scholarly journals Semi-Supervised Machine Learning Enables the Robust Detection of Multireference Character at Low Cost

2020 ◽  
Author(s):  
Chenru Duan ◽  
Fang Liu ◽  
Aditya Nandy ◽  
Heather Kulik
Keyword(s):  
Machine Learning ◽  
High Throughput Screening ◽  
Density Functional ◽  
Low Cost ◽  
Supervised Machine Learning ◽  
Strongly Correlated ◽  
Robust Detection ◽  
Distinct Property ◽  
The Cost ◽  
Decision Engine

Multireference (MR) diagnostics are common tools for identifying strongly correlated electronic structure that makes single reference (SR) methods (e.g., density functional theory or DFT) insufficient for accurate property prediction. However, MR diagnostics typically require computationally demanding correlated wavefunction theory (WFT) calculations, and diagnostics often disagree or fail to predict MR effects on properties. To overcome these challenges, we introduce a semi-supervised machine learning (ML) approach with virtual adversarial training (VAT) of an MR classifier using 15 WFT and DFT MR diagnostics as inputs. In semi-supervised learning, only the most extreme SR or MR points are labeled, and the remaining point labels are learned. The resulting VAT model outperforms the alternatives, as quantified by the distinct property distributions of SR- and MR-classified molecules. To reduce the cost of generating inputs to the VAT model, we leverage the VAT model’s robustness to noisy inputs by replacing WFT MR diagnostics with regression predictions in a MR decision engine workflow that preserves excellent performance. We demonstrate the transferability of our approach to larger molecules and those with distinct chemical composition from the training set. This MR decision engine demonstrates promise as a low-cost, high-accuracy approach to the automatic detection of strong correlation for predictive high-throughput screening.

scholarly journals Semi-Supervised Machine Learning Enables the Robust Detection of Multireference Character at Low Cost

2020 ◽  
Author(s):  
Chenru Duan ◽  
Fang Liu ◽  
Aditya Nandy ◽  
Heather Kulik
Keyword(s):  
Machine Learning ◽  
High Throughput Screening ◽  
Density Functional ◽  
Low Cost ◽  
Supervised Machine Learning ◽  
Strongly Correlated ◽  
Robust Detection ◽  
Distinct Property ◽  
The Cost ◽  
Decision Engine

Multireference (MR) diagnostics are common tools for identifying strongly correlated electronic structure that makes single reference (SR) methods (e.g., density functional theory or DFT) insufficient for accurate property prediction. However, MR diagnostics typically require computationally demanding correlated wavefunction theory (WFT) calculations, and diagnostics often disagree or fail to predict MR effects on properties. To overcome these challenges, we introduce a semi-supervised machine learning (ML) approach with virtual adversarial training (VAT) of an MR classifier using 15 WFT and DFT MR diagnostics as inputs. In semi-supervised learning, only the most extreme SR or MR points are labeled, and the remaining point labels are learned. The resulting VAT model outperforms the alternatives, as quantified by the distinct property distributions of SR- and MR-classified molecules. To reduce the cost of generating inputs to the VAT model, we leverage the VAT model’s robustness to noisy inputs by replacing WFT MR diagnostics with regression predictions in a MR decision engine workflow that preserves excellent performance. We demonstrate the transferability of our approach to larger molecules and those with distinct chemical composition from the training set. This MR decision engine demonstrates promise as a low-cost, high-accuracy approach to the automatic detection of strong correlation for predictive high-throughput screening.

scholarly journals Data-Driven Approaches Can Overcome Limitations in Multireference Diagnostics

2020 ◽  
Author(s):  
Chenru Duan ◽  
Fang Liu ◽  
Aditya Nandy ◽  
Heather Kulik
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Density Functional ◽  
Correlation Energy ◽  
Low Cost ◽  
Small Data ◽  
Data Sets ◽  
Strongly Correlated ◽  
Heavy Atoms ◽  
Computational Screening

High-throughput computational screening typically employs methods (i.e., density functional theory or DFT) that can fail to describe challenging molecules, such as those with strongly correlated electronic structure. In such cases, multireference (MR) correlated wavefunction theory (WFT) would be the appropriate choice but remains more challenging to carry out and automate than single-reference (SR) WFT or DFT. Numerous diagnostics have been proposed for identifying when MR character is likely to have an effect on the predictive power of SR calculations, but conflicting conclusions about diagnostic performance have been reached on small data sets. We compute 15 MR diagnostics, ranging from affordable DFT-based to more costly MR-WFT-based diagnostics, on a set of 3,165 equilibrium and distorted small organic molecules containing up to six heavy atoms. Conflicting MR character assignments and low pairwise linear correlations among diagnostics are also observed over this set. We evaluate the ability of existing diagnostics to predict the percent recovery of the correlation energy, %<i>E</i><sub>corr</sub>. None of the DFT-based diagnostics are nearly as predictive of %<i>E</i><sub>corr</sub> as the best WFT-based diagnostics. To overcome the limitation of this cost–accuracy trade-off, we develop machine learning (ML, i.e., kernel ridge regression) models to predict WFT-based diagnostics from a combination of DFT-based diagnostics and a new, size-independent 3D geometric representation. The ML-predicted diagnostics correlate as well with MR effects as their computed (i.e., with WFT) values, significantly improving over the DFT-based diagnostics on which the models were trained. These ML models thus provide a promising approach to improve upon DFT-based diagnostic accuracy while remaining suitably low cost for high-throughput screening.

