Comprehensive Fitness Landscape of a Multi-Geometry Protein Capsid Informs Machine Learning Models of Assembly

Virus-like particles (VLPs) are non-infections viral-derived nanomaterials poised for biotechnological applications due to their well-defined, modular self-assembling architecture. Although progress has been made in understanding the complex effects that mutations may have on VLPs, nuanced understanding of the influence particle mutability has on quaternary structure has yet to be achieved. Here, we generate and compare the apparent fitness landscapes of two capsid geometries (T=3 and T=1 icosahedral) of the bacteriophage MS2 VLP. We find significant shifts in mutability at the symmetry interfaces of the T=1 capsid when compared to the wildtype T=3 assembly. Furthermore, we use the generated landscapes to benchmark the performance of in silico mutational scanning tools in capturing the effect of missense mutation on complex particle assembly. Finding that predicted stability effects correlated relatively poorly with assembly phenotype, we used a combination of de novo features in tandem with in silico results to train machine learning algorithms for the classification of variant effects on assembly. Our findings not only reveal ways that assembly geometry affects the mutable landscape of a self-assembled particle, but also establish a template for the generation of predictive mutational models of self-assembled capsids using minimal empirical training data.

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Optimization of Diabetes Training DATA using Machine Learning Algorithms

International Journal of Computer Sciences and Engineering ◽

10.26438/ijcse/v6i2.283286 ◽

2018 ◽

Vol 6 (2) ◽

pp. 283-286

Author(s):

M. Samba Siva Rao ◽

◽

M.Yaswanth . ◽

K. Raghavendra Swamy ◽

◽

...

Keyword(s):

Machine Learning ◽

Learning Algorithms ◽

Machine Learning Algorithms ◽

Training Data

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

Journal for ImmunoTherapy of Cancer ◽

10.1136/jitc-2020-sitc2020.0057 ◽

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.

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Drill-Core Mineral Abundance Estimation Using Hyperspectral and High-Resolution Mineralogical Data

Remote Sensing ◽

10.3390/rs12071218 ◽

2020 ◽

Vol 12 (7) ◽

pp. 1218

Author(s):

Laura Tuşa ◽

Mahdi Khodadadzadeh ◽

Cecilia Contreras ◽

Kasra Rafiezadeh Shahi ◽

Margret Fuchs ◽

...

Keyword(s):

Machine Learning ◽

High Resolution ◽

Ore Deposits ◽

Machine Learning Algorithms ◽

Training Data ◽

Support Vector ◽

Drill Core ◽

Data Types ◽

Mineralogical Characterization ◽

Core Samples

Due to the extensive drilling performed every year in exploration campaigns for the discovery and evaluation of ore deposits, drill-core mapping is becoming an essential step. While valuable mineralogical information is extracted during core logging by on-site geologists, the process is time consuming and dependent on the observer and individual background. Hyperspectral short-wave infrared (SWIR) data is used in the mining industry as a tool to complement traditional logging techniques and to provide a rapid and non-invasive analytical method for mineralogical characterization. Additionally, Scanning Electron Microscopy-based image analyses using a Mineral Liberation Analyser (SEM-MLA) provide exhaustive high-resolution mineralogical maps, but can only be performed on small areas of the drill-cores. We propose to use machine learning algorithms to combine the two data types and upscale the quantitative SEM-MLA mineralogical data to drill-core scale. This way, quasi-quantitative maps over entire drill-core samples are obtained. Our upscaling approach increases result transparency and reproducibility by employing physical-based data acquisition (hyperspectral imaging) combined with mathematical models (machine learning). The procedure is tested on 5 drill-core samples with varying training data using random forests, support vector machines and neural network regression models. The obtained mineral abundance maps are further used for the extraction of mineralogical parameters such as mineral association.

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Automatic Grading of Stroke Symptoms for Rapid Assessment Using Optimized Machine Learning and 4-Limb Kinematics: Clinical Validation Study (Preprint)

10.2196/preprints.20641 ◽

2020 ◽

Author(s):

Eunjeong Park ◽

Kijeong Lee ◽

Taehwa Han ◽

Hyo Suk Nam

Keyword(s):

