesting, maceration, fermentation, extraction and aging. These stages require proper monitoring and control, in order to consistently achieve the desired wine properties. The present work focuses on the harvesting stage, where the sugar content of grapes plays a key role as one of the critical maturity parameters. Our approach makes use of hyperspectral imaging technology to rapidly extract information from wine grape berries; the collected spectra are fed to machine learning algorithms that produce estimates of the sugar level. A consistent predictive capability is important for establishing the harvest date, as well as to select the best grapes to produce specific high-quality wines. We compared four different machine learning methods (including deep learning), assessing their generalization capacity for different vintages and varieties not included in the training process. Ridge regression, partial least squares, neural networks and convolutional neural networks were the methods considered to conduct this comparison. The results show that the estimated models can successfully predict the sugar content from hyperspectral data, with the convolutional neural network outperforming the other methods.

57 Precision neoantigen discovery using novel algorithms and expanded HLA-ligandome datasets

2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A62-A62
Author(s):  
Dattatreya Mellacheruvu ◽  
Rachel Pyke ◽  
Charles Abbott ◽  
Nick Phillips ◽  
Sejal Desai ◽  
...  
Keyword(s):  
Machine Learning ◽  
Cell Lines ◽  
Antigen Processing ◽  
Large Scale ◽  
Prediction Models ◽  
K562 Cells ◽  
Machine Learning Algorithms ◽  
Training Data ◽  
High Quality ◽  
Tissue Samples

BackgroundAccurately identified neoantigens can be effective therapeutic agents in both adjuvant and neoadjuvant settings. A key challenge for neoantigen discovery has been the availability of accurate prediction models for MHC peptide presentation. We have shown previously that our proprietary model based on (i) large-scale, in-house mono-allelic data, (ii) custom features that model antigen processing, and (iii) advanced machine learning algorithms has strong performance. We have extended upon our work by systematically integrating large quantities of high-quality, publicly available data, implementing new modelling algorithms, and rigorously testing our models. These extensions lead to substantial improvements in performance and generalizability. Our algorithm, named Systematic HLA Epitope Ranking Pan Algorithm (SHERPA™), is integrated into the ImmunoID NeXT Platform®, our immuno-genomics and transcriptomics platform specifically designed to enable the development of immunotherapies.MethodsIn-house immunopeptidomic data was generated using stably transfected HLA-null K562 cells lines that express a single HLA allele of interest, followed by immunoprecipitation using W6/32 antibody and LC-MS/MS. Public immunopeptidomics data was downloaded from repositories such as MassIVE and processed uniformly using in-house pipelines to generate peptide lists filtered at 1% false discovery rate. Other metrics (features) were either extracted from source data or generated internally by re-processing samples utilizing the ImmunoID NeXT Platform.ResultsWe have generated large-scale and high-quality immunopeptidomics data by using approximately 60 mono-allelic cell lines that unambiguously assign peptides to their presenting alleles to create our primary models. Briefly, our primary ‘binding’ algorithm models MHC-peptide binding using peptide and binding pockets while our primary ‘presentation’ model uses additional features to model antigen processing and presentation. Both primary models have significantly higher precision across all recall values in multiple test data sets, including mono-allelic cell lines and multi-allelic tissue samples. To further improve the performance of our model, we expanded the diversity of our training set using high-quality, publicly available mono-allelic immunopeptidomics data. Furthermore, multi-allelic data was integrated by resolving peptide-to-allele mappings using our primary models. We then trained a new model using the expanded training data and a new composite machine learning architecture. The resulting secondary model further improves performance and generalizability across several tissue samples.ConclusionsImproving technologies for neoantigen discovery is critical for many therapeutic applications, including personalized neoantigen vaccines, and neoantigen-based biomarkers for immunotherapies. Our new and improved algorithm (SHERPA) has significantly higher performance compared to a state-of-the-art public algorithm and furthers this objective.

scholarly journals An Exploratory Study of COVID-19 Information on Twitter in the Greater Region

2021 ◽  
Vol 5 (1) ◽  
pp. 5
Author(s):  
Ninghan Chen ◽  
Zhiqiang Zhong ◽  
Jun Pang
Keyword(s):  
Machine Learning ◽  
Social Networks ◽  
Online Social Networks ◽  
Exploratory Study ◽  
Representation Learning ◽  
Data Driven ◽  
Learning Methods ◽  
Twitter Users ◽  
Over Time

The outbreak of the COVID-19 led to a burst of information in major online social networks (OSNs). Facing this constantly changing situation, OSNs have become an essential platform for people expressing opinions and seeking up-to-the-minute information. Thus, discussions on OSNs may become a reflection of reality. This paper aims to figure out how Twitter users in the Greater Region (GR) and related countries react differently over time through conducting a data-driven exploratory study of COVID-19 information using machine learning and representation learning methods. We find that tweet volume and COVID-19 cases in GR and related countries are correlated, but this correlation only exists in a particular period of the pandemic. Moreover, we plot the changing of topics in each country and region from 22 January 2020 to 5 June 2020, figuring out the main differences between GR and related countries.

scholarly journals Evolutionary Machine Learning for Multi-Objective Class Solutions in Medical Deformable Image Registration

Algorithms ◽  
2019 ◽  
Vol 12 (5) ◽  
pp. 99 ◽  
Author(s):  
Kleopatra Pirpinia ◽  
Peter A. N. Bosman ◽  
Jan-Jakob Sonke ◽  
Marcel van Herk ◽  
Tanja Alderliesten
Keyword(s):  
Machine Learning ◽  
Image Registration ◽  
State Of The Art ◽  
Deformable Image Registration ◽  
Optimization Approach ◽  
High Quality ◽  
Trade Off ◽  
Multi Objective ◽  
Current State ◽  
Image Artefacts

Current state-of-the-art medical deformable image registration (DIR) methods optimize a weighted sum of key objectives of interest. Having a pre-determined weight combination that leads to high-quality results for any instance of a specific DIR problem (i.e., a class solution) would facilitate clinical application of DIR. However, such a combination can vary widely for each instance and is currently often manually determined. A multi-objective optimization approach for DIR removes the need for manual tuning, providing a set of high-quality trade-off solutions. Here, we investigate machine learning for a multi-objective class solution, i.e., not a single weight combination, but a set thereof, that, when used on any instance of a specific DIR problem, approximates such a set of trade-off solutions. To this end, we employed a multi-objective evolutionary algorithm to learn sets of weight combinations for three breast DIR problems of increasing difficulty: 10 prone-prone cases, 4 prone-supine cases with limited deformations and 6 prone-supine cases with larger deformations and image artefacts. Clinically-acceptable results were obtained for the first two problems. Therefore, for DIR problems with limited deformations, a multi-objective class solution can be machine learned and used to compute straightforwardly multiple high-quality DIR outcomes, potentially leading to more efficient use of DIR in clinical practice.

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