Inferring latent learning factors in large-scale cognitive training data

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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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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Estimation of biophysical characteristics for highly variable mixed-conifer stands using small-footprint lidar

Canadian Journal of Forest Research ◽

10.1139/x06-007 ◽

2006 ◽

Vol 36 (5) ◽

pp. 1129-1138 ◽

Cited By ~ 40

Author(s):

Jennifer L. Rooker Jensen ◽

Karen S Humes ◽

Tamara Conner ◽

Christopher J Williams ◽

John DeGroot

Keyword(s):

Regression Model ◽

Large Scale ◽

Canopy Height ◽

Training Data ◽

Lidar Data ◽

Mixed Conifer ◽

Wood Volume ◽

Small Footprint ◽

Mean Square Errors ◽

Single Regression

Although lidar data are widely available from commercial contractors, operational use in North America is still limited by both cost and the uncertainty of large-scale application and associated model accuracy issues. We analyzed whether small-footprint lidar data obtained from five noncontiguous geographic areas with varying species and structural composition, silvicultural practices, and topography could be used in a single regression model to produce accurate estimates of commonly obtained forest inventory attributes on the Nez Perce Reservation in northern Idaho, USA. Lidar-derived height metrics were used as predictor variables in a best-subset multiple linear regression procedure to determine whether a suite of stand inventory variables could be accurately estimated. Empirical relationships between lidar-derived height metrics and field-measured dependent variables were developed with training data and acceptable models validated with an independent subset. Models were then fit with all data, resulting in coefficients of determination and root mean square errors (respectively) for seven biophysical characteristics, including maximum canopy height (0.91, 3.03 m), mean canopy height (0.79, 2.64 m), quadratic mean DBH (0.61, 6.31 cm), total basal area (0.91, 2.99 m2/ha), ellipsoidal crown closure (0.80, 0.08%), total wood volume (0.93, 24.65 m3/ha), and large saw-wood volume (0.75, 28.76 m3/ha). Although these regression models cannot be generalized to other sites without additional testing, the results obtained in this study suggest that for these types of mixed-conifer forests, some biophysical characteristics can be adequately estimated using a single regression model over stands with highly variable structural characteristics and topography.

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MetaTP

Proceedings of the ACM on Interactive Mobile Wearable and Ubiquitous Technologies ◽

10.1145/3478083 ◽

2021 ◽

Vol 5 (3) ◽

pp. 1-28

Author(s):

Weida Zhong ◽

Qiuling Suo ◽

Abhishek Gupta ◽

Xiaowei Jia ◽

Chunming Qiao ◽

...

Keyword(s):

Time Series ◽

Large Scale ◽

Multivariate Time Series ◽

Modern Society ◽

Training Data ◽

Traffic Prediction ◽

Temporal Prediction ◽

Reference Space ◽

Meta Learning ◽

Real World Datasets

With the popularity of smartphones, large-scale road sensing data is being collected to perform traffic prediction, which is an important task in modern society. Due to the nature of the roving sensors on smartphones, the collected traffic data which is in the form of multivariate time series, is often temporally sparse and unevenly distributed across regions. Moreover, different regions can have different traffic patterns, which makes it challenging to adapt models learned from regions with sufficient training data to target regions. Given that many regions may have very sparse data, it is also impossible to build individual models for each region separately. In this paper, we propose a meta-learning based framework named MetaTP to overcome these challenges. MetaTP has two key parts, i.e., basic traffic prediction network (base model) and meta-knowledge transfer. In base model, a two-layer interpolation network is employed to map original time series onto uniformly-spaced reference time points, so that temporal prediction can be effectively performed in the reference space. The meta-learning framework is employed to transfer knowledge from source regions with a large amount of data to target regions with a few data examples via fast adaptation, in order to improve model generalizability on target regions. Moreover, we use two memory networks to capture the global patterns of spatial and temporal information across regions. We evaluate the proposed framework on two real-world datasets, and experimental results show the effectiveness of the proposed framework.

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