Polling India via regression and post-stratification of non-probability online samples

Recent technological advances have facilitated the collection of large-scale administrative data and the online surveying of the Indian population. Building on these we propose a strategy for more robust, frequent and transparent projections of the Indian vote during the campaign. We execute a modified MrP model of Indian vote preferences that proposes innovations to each of its three core components: stratification frame, training data, and a learner. For the post-stratification frame we propose a novel Data Integration approach that allows the simultaneous estimation of counts from multiple complementary sources, such as census tables and auxiliary surveys. For the training data we assemble panels of respondents from two unorthodox online populations: Amazon Mechanical Turks workers and Facebook users. And as a modeling tool, we replace the Bayesian multilevel regression learner with Random Forests. Our 2019 pre-election forecasts for the two largest Lok Sahba coalitions were very close to actual outcomes: we predicted 41.8% for the NDA, against an observed value of 45.0% and 30.8% for the UPA against an observed vote share of just under 31.3%. Our uniform-swing seat projection outperforms other pollsters—we had the lowest absolute error of 89 seats (along with a poll from ‘Jan Ki Baat’); the lowest error on the NDA-UPA lead (a mere 8 seats), and we are the only pollster that can capture real-time preference shifts due to salient campaign events.

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Scalable Approach to High Coverages on Oxides via Iterative Training of a Machine-Learning Algorithm

10.26434/chemrxiv.10288514.v1 ◽

2019 ◽

Author(s):

Andrew Medford ◽

Shengchun Yang ◽

Fuzhu Liu

Keyword(s):

Machine Learning ◽

Chemical Potential ◽

Learning Algorithm ◽

Absolute Error ◽

Low Energy ◽

Training Data ◽

High Coverage ◽

Metal Compounds ◽

Adsorption Energies ◽

The Stability

Understanding the interaction of multiple types of adsorbate molecules on solid surfaces is crucial to establishing the stability of catalysts under various chemical environments. Computational studies on the high coverage and mixed coverages of reaction intermediates are still challenging, especially for transition-metal compounds. In this work, we present a framework to predict differential adsorption energies and identify low-energy structures under high- and mixed-adsorbate coverages on oxide materials. The approach uses Gaussian process machine-learning models with quantified uncertainty in conjunction with an iterative training algorithm to actively identify the training set. The framework is demonstrated for the mixed adsorption of CHx, NHx and OHx species on the oxygen vacancy and pristine rutile TiO2(110) surface sites. The results indicate that the proposed algorithm is highly efficient at identifying the most valuable training data, and is able to predict differential adsorption energies with a mean absolute error of ~0.3 eV based on <25% of the total DFT data. The algorithm is also used to identify 76% of the low-energy structures based on <30% of the total DFT data, enabling construction of surface phase diagrams that account for high and mixed coverage as a function of the chemical potential of C, H, O, and N. Furthermore, the computational scaling indicates the algorithm scales nearly linearly (N1.12) as the number of adsorbates increases. This framework can be directly extended to metals, metal oxides, and other materials, providing a practical route toward the investigation of the behavior of catalysts under high-coverage conditions.

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Benchmark of Simplified Time-Dependent Density Functional Theory for UV-Vis Spectral Properties of Porphyrinoids

10.26434/chemrxiv.9912860 ◽

2019 ◽

Author(s):

Kamal Batra ◽

Stefan Zahn ◽

Thomas Heine

Keyword(s):

Density Functional Theory ◽

Density Functional ◽

Large Scale ◽

Absolute Error ◽

Time Dependent ◽

Basis Set ◽

Basis Sets ◽

Functional Theory ◽

Framework Materials ◽

Dependent Density

We thoroughly benchmark time-dependent density- functional theory for the predictive calculation of UV/Vis spectra of porphyrin derivatives. With the aim to provide an approach that is computationally feasible for large-scale applications such as biological systems or molecular framework materials, albeit performing with high accuracy for the Q-bands, we compare the results given by various computational protocols, including basis sets, density-functionals (including gradient corrected local functionals, hybrids, double hybrids and range-separated functionals), and various variants of time-dependent density-functional theory, including the simplified Tamm-Dancoff approximation. An excellent choice for these calculations is the range-separated functional CAM-B3LYP in combination with the simplified Tamm-Dancoff approximation and a basis set of double-ζ quality def2-SVP (mean absolute error [MAE] of ~0.05 eV). This is not surpassed by more expensive approaches, not even by double hybrid functionals, and solely systematic excitation energy scaling slightly improves the results (MAE ~0.04 eV).

