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There have been a number of recent proposals to enhance the performance of machine learning strategies for collider physics by combining many distinct events into a single ensemble feature. To evaluate the efficacy of these proposals, we study the connection between single-event classifiers and multievent classifiers under the assumption that collider events are independent and identically distributed. We show how one can build optimal multievent classifiers from single-event classifiers, and we also show how to construct multievent classifiers such that they produce optimal single-event classifiers. This is illustrated for a Gaussian example as well as for classification tasks relevant for searches and measurements at the Large Hadron Collider. We extend our discussion to regression tasks by showing how they can be phrased in terms of parametrized classifiers. Empirically, we find that training a single-event (per-instance) classifier is more effective than training a multievent (per-ensemble) classifier, as least for the cases we studied, and we relate this fact to properties of the loss function gradient in the two cases. While we did not identify a clear benefit from using multievent classifiers in the collider context, we speculate on the potential value of these methods in cases involving only approximate independence, as relevant for jet substructure studies.
High-throughput analysis of biomass is necessary to ensure consistent and uniform feedstocks for agricultural and bioenergy applications and is needed to inform genomics and systems biology models. Pyrolysis followed by mass spectrometry such as molecular beam mass spectrometry (py-MBMS) analyses are becoming increasingly popular for the rapid analysis of biomass cell wall composition and typically require the use of different data analysis tools depending on the need and application. Here, the authors report the py-MBMS analysis of several types of lignocellulosic biomass to gain an understanding of spectral patterns and variation with associated biomass composition and use machine learning approaches to classify, differentiate, and predict biomass types on the basis of py-MBMS spectra. Py-MBMS spectra were also corrected for instrumental variance using generalized linear modeling (GLM) based on the use of select ions relative abundances as spike-in controls. Machine learning classification algorithms e.g., random forest, k-nearest neighbor, decision tree, Gaussian Naïve Bayes, gradient boosting, and multilayer perceptron classifiers were used. The k-nearest neighbors (k-NN) classifier generally performed the best for classifications using raw spectral data, and the decision tree classifier performed the worst. After normalization of spectra to account for instrumental variance, all the classifiers had comparable and generally acceptable performance for predicting the biomass types, although the k-NN and decision tree classifiers were not as accurate for prediction of specific sample types. Gaussian Naïve Bayes (GNB) and extreme gradient boosting (XGB) classifiers performed better than the k-NN and the decision tree classifiers for the prediction of biomass mixtures. The data analysis workflow reported here could be applied and extended for comparison of biomass samples of varying types, species, phenotypes, and/or genotypes or subjected to different treatments, environments, etc. to further elucidate the sources of spectral variance, patterns, and to infer compositional information based on spectral analysis, particularly for analysis of data without a priori knowledge of the feedstock composition or identity.