Machine Learning ◽

Medical Staff ◽

Machine Learning Algorithms ◽

Training Data ◽

Support Vector ◽

Grading System ◽

Operating Characteristics ◽

Stroke Patients ◽

Motor Weakness ◽

Automatic Grading

BACKGROUND Subtle abnormal motor signs are indications of serious neurological diseases. Although neurological deficits require fast initiation of treatment in a restricted time, it is difficult for nonspecialists to detect and objectively assess the symptoms. In the clinical environment, diagnoses and decisions are based on clinical grading methods, including the National Institutes of Health Stroke Scale (NIHSS) score or the Medical Research Council (MRC) score, which have been used to measure motor weakness. Objective grading in various environments is necessitated for consistent agreement among patients, caregivers, paramedics, and medical staff to facilitate rapid diagnoses and dispatches to appropriate medical centers. OBJECTIVE In this study, we aimed to develop an autonomous grading system for stroke patients. We investigated the feasibility of our new system to assess motor weakness and grade NIHSS and MRC scores of 4 limbs, similar to the clinical examinations performed by medical staff. METHODS We implemented an automatic grading system composed of a measuring unit with wearable sensors and a grading unit with optimized machine learning. Inertial sensors were attached to measure subtle weaknesses caused by paralysis of upper and lower limbs. We collected 60 instances of data with kinematic features of motor disorders from neurological examination and demographic information of stroke patients with NIHSS 0 or 1 and MRC 7, 8, or 9 grades in a stroke unit. Training data with 240 instances were generated using a synthetic minority oversampling technique to complement the imbalanced number of data between classes and low number of training data. We trained 2 representative machine learning algorithms, an ensemble and a support vector machine (SVM), to implement auto-NIHSS and auto-MRC grading. The optimized algorithms performed a 5-fold cross-validation and were searched by Bayes optimization in 30 trials. The trained model was tested with the 60 original hold-out instances for performance evaluation in accuracy, sensitivity, specificity, and area under the receiver operating characteristics curve (AUC). RESULTS The proposed system can grade NIHSS scores with an accuracy of 83.3% and an AUC of 0.912 using an optimized ensemble algorithm, and it can grade with an accuracy of 80.0% and an AUC of 0.860 using an optimized SVM algorithm. The auto-MRC grading achieved an accuracy of 76.7% and a mean AUC of 0.870 in SVM classification and an accuracy of 78.3% and a mean AUC of 0.877 in ensemble classification. CONCLUSIONS The automatic grading system quantifies proximal weakness in real time and assesses symptoms through automatic grading. The pilot outcomes demonstrated the feasibility of remote monitoring of motor weakness caused by stroke. The system can facilitate consistent grading with instant assessment and expedite dispatches to appropriate hospitals and treatment initiation by sharing auto-MRC and auto-NIHSS scores between prehospital and hospital responses as an objective observation.

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X-MOL: large-scale pre-training for molecular understanding and diverse molecular analysis

10.1101/2020.12.23.424259 ◽

2020 ◽

Author(s):

Dongyu Xue ◽

Han Zhang ◽

Dongling Xiao ◽

Yukang Gong ◽

Guohui Chuai ◽

...

Keyword(s):

Molecular Analysis ◽

In Silico ◽

Large Scale ◽

De Novo ◽

Representation Learning ◽

Training Data ◽

Fine Tuning ◽

Model Interpretation ◽

Unlabelled Data ◽

Super Computing

AbstractIn silico modelling and analysis of small molecules substantially accelerates the process of drug development. Representing and understanding molecules is the fundamental step for various in silico molecular analysis tasks. Traditionally, these molecular analysis tasks have been investigated individually and separately. In this study, we presented X-MOL, which applies large-scale pre-training technology on 1.1 billion molecules for molecular understanding and representation, and then, carefully designed fine-tuning was performed to accommodate diverse downstream molecular analysis tasks, including molecular property prediction, chemical reaction analysis, drug-drug interaction prediction, de novo generation of molecules and molecule optimization. As a result, X-MOL was proven to achieve state-of-the-art results on all these molecular analysis tasks with good model interpretation ability. Collectively, taking advantage of super large-scale pre-training data and super-computing power, our study practically demonstrated the utility of the idea of “mass makes miracles” in molecular representation learning and downstream in silico molecular analysis, indicating the great potential of using large-scale unlabelled data with carefully designed pre-training and fine-tuning strategies to unify existing molecular analysis tasks and substantially enhance the performance of each task.

