scholarly journals MatClassRSA: A Matlab toolbox for M/EEG classification and visualization of proximity matrices

2017 ◽  
Author(s):  
Bernard C. Wang ◽  
Anthony M. Norcia ◽  
Blair Kaneshiro
Keyword(s):  
Machine Learning ◽  
Cognitive Neuroscience ◽  
Matlab Toolbox ◽  
Eeg Classification ◽  
High Level ◽  
Confusion Matrices ◽  
Proximity Matrices

AbstractMatClassRSA is a Matlab toolbox that performs M/EEG classification and produces various visualizations of the resulting confusion matrices. This toolbox is aimed toward cognitive neuroscience researchers who wish to apply classification-style analyses to repeated trials of data. The functionalities of the toolbox fall into three categories: (1) M/EEG classification, (2) computation of Representational Dissimilarity Matrices (RDMs) from confusion or other proximity matrices, and (3) clustering and tree visualizations of RDMs. MatClassRSA combines out-of-the-box functionality with a variety of customization options. Usage of the toolbox requires only a high-level understanding of machine learning and the ability to call Matlab functions from scripts.

BAND NN: A Deep Learning Framework For Energy Prediction and Geometry Optimization of Organic Small Molecules

2019 ◽  
Author(s):  
Siddhartha Laghuvarapu ◽  
Yashaswi Pathak ◽  
U. Deva Priyakumar
Keyword(s):  
Machine Learning ◽  
Density Functional ◽  
Computational Cost ◽  
Geometry Optimization ◽  
Dft Methods ◽  
Energy Prediction ◽  
Machine Learning Model ◽  
Equilibrium Structures ◽  
High Level ◽  
Non Equilibrium

Recent advances in artificial intelligence along with development of large datasets of energies calculated using quantum mechanical (QM)/density functional theory (DFT) methods have enabled prediction of accurate molecular energies at reasonably low computational cost. However, machine learning models that have been reported so far requires the atomic positions obtained from geometry optimizations using high level QM/DFT methods as input in order to predict the energies, and do not allow for geometry optimization. In this paper, a transferable and molecule-size independent machine learning model (BAND NN) based on a chemically intuitive representation inspired by molecular mechanics force fields is presented. The model predicts the atomization energies of equilibrium and non-equilibrium structures as sum of energy contributions from bonds (B), angles (A), nonbonds (N) and dihedrals (D) at remarkable accuracy. The robustness of the proposed model is further validated by calculations that span over the conformational, configurational and reaction space. The transferability of this model on systems larger than the ones in the dataset is demonstrated by performing calculations on select large molecules. Importantly, employing the BAND NN model, it is possible to perform geometry optimizations starting from non-equilibrium structures along with predicting their energies.

COVID-19 Outbreak Prediction with Machine Learning

2020 ◽  
Author(s):  
Sina Faizollahzadeh Ardabili ◽  
Amir Mosavi ◽  
Pedram Ghamisi ◽  
Filip Ferdinand ◽  
Annamaria R. Varkonyi-Koczy ◽  
...  
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Fuzzy Inference ◽  
Control Measures ◽  
Future Research ◽  
Complex Nature ◽  
Inference System ◽  
Wide Range ◽  
Standard Models ◽  
High Level

Several outbreak prediction models for COVID-19 are being used by officials around the world to make informed-decisions and enforce relevant control measures. Among the standard models for COVID-19 global pandemic prediction, simple epidemiological and statistical models have received more attention by authorities, and they are popular in the media. Due to a high level of uncertainty and lack of essential data, standard models have shown low accuracy for long-term prediction. Although the literature includes several attempts to address this issue, the essential generalization and robustness abilities of existing models needs to be improved. This paper presents a comparative analysis of machine learning and soft computing models to predict the COVID-19 outbreak as an alternative to SIR and SEIR models. Among a wide range of machine learning models investigated, two models showed promising results (i.e., multi-layered perceptron, MLP, and adaptive network-based fuzzy inference system, ANFIS). Based on the results reported here, and due to the highly complex nature of the COVID-19 outbreak and variation in its behavior from nation-to-nation, this study suggests machine learning as an effective tool to model the outbreak. This paper provides an initial benchmarking to demonstrate the potential of machine learning for future research. Paper further suggests that real novelty in outbreak prediction can be realized through integrating machine learning and SEIR models.