There is an increasing need to create predictive models for defect classification in concrete using the output of non-destructive testing (NDT) techniques. Recent advancement of machine-learning algorithms has offered several techniques for developing classification models for different types of data sets. However, the performance of these algorithms is very uncertain, mainly when applied to small and noisy datasets. For example, when human access is limited (e.g., nuclear facility), robot-based NDT is preferred. But compared to manual tests with humans present on site, the data sets are small, and more noise can exist. Therefore, it is imperative to develop new approaches to ensure a consistently high classification accuracy for inadequate data sets. This study explores the classification performance on NDT dataset using classifiers from different machine-learning algorithms, namely k-Nearest Neighbor (kNN), Decision Tree, Naive Bayes, Logistic Regression, and Support Vector Machine (SVM). The authors further integrated the predictions from these classifiers using proposed methods. The integration strategy combines the output of the classifiers based on two different measures, accuracy, and performance (ACC and PERF), using equations such as sum, average, and square-root-of-sums-of-squares (SRSS). Our results reveal varying classification accuracies across individual classifiers with different misclassifications across the test data set. The integration strategy provided significant improvement in the classification accuracy compared to the individual classifiers. Furthermore, the results indicate minimal variation across the integration methods as compared to the variation across the individual classifiers. To conclude, prediction integration offers a unique approach for combining the output of multiple classifiers to create redundancies with the potential of achieving high classification performance and improved reliability in predictive models for defect detection in concrete. (authors)
Purpose In clinical practice, invasiveness is an important reference indicator for differentiating the malignant degree of subsolid pulmonary nodules. These nodules can be classified as atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA), or invasive adenocarcinoma (IAC). The automatic determination of a nodule's invasiveness based on chest CT scans can guide treatment planning. However, it is challenging, owing to the insufficiency of training data and their interclass similarity and intraclass variation. To address these challenges, we propose a two‐stage deep learning strategy for this task: prior‐feature learning followed by adaptive‐boost deep learning. Methods The adaptive‐boost deep learning is proposed to train a strong classifier for invasiveness classification of subsolid nodules in chest CT images, using multiple 3D convolutional neural network (CNN)‐based weak classifiers. Because ensembles of multiple deep 3D CNN models have a huge number of parameters and require large computing resources along with more training and testing time, the prior‐feature learning is proposed to reduce the computations by sharing the CNN layers between all weak classifiers. Using this strategy, all weak classifiers can be integrated into a single network. Results Tenfold cross validation of binary classification was conducted on a total of 1357 nodules, including 765 noninvasive (AAH and AIS) and 592 invasive nodules (MIA and IAC). Ablation experimental results indicated that the proposed binary classifier achieved an accuracy of with an AUC of 81.3 . These results are superior compared to those achieved by three experienced chest imaging specialists who achieved an accuracy of , , and , respectively. About 200 additional nodules were also collected. These nodules covered 50 cases for each category (AAH, AIS, MIA, and IAC, respectively). Both binary and multiple classifications were performed on these data and the results demonstrated that the proposed method definitely achieves better performance than the performance achieved by nonensemble deep learning methods. Conclusions It can be concluded that the proposed adaptive‐boost deep learning can significantly improve the performance of invasiveness classification of pulmonary subsolid nodules in CT images, while the prior‐feature learning can significantly reduce the total size of deep models. The promising results on clinical data show that the trained models can be used as an effective lung cancer screening tool in hospitals. Moreover, the proposed strategy can be easily extended to other similar classification tasks in 3D medical images.
Many measurements in the physical sciences can be cast as counting experiments, where the number of occurrences of a physical phenomenon informs the prevalence of the phenomenon's source. Often, detection of the physical phenomenon (termed signal) is difficult to distinguish from naturally occurring phenomena (termed background). In this case, the discrimination of signal events from background can be performed using classifiers, and they may range from simple, threshold-based classifiers to sophisticated neural networks. These classifiers are often trained and validated to obtain optimal accuracy, however we show that the optimal accuracy classifier does not generally coincide with a classifier that provides the lowest detection limit, nor the lowest quantification uncertainty. Here, we present a derivation of the detection limit and quantification uncertainty in the classifier-based counting experiment case. We also present a novel abstention mechanism to minimize the detection limit or quantification uncertainty a posteriori. We illustrate the method on two data sets from the physical sciences, discriminating Ar-37 and Ar-39 radioactive decay from non-radioactive events in a gas proportional counter, and discriminating neutrons from gammas in an inorganic scintillator and report results therefrom.