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DeepSSPred: A Deep Learning Based Sulfenylation site predictor via a novel n-segmented optimize federated feature encoder

Protein and Peptide Letters ◽

10.2174/0929866527666201202103411 ◽

2020 ◽

Vol 27 ◽

Author(s):

Zaheer Ullah Khan ◽

Dechang Pi

Keyword(s):

Large Scale ◽

Computational Models ◽

Research Work ◽

Training Data ◽

Training Dataset ◽

Validation Dataset ◽

Cytokine Signaling ◽

Minority Class ◽

Independent Dataset ◽

Feature Encoding

Background: S-sulfenylation (S-sulphenylation, or sulfenic acid) proteins, are special kinds of post-translation modification, which plays an important role in various physiological and pathological processes such as cytokine signaling, transcriptional regulation, and apoptosis. Despite these aforementioned significances, and by complementing existing wet methods, several computational models have been developed for sulfenylation cysteine sites prediction. However, the performance of these models was not satisfactory due to inefficient feature schemes, severe imbalance issues, and lack of an intelligent learning engine. Objective: In this study, our motivation is to establish a strong and novel computational predictor for discrimination of sulfenylation and non-sulfenylation sites. Methods: In this study, we report an innovative bioinformatics feature encoding tool, named DeepSSPred, in which, resulting encoded features is obtained via n-segmented hybrid feature, and then the resampling technique called synthetic minority oversampling was employed to cope with the severe imbalance issue between SC-sites (minority class) and non-SC sites (majority class). State of the art 2DConvolutional Neural Network was employed over rigorous 10-fold jackknife cross-validation technique for model validation and authentication. Results: Following the proposed framework, with a strong discrete presentation of feature space, machine learning engine, and unbiased presentation of the underline training data yielded into an excellent model that outperforms with all existing established studies. The proposed approach is 6% higher in terms of MCC from the first best. On an independent dataset, the existing first best study failed to provide sufficient details. The model obtained an increase of 7.5% in accuracy, 1.22% in Sn, 12.91% in Sp and 13.12% in MCC on the training data and12.13% of ACC, 27.25% in Sn, 2.25% in Sp, and 30.37% in MCC on an independent dataset in comparison with 2nd best method. These empirical analyses show the superlative performance of the proposed model over both training and Independent dataset in comparison with existing literature studies. Conclusion : In this research, we have developed a novel sequence-based automated predictor for SC-sites, called DeepSSPred. The empirical simulations outcomes with a training dataset and independent validation dataset have revealed the efficacy of the proposed theoretical model. The good performance of DeepSSPred is due to several reasons, such as novel discriminative feature encoding schemes, SMOTE technique, and careful construction of the prediction model through the tuned 2D-CNN classifier. We believe that our research work will provide a potential insight into a further prediction of S-sulfenylation characteristics and functionalities. Thus, we hope that our developed predictor will significantly helpful for large scale discrimination of unknown SC-sites in particular and designing new pharmaceutical drugs in general.

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Knowledge Transfer with Weighted Adversarial Network for Cold-Start Store Site Recommendation

ACM Transactions on Knowledge Discovery from Data ◽

10.1145/3442203 ◽

2021 ◽

Vol 15 (3) ◽

pp. 1-27

Author(s):

Yan Liu ◽

Bin Guo ◽

Daqing Zhang ◽

Djamal Zeghlache ◽

Jingmin Chen ◽

...

Keyword(s):

Large Scale ◽

Cold Start ◽

Weighting Scheme ◽

Training Data ◽

Chain Store ◽

Useful Knowledge ◽

Adversarial Network ◽

Brick And Mortar ◽

New City ◽

Learning Machine

Store site recommendation aims to predict the value of the store at candidate locations and then recommend the optimal location to the company for placing a new brick-and-mortar store. Most existing studies focus on learning machine learning or deep learning models based on large-scale training data of existing chain stores in the same city. However, the expansion of chain enterprises in new cities suffers from data scarcity issues, and these models do not work in the new city where no chain store has been placed (i.e., cold-start problem). In this article, we propose a unified approach for cold-start store site recommendation, Weighted Adversarial Network with Transferability weighting scheme (WANT), to transfer knowledge learned from a data-rich source city to a target city with no labeled data. In particular, to promote positive transfer, we develop a discriminator to diminish distribution discrepancy between source city and target city with different data distributions, which plays the minimax game with the feature extractor to learn transferable representations across cities by adversarial learning. In addition, to further reduce the risk of negative transfer, we design a transferability weighting scheme to quantify the transferability of examples in source city and reweight the contribution of relevant source examples to transfer useful knowledge. We validate WANT using a real-world dataset, and experimental results demonstrate the effectiveness of our proposed model over several state-of-the-art baseline models.