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Android Malware Detection using Machine Learning

International Journal of Recent Technology and Engineering - 2 ◽

10.35940/ijrte.b1011.0982s1219 ◽

2020 ◽

Vol 8 (2S12) ◽

pp. 65-70

Keyword(s):

Machine Learning ◽

Nearest Neighbor ◽

Machine Learning Algorithms ◽

Training Data ◽

Machine Learning Techniques ◽

Support Vector ◽

K Nearest Neighbor ◽

User Interest ◽

Android Malware ◽

Android Malware Detection

Machine Learning is empowering many aspects of day-to-day lives from filtering the content on social networks to suggestions of products that we may be looking for. This technology focuses on taking objects as image input to find new observations or show items based on user interest. The major discussion here is the Machine Learning techniques where we use supervised learning where the computer learns by the input data/training data and predict result based on experience. We also discuss the machine learning algorithms: Naïve Bayes Classifier, K-Nearest Neighbor, Random Forest, Decision Tress, Boosted Trees, Support Vector Machine, and use these classifiers on a dataset Malgenome and Drebin which are the Android Malware Dataset. Android is an operating system that is gaining popularity these days and with a rise in demand of these devices the rise in Android Malware. The traditional techniques methods which were used to detect malware was unable to detect unknown applications. We have run this dataset on different machine learning classifiers and have recorded the results. The experiment result provides a comparative analysis that is based on performance, accuracy, and cost.

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PSIX-15 Assessment of machine learning algorithms for prediction of Aleutian disease in American mink

Journal of Animal Science ◽

10.1093/jas/skab235.484 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 264-265

Author(s):

Duy Ngoc Do ◽

Guoyu Hu ◽

Younes Miar

Keyword(s):

Machine Learning ◽

Random Forest ◽

Linear Models ◽

American Mink ◽

Learning Algorithms ◽

Machine Learning Algorithms ◽

Training Data ◽

Enzyme Linked Immunosorbent Assay ◽

Linear Discriminant ◽

Machine Learning Classification

Abstract American mink (Neovison vison) is the major source of fur for the fur industries worldwide and Aleutian disease (AD) is causing severe financial losses to the mink industry. Different methods have been used to diagnose the AD in mink, but the combination of several methods can be the most appropriate approach for the selection of AD resilient mink. Iodine agglutination test (IAT) and counterimmunoelectrophoresis (CIEP) methods are commonly employed in test-and-remove strategy; meanwhile, enzyme-linked immunosorbent assay (ELISA) and packed-cell volume (PCV) methods are complementary. However, using multiple methods are expensive; and therefore, hindering the corrected use of AD tests in selection. This research presented the assessments of the AD classification based on machine learning algorithms. The Aleutian disease was tested on 1,830 individuals using these tests in an AD positive mink farm (Canadian Centre for Fur Animal Research, NS, Canada). The accuracy of classification for CIEP was evaluated based on the sex information, and IAT, ELISA and PCV test results implemented in seven machine learning classification algorithms (Random Forest, Artificial Neural Networks, C50Tree, Naive Bayes, Generalized Linear Models, Boost, and Linear Discriminant Analysis) using the Caret package in R. The accuracy of prediction varied among the methods. Overall, the Random Forest was the best-performing algorithm for the current dataset with an accuracy of 0.89 in the training data and 0.94 in the testing data. Our work demonstrated the utility and relative ease of using machine learning algorithms to assess the CIEP information, and consequently reducing the cost of AD tests. However, further works require the inclusion of production and reproduction information in the models and extension of phenotypic collection to increase the accuracy of current methods.

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PREDICTION AND ANALYSIS OF GEOMECHANICAL PROPERTIES OF JIMUSAER SHALE USING A MACHINE LEARNING APPROACH

10.30632/spwla-2021-0089 ◽

2021 ◽

Author(s):

Lianteng Song ◽

◽

Zhonghua Liu ◽

Chaoliu Li ◽

Congqian Ning ◽

...

Keyword(s):