In this work, we apply machine learning approaches sparse multinomial logistic regression to classify aerosol mass spectrometer (AMS) unit mass resolution (UMR) data followed by an ensemble regression technique for source apportionment of organic aerosols (OA). The classifier was trained on 60 well characterized laboratory and positive matrix factorization (PMF) deconvolved reference spectra to identify eight OA types. These include four laboratory-derived secondary organic aerosol (SOA) spectra, which include isoprene photooxidation SOA, isoprene epoxydiols (IEPOX) SOA, a monoterpene SOA type that includes a-pinene and ß-pinene SOA, and aromatic SOA from oxidation of naphthalene and m-xylene precursors, as well as PMF deconvolved spectra for three primary organic aerosol (POA) types, namely, hydrocarbon-like organic aerosol (HOA), biomass burning organic aerosol (BBOA), and cooking OA (COA), and a more oxidized oxygenated OA type (MO-OOA). A 5-fold cross-validation strategy, repeated 10 times, was used to assess the classifier’s performance. The classifier had high classification accuracy for COA, aromatic SOA, and isoprene SOA spectra but incorrectly classified ~9% by number of MO-OOA spectra as BBOA, 12% of BBOA spectra as HOA (and vice versa), and 18% of IEPOX-SOA spectra as aromatic SOA. Next, an ensemble regression model was trained on an artificially generated dataset consisting of mixtures of different OA types to assess its ability to predict fractional mass abundances from classification probabilities of various OA species obtained from the multinomial logistic regression classifier trained on the reference spectra. Ultimately, the proposed approach was applied for source apportionment of aircraft-based AMS measurements of OA UMR spectra during the HI-SCALE field campaign. On two representative days (May 6th and 18th, 2016), the algorithm determined that ~50-60% of OA by mass was MO-OOA, which represented a highly aged organic aerosol mixture from different sources. On both days, BBOA was determined to contribute less than 10% to OA by mass. However, on May 18th, the aromatic SOA fraction was higher compared to that on May 6th. The proposed approach is capable of rapidly analyzing AMS data in real time, making it suitable for applications where rapid source apportionment of AMS OA spectra is desirable.
Abstract The Structural Classification of Proteins—extended (SCOPe, https://scop.berkeley.edu) knowledgebase aims to provide an accurate, detailed, and comprehensive description of the structural and evolutionary relationships amongst the majority of proteins of known structure, along with resources for analyzing the protein structures and their sequences. Structures from the PDB are divided into domains and classified using a combination of manual curation and highly precise automated methods. In the current release of SCOPe, 2.08, we have developed search and display tools for analysis of genetic variants we mapped to structures classified in SCOPe. In order to improve the utility of SCOPe to automated methods such as deep learning classifiers that rely on multiple alignment of sequences of homologous proteins, we have introduced new machine-parseable annotations that indicate aberrant structures as well as domains that are distinguished by a smaller repeat unit. We also classified structures from 74 of the largest Pfam families not previously classified in SCOPe, and we improved our algorithm to remove N- and C-terminal cloning, expression and purification sequences from SCOPe domains. SCOPe 2.08-stable classifies 106 976 PDB entries (about 60% of PDB entries).
Introduction: The purpose of this study was to evaluate the treatment efficacy of transcatheter arterial chemoembolization (TACE) for treatment-naive hepatocellular carcinoma (HCC) according to tumor location and burden. Methods: Between 2010 and 2019, consecutive patients who underwent TACE as the first treatment were enrolled. Tumors were classified into two categories based on their location, as central or peripheral tumors. Tumors in the central zone, which is within 1 cm of the main trunk or the first branch of the portal vein, were classified as central tumors, while those located in the peripheral zone were classified as peripheral tumors. Patients were grouped according to the HCC location and up-to-7 criteria. Patients with central tumors were classified into the central arm and those with only peripheral tumors were classified into the peripheral arm. Patients within and beyond the up-to-7 criteria were classified into the up-to-7 in and up-to-7 out-groups, respectively. Local recurrence-free survival (LRFS) and progression-free survival (PFS) were compared per nodule (central tumor vs. peripheral tumor) and per patient (central arm vs. peripheral arm), respectively. The prognostic factors of LRFS and PFS were analyzed by univariate and multivariate analyses. Results: A total of 174 treatment-naive patients with 352 HCCs were retrospectively enrolled. Ninety-six patients and 130 lesions were selected by propensity score matching. Median LRFS was longer for peripheral tumors than central tumors (not reached vs. 3.3 months, p < 0.001). Median PFS was 17.1 months (8.3–24.9) in the peripheral arm and up-to-7 in, 7.0 months (3.3–12.7) in the peripheral arm and up-to-7 out, 8.4 months (4.0–12.6) in the central arm and up-to-7 in, and 3.0 months (1.2–4.9) in the central arm and up-to-7 out-groups. The peripheral arm and up-to-7 in-groups had significantly longer PFS than the other three groups (p = 0.013, p = 0.015, p < 0.001, respectively). Multivariate analysis confirmed that the central zone and central arm were associated with high adjusted hazard ratios for tumor recurrence or death (2.87, p < 0.001; 2.89, p < 0.001, respectively). Conclusion: Treatment-naive HCCs in the peripheral zone had a longer LRFS and PFS following TACE compared to those in the central zone.