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Sampling weights in multilevel modelling: an investigation using PISA sampling structures

Large-scale Assessments in Education ◽

10.1186/s40536-021-00099-0 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Julia Mang ◽

Helmut Küchenhoff ◽

Sabine Meinck ◽

Manfred Prenzel

Keyword(s):

Hierarchical Models ◽

Large Scale ◽

Practical Importance ◽

Multilevel Modelling ◽

Likelihood Method ◽

Multilevel Regression ◽

Sampling Weights ◽

International Student Assessment ◽

Software Packages ◽

Software Programs

Abstract Background Standard methods for analysing data from large-scale assessments (LSA) cannot merely be adopted if hierarchical (or multilevel) regression modelling should be applied. Currently various approaches exist; they all follow generally a design-based model of estimation using the pseudo maximum likelihood method and adjusted weights for the corresponding hierarchies. Specifically, several different approaches to using and scaling sampling weights in hierarchical models are promoted, yet no study has compared them to provide evidence of which method performs best and therefore should be preferred. Furthermore, different software programs implement different estimation algorithms, leading to different results. Objective and method In this study, we determine based on a simulation, the estimation procedure showing the smallest distortion to the actual population features. We consider different estimation, optimization and acceleration methods, and different approaches on using sampling weights. Three scenarios have been simulated using the statistical program R. The analyses have been performed with two software packages for hierarchical modelling of LSA data, namely Mplus and SAS. Results and conclusions The simulation results revealed three weighting approaches performing best in retrieving the true population parameters. One of them implies using only level two weights (here: final school weights) and is because of its simple implementation the most favourable one. This finding should provide a clear recommendation to researchers for using weights in multilevel modelling (MLM) when analysing LSA data, or data with a similar structure. Further, we found only little differences in the performance and default settings of the software programs used, with the software package Mplus providing slightly more precise estimates. Different algorithm starting settings or different accelerating methods for optimization could cause these distinctions. However, it should be emphasized that with the recommended weighting approach, both software packages perform equally well. Finally, two scaling techniques for student weights have been investigated. They provide both nearly identical results. We use data from the Programme for International Student Assessment (PISA) 2015 to illustrate the practical importance and relevance of weighting in analysing large-scale assessment data with hierarchical models.

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Classification of Very-High-Spatial-Resolution Aerial Images Based on Multiscale Features with Limited Semantic Information

Remote Sensing ◽

10.3390/rs13030364 ◽

2021 ◽

Vol 13 (3) ◽

pp. 364

Author(s):

Han Gao ◽

Jinhui Guo ◽

Peng Guo ◽

Xiuwan Chen

Keyword(s):

Deep Learning ◽

Land Cover ◽

Spatial Resolution ◽

Large Scale ◽

High Spatial Resolution ◽

Training Data ◽

Aerial Images ◽

Rural Landscapes ◽

Feature Representations ◽

Object Based

Recently, deep learning has become the most innovative trend for a variety of high-spatial-resolution remote sensing imaging applications. However, large-scale land cover classification via traditional convolutional neural networks (CNNs) with sliding windows is computationally expensive and produces coarse results. Additionally, although such supervised learning approaches have performed well, collecting and annotating datasets for every task are extremely laborious, especially for those fully supervised cases where the pixel-level ground-truth labels are dense. In this work, we propose a new object-oriented deep learning framework that leverages residual networks with different depths to learn adjacent feature representations by embedding a multibranch architecture in the deep learning pipeline. The idea is to exploit limited training data at different neighboring scales to make a tradeoff between weak semantics and strong feature representations for operational land cover mapping tasks. We draw from established geographic object-based image analysis (GEOBIA) as an auxiliary module to reduce the computational burden of spatial reasoning and optimize the classification boundaries. We evaluated the proposed approach on two subdecimeter-resolution datasets involving both urban and rural landscapes. It presented better classification accuracy (88.9%) compared to traditional object-based deep learning methods and achieves an excellent inference time (11.3 s/ha).