scholarly journals Data-Driven Approaches Can Overcome Limitations in Multireference Diagnostics

2020 ◽  
Author(s):  
Chenru Duan ◽  
Fang Liu ◽  
Aditya Nandy ◽  
Heather Kulik
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Density Functional ◽  
Correlation Energy ◽  
Low Cost ◽  
Small Data ◽  
Data Sets ◽  
Strongly Correlated ◽  
Heavy Atoms ◽  
Computational Screening

High-throughput computational screening typically employs methods (i.e., density functional theory or DFT) that can fail to describe challenging molecules, such as those with strongly correlated electronic structure. In such cases, multireference (MR) correlated wavefunction theory (WFT) would be the appropriate choice but remains more challenging to carry out and automate than single-reference (SR) WFT or DFT. Numerous diagnostics have been proposed for identifying when MR character is likely to have an effect on the predictive power of SR calculations, but conflicting conclusions about diagnostic performance have been reached on small data sets. We compute 15 MR diagnostics, ranging from affordable DFT-based to more costly MR-WFT-based diagnostics, on a set of 3,165 equilibrium and distorted small organic molecules containing up to six heavy atoms. Conflicting MR character assignments and low pairwise linear correlations among diagnostics are also observed over this set. We evaluate the ability of existing diagnostics to predict the percent recovery of the correlation energy, %<i>E</i><sub>corr</sub>. None of the DFT-based diagnostics are nearly as predictive of %<i>E</i><sub>corr</sub> as the best WFT-based diagnostics. To overcome the limitation of this cost–accuracy trade-off, we develop machine learning (ML, i.e., kernel ridge regression) models to predict WFT-based diagnostics from a combination of DFT-based diagnostics and a new, size-independent 3D geometric representation. The ML-predicted diagnostics correlate as well with MR effects as their computed (i.e., with WFT) values, significantly improving over the DFT-based diagnostics on which the models were trained. These ML models thus provide a promising approach to improve upon DFT-based diagnostic accuracy while remaining suitably low cost for high-throughput screening.

scholarly journals Infinity Flow: High-throughput single-cell quantification of 100s of proteins using conventional flow cytometry and machine learning

2020 ◽  
Author(s):  
Etienne Becht ◽  
Daniel Tolstrup ◽  
Charles-Antoine Dutertre ◽  
Florent Ginhoux ◽  
Evan W. Newell ◽  
...  
Keyword(s):  
Machine Learning ◽  
Flow Cytometry ◽  
Single Cell ◽  
Low Cost ◽  
Expression Patterns ◽  
Cell Types ◽  
Cellular Heterogeneity ◽  
Supervised Machine Learning ◽  
Melanoma Metastasis ◽  
Immunologic Research

AbstractModern immunologic research increasingly requires high-dimensional analyses in order to understand the complex milieu of cell-types that comprise the tissue microenvironments of disease. To achieve this, we developed Infinity Flow combining hundreds of overlapping flow cytometry panels using machine learning to enable the simultaneous analysis of the co-expression patterns of 100s of surface-expressed proteins across millions of individual cells. In this study, we demonstrate that this approach allows the comprehensive analysis of the cellular constituency of the steady-state murine lung and to identify novel cellular heterogeneity in the lungs of melanoma metastasis bearing mice. We show that by using supervised machine learning, Infinity Flow enhances the accuracy and depth of clustering or dimensionality reduction algorithms. Infinity Flow is a highly scalable, low-cost and accessible solution to single cell proteomics in complex tissues.

scholarly journals The prototype device for non-invasive diagnosis of arteriovenous fistula condition using machine learning methods

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Marcin Grochowina ◽  
Lucyna Leniowska ◽  
Agnieszka Gala-Błądzińska
Keyword(s):  
Machine Learning ◽  
Arteriovenous Fistula ◽  
Low Cost ◽  
Principal Component ◽  
Special Kind ◽  
Classification Model ◽  
Supervised Machine Learning ◽  
Signal Acquisition ◽  
Non Invasive ◽  
Prototype Device