Abstract A vast amount of ice crystal imagery exists from a variety of field campaign initiatives that can be utilized for cloud microphysical research. Here, nine convolutional neural networks are used to classify particles into nine regimes on over 10 million images from the Cloud Particle Imager probe, including liquid and frozen states and particles with evidence of riming. A transfer learning approach proves that the Visual Geometry Group (VGG-16) network best classifies imagery with respect to multiple performance metrics. Classification accuracies on a validation dataset reach 97% and surpass traditional automated classification. Furthermore, after initial model training and preprocessing, 10 000 images can be classified in approximately 35 s using 20 central processing unit cores and two graphics processing units, which reaches real-time classification capabilities. Statistical analysis of the classified images indicates that a large portion (57%) of the dataset is unusable, meaning the images are too blurry or represent indistinguishable small fragments. In addition, 19% of the dataset is classified as liquid drops. After removal of fragments, blurry images, and cloud drops, 38% of the remaining ice particles are largely intersecting the image border (≥10% cutoff) and therefore are considered unusable because of the inability to properly classify and dimensionalize. After this filtering, an unprecedented database of 1 560 364 images across all campaigns is available for parameter extraction and bulk statistics on specific particle types in a wide variety of storm systems, which can act to improve the current state of microphysical parameterizations.
Background: Health authorities can minimize the impact of an emergent infectious disease outbreak through effective and timely risk communication, which can build trust and adherence to subsequent behavioral messaging. Monitoring the psychological impacts of an outbreak, as well as public adherence to such messaging, is also important for minimizing long-term effects of an outbreak. Objective: We used social media data from Twitter to identify human behaviors relevant to COVID-19 transmission, as well as the perceived impacts of COVID-19 on individuals, as a first step toward real-time monitoring of public perceptions to inform public health communications. Methods: We developed a coding schema for 6 categories and 11 subcategories, which included both a wide number of behaviors as well codes focused on the impacts of the pandemic (eg, economic and mental health impacts). We used this to develop training data and develop supervised learning classifiers for classes with sufficient labels. Classifiers that performed adequately were applied to our remaining corpus, and temporal and geospatial trends were assessed. We compared the classified patterns to ground truth mobility data and actual COVID-19 confirmed cases to assess the signal achieved here. Results: We applied our labeling schema to approximately 7200 tweets. The worst-performing classifiers had F1 scores of only 0.18 to 0.28 when trying to identify tweets about monitoring symptoms and testing. Classifiers about social distancing, however, were much stronger, with F1 scores of 0.64 to 0.66. We applied the social distancing classifiers to over 228 million tweets. We showed temporal patterns consistent with real-world events, and we showed correlations of up to –0.5 between social distancing signals on Twitter and ground truth mobility throughout the United States. Conclusions: Behaviors discussed on Twitter are exceptionally varied. Twitter can provide useful information for parameterizing models that incorporate human behavior, as well as for informing public health communication strategies by describing awareness of and compliance with suggested behaviors.