scholarly journals Machine Learning–enabled Scalable Performance Prediction of Scientific Codes

2021 ◽  
Vol 31 (2) ◽  
pp. 1-28
Author(s):  
Gopinath Chennupati ◽  
Nandakishore Santhi ◽  
Phill Romero ◽  
Stephan Eidenbenz
Keyword(s):  
Machine Learning ◽  
Performance Prediction ◽  
Prediction Models ◽  
Radiation Transport ◽  
Discrete Event ◽  
Basic Block ◽  
Distribution Models ◽  
Scientific Application ◽  
High Level ◽  
Access Patterns

Hardware architectures become increasingly complex as the compute capabilities grow to exascale. We present the Analytical Memory Model with Pipelines (AMMP) of the Performance Prediction Toolkit (PPT). PPT-AMMP takes high-level source code and hardware architecture parameters as input and predicts runtime of that code on the target hardware platform, which is defined in the input parameters. PPT-AMMP transforms the code to an (architecture-independent) intermediate representation, then (i) analyzes the basic block structure of the code, (ii) processes architecture-independent virtual memory access patterns that it uses to build memory reuse distance distribution models for each basic block, and (iii) runs detailed basic-block level simulations to determine hardware pipeline usage. PPT-AMMP uses machine learning and regression techniques to build the prediction models based on small instances of the input code, then integrates into a higher-order discrete-event simulation model of PPT running on Simian PDES engine. We validate PPT-AMMP on four standard computational physics benchmarks and present a use case of hardware parameter sensitivity analysis to identify bottleneck hardware resources on different code inputs. We further extend PPT-AMMP to predict the performance of a scientific application code, namely, the radiation transport mini-app SNAP. To this end, we analyze multi-variate regression models that accurately predict the reuse profiles and the basic block counts. We validate predicted SNAP runtimes against actual measured times.

scholarly journals Semi-automated classification of colonial Microcystis by FlowCAM imaging flow cytometry in mesocosm experiment reveals high heterogeneity during seasonal bloom

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yersultan Mirasbekov ◽  
Adina Zhumakhanova ◽  
Almira Zhantuyakova ◽  
Kuanysh Sarkytbayev ◽  
Dmitry V. Malashenkov ◽  
...  
Keyword(s):  
Machine Learning ◽  
Flow Cytometry ◽  
Spatial Resolution ◽  
Mesocosm Experiment ◽  
Imaging Flow Cytometry ◽  
Leibler Divergence ◽  
Temporal And Spatial ◽  
High Level ◽  
Training Sets

AbstractA machine learning approach was employed to detect and quantify Microcystis colonial morphospecies using FlowCAM-based imaging flow cytometry. The system was trained and tested using samples from a long-term mesocosm experiment (LMWE, Central Jutland, Denmark). The statistical validation of the classification approaches was performed using Hellinger distances, Bray–Curtis dissimilarity, and Kullback–Leibler divergence. The semi-automatic classification based on well-balanced training sets from Microcystis seasonal bloom provided a high level of intergeneric accuracy (96–100%) but relatively low intrageneric accuracy (67–78%). Our results provide a proof-of-concept of how machine learning approaches can be applied to analyze the colonial microalgae. This approach allowed to evaluate Microcystis seasonal bloom in individual mesocosms with high level of temporal and spatial resolution. The observation that some Microcystis morphotypes completely disappeared and re-appeared along the mesocosm experiment timeline supports the hypothesis of the main transition pathways of colonial Microcystis morphoforms. We demonstrated that significant changes in the training sets with colonial images required for accurate classification of Microcystis spp. from time points differed by only two weeks due to Microcystis high phenotypic heterogeneity during the bloom. We conclude that automatic methods not only allow a performance level of human taxonomist, and thus be a valuable time-saving tool in the routine-like identification of colonial phytoplankton taxa, but also can be applied to increase temporal and spatial resolution of the study.