Abstract Pattern recognition and automatic decision support methods provide significant advantages in the area of health protection. The aim of this work is to develop a low-cost tool for monitoring arteriovenous fistula (AVF) with the use of phono-angiography method. This article presents a developed and diagnostic device that implements classification algorithms to identify 38 patients with end stage renal disease, chronically hemodialysed using an AVF, at risk of vascular access stenosis. We report on the design, fabrication, and preliminary testing of a prototype device for non-invasive diagnosis which is very important for hemodialysed patients. The system includes three sub-modules: AVF signal acquisition, information processing and classification and a unit for presenting results. This is a non-invasive and inexpensive procedure for evaluating the sound pattern of bruit produced by AVF. With a special kind of head which has a greater sensitivity than conventional stethoscope, a sound signal from fistula was recorded. The proces of signal acquisition was performed by a dedicated software, written specifically for the purpose of our study. From the obtained phono-angiogram, 23 features were isolated for vectors used in a decision-making algorithm, including 6 features based on the waveform of time domain, and 17 features based on the frequency spectrum. Final definition of the feature vector composition was obtained by using several selection methods: the feature-class correlation, forward search, Principal Component Analysis and Joined-Pairs method. The supervised machine learning technique was then applied to develop the best classification model.

scholarly journals Application of DFT-based machine learning for developing molecular electrode materials in Li-ion batteries

RSC Advances ◽  
2018 ◽  
Vol 8 (69) ◽  
pp. 39414-39420 ◽  
Author(s):  
Omar Allam ◽  
Byung Woo Cho ◽  
Ki Chul Kim ◽  
Seung Soon Jang
Keyword(s):  
Machine Learning ◽  
Density Functional Theory ◽  
High Throughput Screening ◽  
Density Functional ◽  
Electrode Materials ◽  
Screening Method ◽  
Li Ion Batteries ◽  
Functional Theory ◽  
Learning Framework ◽  
Li Ion

In this study, we utilize a density functional theory-machine learning framework to develop a high-throughput screening method for designing new molecular electrode materials.

scholarly journals Active Learning Approaches for Labeling Text: Review and Assessment of the Performance of Active Learning Approaches

2020 ◽  
Vol 28 (4) ◽  
pp. 532-551
Author(s):  
Blake Miller ◽  
Fridolin Linder ◽  
Walter R. Mebane
Keyword(s):  
Machine Learning ◽  
Active Learning ◽  
Random Sampling ◽  
Supervised Machine Learning ◽  
Learning Approaches ◽  
Simulation Studies ◽  
Text Data ◽  
Passive Learning ◽  
Machine Learning Model ◽  
The Cost

Supervised machine learning methods are increasingly employed in political science. Such models require costly manual labeling of documents. In this paper, we introduce active learning, a framework in which data to be labeled by human coders are not chosen at random but rather targeted in such a way that the required amount of data to train a machine learning model can be minimized. We study the benefits of active learning using text data examples. We perform simulation studies that illustrate conditions where active learning can reduce the cost of labeling text data. We perform these simulations on three corpora that vary in size, document length, and domain. We find that in cases where the document class of interest is not balanced, researchers can label a fraction of the documents one would need using random sampling (or “passive” learning) to achieve equally performing classifiers. We further investigate how varying levels of intercoder reliability affect the active learning procedures and find that even with low reliability, active learning performs more efficiently than does random sampling.

scholarly journals Data-driven Discovery of Photoactive Quaternary Oxides using First-principles Machine Learning

2019 ◽  
Author(s):  
Daniel Davies ◽  
Keith T. Butler ◽  
Aron Walsh
Keyword(s):  
Machine Learning ◽  
First Principles ◽  
Chemical Space ◽  
Low Cost ◽  
Probability Model ◽  
Solar Spectrum ◽  
Inorganic Materials ◽  
Supervised Machine Learning ◽  
Visible Range ◽  
Energy Applications

<div> <div> <div> <p>We present a low-cost, virtual high-throughput materials design workflow and use it to identify earth-abundant materials for solar energy applications from the quaternary oxide chemical space. A statistical model that predicts bandgap from chemical composition is built using supervised machine learning. The trained model forms the first in a hierarchy of screening steps. An ionic substitution algorithm is used to assign crystal structures, and an oxidation state probability model is used to discard unlikely chemistries. We demonstrate the utility of this process for screening over 1 million oxide compositions. We find that, despite the difficulties inherent to identifying stable multi-component inorganic materials, several compounds produced by our workflow are calculated to be thermodynamically stable or metastable and have desirable optoelectronic properties according to first-principles calculations. The predicted oxides are Li2MnSiO5, MnAg(SeO3)2 and two polymorphs of MnCdGe2O6, all four of which are found to have direct electronic bandgaps in the visible range of the solar spectrum. </p> </div> </div> </div>

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