We consider two streams of data or measurements with disparate qualities and time resolutions that need to be classified. The first stream consists of higher quality data at a coarser time resolution, and the other consists of lower quality data at a finer time resolution. We present a fuser-switch method that fuses the set of classifiers of each stream separately and switches between them. We show that this method provides classification decisions at a finer time resolution with superior detection and false alarm probabilities compared to individual classifiers, under the statistical independence and time resolution ratio conditions. When classifiers are trained using machine learning methods, we show that this superior performance is guaranteed with a confidence probability specified by the classifiers' generalization equations. We use these results to provide analytical foundations for previous practical results that achieved significant performance improvements in classifying Pu/Np target dissolution events at a radiochemical processing facility.
Abstract The Red Snapper Lutjanus campechanus is a structure‐associated species occurring across a wide depth range in the northern Gulf of Mexico. We used the random forest machine learning algorithm to understand which habitat and individual fish characteristics could predict reproductive parameters of female Red Snapper. We evaluated fish captured from 2016 to 2018 on three artificial structure types with various structure heights at depths of 100 m or less. Overall, we found that depth and month were important predictors for most reproductive parameters, but the type of structure (artificial reefs, oil platforms, and rigs‐to‐reefs structures) was not important. Maturity was correctly classified in 88.9% of the cases when using the random forest ensemble model, with important predictors including FL, depth, structure height, and month of collection. Spawning seasonality (measured as gonadosomatic index [GSI]) was correctly classified in 59.5% of the cases when using histology reproductive phase, FL, month, and depth variables. Reproductively active or inactive females were correctly classified in 89.3% of the cases using GSI, month, FL, and depth, while females in the developing versus spawning capable phases were correctly classified in 82.2% of the cases using GSI, FL, month, and depth. Histological indicators that show potential spawning within a 36‐h period were correctly classified 61.5% of the time, with the best predictors being depth, FL, GSI, and month. Stepwise regression indicated that month was the only factor that significantly predicted contrasts in relative batch fecundity, with significantly greater values in August compared to all other months. Our findings suggest that female Red Snapper reproductive effort is not consistently or well predicted by artificial structure type or height but that a combination of fish FL, month, and depth can predict reproductive characteristics of female Red Snapper.
Context. In modern astronomy, machine learning has proved to be efficient and effective in mining big data from the newest telescopes. Aims. In this study, we construct a supervised machine-learning algorithm to classify the objects in the Javalambre Photometric Local Universe Survey first data release (J-PLUS DR1). Methods. The sample set is featured with 12-waveband photometry and labeled with spectrum-based catalogs, including Sloan Digital Sky Survey spectroscopic data, the Large Sky Area Multi-Object Fiber Spectroscopic Telescope, and VERONCAT – the Veron Catalog of Quasars & AGN. The performance of the classifier is presented with the applications of blind test validations based on RAdial Velocity Extension, the Kepler Input Catalog, the Two Micron All Sky Survey Redshift Survey, and the UV-bright Quasar Survey. A new algorithm was applied to constrain the potential extrapolation that could decrease the performance of the machine-learning classifier. Results. The accuracies of the classifier are 96.5% in the blind test and 97.0% in training cross-validation. The F1-scores for each class are presented to show the balance between the precision and the recall of the classifier. We also discuss different methods to constrain the potential extrapolation.
We describe a novel application of the end-to-end deep learning technique to the task of discriminating top quark-initiated jets from those originating from the hadronization of a light quark or a gluon. The end-to-end deep learning technique combines deep learning algorithms and low-level detector representation of the high-energy collision event. In this study, we use lowlevel detector information from the simulated CMS Open Data samples to construct the top jet classifiers. To optimize classifier performance we progressively add low-level information from the CMS tracking detector, including pixel detector reconstructed hits and impact parameters, and demonstrate the value of additional tracking information even when no new spatial structures are added. Relying only on calorimeter energy deposits and reconstructed pixel detector hits, the end-to-end classifier achieves a ROC-AUC score of 0.975±0.002 for the task of classifying boosted top quark jets. After adding derived track quantities, the classifier ROC-AUC score increases to 0.9824±0.0013, serving as the first performance benchmark for these CMS Open Data samples.