scholarly journals A transferable active-learning strategy for reactive molecular force fields

2021 ◽  
Author(s):  
Tom Young ◽  
Tristan Johnston-Wood ◽  
Volker L. Deringer ◽  
Fernanda Duarte
Keyword(s):  
Machine Learning ◽  
Active Learning ◽  
Learning Strategy ◽  
Force Fields ◽  
Molecular Simulations ◽  
Quantum Mechanical ◽  
Interatomic Potentials ◽  
Molecular Force ◽  
High Level ◽  
Active Learning Strategy

Predictive molecular simulations require fast, accurate and reactive interatomic potentials. Machine learning offers a promising approach to construct such potentials by fitting energies and forces to high-level quantum-mechanical data, but...

scholarly journals Entity Type Recognition for Heterogeneous Semantic Graphs

AI Magazine ◽  
2015 ◽  
Vol 36 (1) ◽  
pp. 75-86 ◽  
Author(s):  
Jennifer Sleeman ◽  
Tim Finin ◽  
Anupam Joshi
Keyword(s):  
Machine Learning ◽  
Background Knowledge ◽  
Knowledge Bases ◽  
Heterogeneous Data ◽  
Unstructured Data ◽  
Supervised Machine Learning ◽  
Coreference Resolution ◽  
Multiple Sources ◽  
Fine Grained ◽  
High Level

We describe an approach for identifying fine-grained entity types in heterogeneous data graphs that is effective for unstructured data or when the underlying ontologies or semantic schemas are unknown. Identifying fine-grained entity types, rather than a few high-level types, supports coreference resolution in heterogeneous graphs by reducing the number of possible coreference relations that must be considered. Big data problems that involve integrating data from multiple sources can benefit from our approach when the datas ontologies are unknown, inaccessible or semantically trivial. For such cases, we use supervised machine learning to map entity attributes and relations to a known set of attributes and relations from appropriate background knowledge bases to predict instance entity types. We evaluated this approach in experiments on data from DBpedia, Freebase, and Arnetminer using DBpedia as the background knowledge base.

scholarly journals MALINI (Machine Learning in NeuroImaging): A MATLAB toolbox for aiding clinical diagnostics using resting-state fMRI data

Data in Brief ◽  
2020 ◽  
Vol 29 ◽  
pp. 105213 ◽  
Author(s):  
Pradyumna Lanka ◽  
D. Rangaprakash ◽  
Sai Sheshan Roy Gotoor ◽  
Michael N. Dretsch ◽  
Jeffrey S. Katz ◽  
...  
Keyword(s):  
Machine Learning ◽  
Resting State ◽  
Resting State Fmri ◽  
Clinical Diagnostics ◽  
Fmri Data ◽  
Matlab Toolbox

scholarly journals Functional Correlations in the Pursuit of Performance Assessment of Classifiers

2020 ◽  
Vol 34 (13) ◽  
pp. 2051013
Author(s):  
Nadezhda Gribkova ◽  
Ričardas Zitikis
Keyword(s):  
Machine Learning ◽  
Performance Assessment ◽  
Correlation Coefficients ◽  
Statistical Classification ◽  
Measures Of Association ◽  
Confusion Matrices

In statistical classification and machine learning, as well as in social and other sciences, a number of measures of association have been proposed for assessing and comparing individual classifiers, raters, as well as their groups. In this paper, we introduce, justify, and explore several new measures of association, which we call CO-, ANTI-, and COANTI-correlation coefficients, that we demonstrate to be powerful tools for classifying confusion matrices. We illustrate the performance of these new coefficients using a number of examples, from which we also conclude that the coefficients are new objects in the sense that they differ from those already in the literature.

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