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Gravity Control-Based Data Augmentation Technique for Improving VR User Activity Recognition

Symmetry ◽

10.3390/sym13050845 ◽

2021 ◽

Vol 13 (5) ◽

pp. 845

Author(s):

Dongheun Han ◽

Chulwoo Lee ◽

Hyeongyeop Kang

Keyword(s):

Activity Recognition ◽

Large Scale ◽

Data Augmentation ◽

Training Data ◽

Measurement Unit ◽

Gravitational Acceleration ◽

The Neural Network ◽

Typical Data ◽

Robust Recognition ◽

Gravity Acceleration

The neural-network-based human activity recognition (HAR) technique is being increasingly used for activity recognition in virtual reality (VR) users. The major issue of a such technique is the collection large-scale training datasets which are key for deriving a robust recognition model. However, collecting large-scale data is a costly and time-consuming process. Furthermore, increasing the number of activities to be classified will require a much larger number of training datasets. Since training the model with a sparse dataset can only provide limited features to recognition models, it can cause problems such as overfitting and suboptimal results. In this paper, we present a data augmentation technique named gravity control-based augmentation (GCDA) to alleviate the sparse data problem by generating new training data based on the existing data. The benefits of the symmetrical structure of the data are that it increased the number of data while preserving the properties of the data. The core concept of GCDA is two-fold: (1) decomposing the acceleration data obtained from the inertial measurement unit (IMU) into zero-gravity acceleration and gravitational acceleration, and augmenting them separately, and (2) exploiting gravity as a directional feature and controlling it to augment training datasets. Through the comparative evaluations, we validated that the application of GCDA to training datasets showed a larger improvement in classification accuracy (96.39%) compared to the typical data augmentation methods (92.29%) applied and those that did not apply the augmentation method (85.21%).

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Data Quality Measures and Efficient Evaluation Algorithms for Large-Scale High-Dimensional Data

Applied Sciences ◽

10.3390/app11020472 ◽

2021 ◽

Vol 11 (2) ◽

pp. 472

Author(s):

Hyeongmin Cho ◽

Sangkyun Lee

Keyword(s):

Machine Learning ◽

Data Quality ◽

Large Scale ◽

High Dimensional Data ◽

Quality Measures ◽

Training Data ◽

Measure Data ◽

High Dimensional ◽

Small Scale ◽

Class Separability

Machine learning has been proven to be effective in various application areas, such as object and speech recognition on mobile systems. Since a critical key to machine learning success is the availability of large training data, many datasets are being disclosed and published online. From a data consumer or manager point of view, measuring data quality is an important first step in the learning process. We need to determine which datasets to use, update, and maintain. However, not many practical ways to measure data quality are available today, especially when it comes to large-scale high-dimensional data, such as images and videos. This paper proposes two data quality measures that can compute class separability and in-class variability, the two important aspects of data quality, for a given dataset. Classical data quality measures tend to focus only on class separability; however, we suggest that in-class variability is another important data quality factor. We provide efficient algorithms to compute our quality measures based on random projections and bootstrapping with statistical benefits on large-scale high-dimensional data. In experiments, we show that our measures are compatible with classical measures on small-scale data and can be computed much more efficiently on large-scale high-dimensional datasets.

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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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Maximum Variance Hashing via Column Generation

Mathematical Problems in Engineering ◽

10.1155/2013/379718 ◽

2013 ◽

Vol 2013 ◽

pp. 1-10

Author(s):

Lei Luo ◽

Chao Zhang ◽

Yongrui Qin ◽

Chunyuan Zhang

Keyword(s):

Column Generation ◽

Large Scale ◽

Web Search ◽

Nearest Neighbor ◽

Computational Cost ◽

Multimedia Retrieval ◽

Training Data ◽

Nonlinear Dimensionality Reduction ◽

Maximum Variance ◽

Data Volume

With the explosive growth of the data volume in modern applications such as web search and multimedia retrieval, hashing is becoming increasingly important for efficient nearest neighbor (similar item) search. Recently, a number of data-dependent methods have been developed, reflecting the great potential of learning for hashing. Inspired by the classic nonlinear dimensionality reduction algorithm—maximum variance unfolding, we propose a novel unsupervised hashing method, named maximum variance hashing, in this work. The idea is to maximize the total variance of the hash codes while preserving the local structure of the training data. To solve the derived optimization problem, we propose a column generation algorithm, which directly learns the binary-valued hash functions. We then extend it using anchor graphs to reduce the computational cost. Experiments on large-scale image datasets demonstrate that the proposed method outperforms state-of-the-art hashing methods in many cases.

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