Abstract Motivation Two key steps in the analysis of uncultured viruses recovered from metagenomes are the taxonomic classification of the viral sequences and the identification of putative host(s). Both steps rely mainly on the assignment of viral proteins to orthologs in cultivated viruses. Viral Protein Families (VPFs) can be used for the robust identification of new viral sequences in large metagenomics datasets. Despite the importance of VPF information for viral discovery, VPFs have not yet been explored for determining viral taxonomy and host targets. Results In this work, we classified the set of VPFs from the IMG/VR database and developed VPF-Class. VPF-Class is a tool that automates the taxonomic classification and host prediction of viral contigs based on the assignment of their proteins to a set of classified VPFs. Applying VPF-Class on 731K uncultivated virus contigs from the IMG/VR database, we were able to classify 363K contigs at the genus level and predict the host of over 461K contigs. In the RefSeq database, VPF-class reported an accuracy of nearly 100% to classify dsDNA, ssDNA and retroviruses, at the genus level, considering a membership ratio and a confidence score of 0.2. The accuracy in host prediction was 86.4%, also at the genus level, considering a membership ratio of 0.3 and a confidence score of 0.5. And, in the prophages dataset, the accuracy in host prediction was 86% considering a membership ratio of 0.6 and a confidence score of 0.8. Moreover, from the Global Ocean Virome dataset, over 817K viral contigs out of 1 million were classified. Availability and implementation The implementation of VPF-Class can be downloaded from https://github.com/biocom-uib/vpf-tools. Supplementary information Supplementary data are available at Bioinformatics online.
ABSTRACT The arrival of the Vera C. Rubin Observatory’s Legacy Survey of Space and Time (LSST), Euclid-Wide and Roman wide-area sensitive surveys will herald a new era in strong lens science in which the number of strong lenses known is expected to rise from $\mathcal {O}(10^3)$ to $\mathcal {O}(10^5)$. However, current lens-finding methods still require time-consuming follow-up visual inspection by strong lens experts to remove false positives which is only set to increase with these surveys. In this work, we demonstrate a range of methods to produce calibrated probabilities to help determine the veracity of any given lens candidate. To do this we use the classifications from citizen science and multiple neural networks for galaxies selected from the Hyper Suprime-Cam survey. Our methodology is not restricted to particular classifier types and could be applied to any strong lens classifier which produces quantitative scores. Using these calibrated probabilities, we generate an ensemble classifier, combining citizen science, and neural network lens finders. We find such an ensemble can provide improved classification over the individual classifiers. We find a false-positive rate of 10−3 can be achieved with a completeness of 46 per cent, compared to 34 per cent for the best individual classifier. Given the large number of galaxy–galaxy strong lenses anticipated in LSST, such improvement would still produce significant numbers of false positives, in which case using calibrated probabilities will be essential for population analysis of large populations of lenses and to help prioritize candidates for follow-up.
Here we describe a novel application of the end-to-end deep learning technique to the task of discriminating top quark-initiated jets from those originating from the hadronization of a light quark or a gluon. The end-to-end deep learning technique uses low-level detector representation of high-energy collision event as inputs to deep learning algorithms. In this study, we use low-level detector information from the simulated Compact Muon Solenoid (CMS) open data samples to construct the top jet classifiers. To optimize classifier performance we progressively add low-level information from the CMS tracking detector, including pixel detector reconstructed hits and impact parameters, and demonstrate the value of additional tracking information even when no new spatial structures are added. Relying only on calorimeter energy deposits and reconstructed pixel detector hits, the end-to-end classifier achieves an area under the receiver operator curve (AUC) score of 0.975 ± 0.002 for the task of classifying boosted top quark jets. After adding derived track quantities, the classifier AUC score increases to 0.9824 ± 0.0013, serving as the first performance benchmark for these CMS open data samples.