Machine Learning ◽

Cross Validation ◽

Gamma Ray ◽

Short Term Memory ◽

Machine Learning Algorithms ◽

Training Data ◽

Sequential Data ◽

Log Data ◽

Geomechanical Properties ◽

Single Well

Geomechanical properties are essential for safe drilling, successful completion, and exploration of both conven-tional and unconventional reservoirs, e.g. deep shale gas and shale oil. Typically, these properties could be calcu-lated from sonic logs. However, in shale reservoirs, it is time-consuming and challenging to obtain reliable log-ging data due to borehole complexity and lacking of in-formation, which often results in log deficiency and high recovery cost of incomplete datasets. In this work, we propose the bidirectional long short-term memory (BiL-STM) which is a supervised neural network algorithm that has been widely used in sequential data-based pre-diction to estimate geomechanical parameters. The pre-diction from log data can be conducted from two differ-ent aspects. 1) Single-Well prediction, the log data from a single well is divided into training data and testing data for cross validation; 2) Cross-Well prediction, a group of wells from the same geographical region are divided into training set and testing set for cross validation, as well. The logs used in this work were collected from 11 wells from Jimusaer Shale, which includes gamma ray, bulk density, resistivity, and etc. We employed 5 vari-ous machine learning algorithms for comparison, among which BiLSTM showed the best performance with an R-squared of more than 90% and an RMSE of less than 10. The predicted results can be directly used to calcu-late geomechanical properties, of which accuracy is also improved in contrast to conventional methods.

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A Comparison of Machine Learning Algorithms for the Segmentation and Classification of Snow Micro Penetrometer Profiles on Arctic Sea Ice

10.5194/egusphere-egu21-15637 ◽

2021 ◽

Author(s):

Julia Kaltenborn ◽

Viviane Clay ◽

Amy R. Macfarlane ◽

Joshua Michael Lloyd King ◽

Martin Schneebeli

Keyword(s):

Machine Learning ◽

Sea Ice ◽

Arctic Sea Ice ◽

Machine Learning Algorithms ◽

Training Data ◽

Support Vector ◽

Snow Layer ◽

Arctic Sea ◽

Execution Speed

Snow-layer classification is an essential diagnostic task for a wide variety of cryospheric science and climate research applications. Traditionally, these measurements are made in snow pits, requiring trained operators and a substantial time commitment. The SnowMicroPen (SMP), a portable high-resolution snow penetrometer, has been demonstrated as a capable tool for rapid snow grain classification and layer type segmentation through statistical inversion of its mechanical signal. The manual classification of the SMP profiles requires time and training and becomes infeasible for large datasets.Here, we introduce a novel set of SMP measurements collected during the MOSAiC expedition and apply Machine Learning (ML) algorithms to automatically classify and segment SMP profiles of snow on Arctic sea ice. To this end, different supervised and unsupervised ML methods, including Random Forests, Support Vector Machines, Artificial Neural Networks, and k-means Clustering, are compared. A subsequent segmentation of the classified data results in distinct layers and snow grain markers for the SMP profiles. The models are trained with the dataset by King et al. (2020) and the MOSAiC SMP dataset. The MOSAiC dataset is a unique and extensive dataset characterizing seasonal and spatial variation of snow on the central Arctic sea-ice.We will test and compare the different algorithms and evaluate the algorithms&#8217; effectiveness based on the need for initial dataset labeling, execution speed, and ease of implementation. In particular, we will compare supervised to unsupervised methods, which are distinguished by their need for labeled training data.The implementation of different ML algorithms for SMP profile classification could provide a fast and automatic grain type classification and snow layer segmentation. Based on the gained knowledge from the algorithms&#8217; comparison, a tool can be built to provide scientists from different fields with an immediate SMP profile classification and segmentation.&#160;&#160;King, J., Howell, S., Brady, M., Toose, P., Derksen, C., Haas, C., & Beckers, J. (2020). Local-scale variability of snow density on Arctic sea ice. The Cryosphere, 14(12), 4323-4339, https://doi.org/10.5194/tc-14-4323-2020.

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Convolutional Neural Network

10.4018/978-1-6684-2408-7.ch077 ◽

2022 ◽

pp. 1559-1575

Author(s):

Mário Pereira Véstias

Keyword(s):

Neural Network ◽

Machine Learning ◽

Neural Networks ◽

Artificial Neural Networks ◽

Deep Learning ◽

Convolutional Neural Network ◽

Machine Learning Algorithms ◽

Training Data ◽

Machine Learning Model ◽

Artificial Neural

Machine learning is the study of algorithms and models for computing systems to do tasks based on pattern identification and inference. When it is difficult or infeasible to develop an algorithm to do a particular task, machine learning algorithms can provide an output based on previous training data. A well-known machine learning model is deep learning. The most recent deep learning models are based on artificial neural networks (ANN). There exist several types of artificial neural networks including the feedforward neural network, the Kohonen self-organizing neural network, the recurrent neural network, the convolutional neural network, the modular neural network, among others. This article focuses on convolutional neural networks with a description of the model, the training and inference processes and its applicability. It will also give an overview of the most used CNN models and what to expect from the next generation of CNN models.

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