Personalized Recommendation using Similarity Powered Pairwise Amplifier Network

SummaryAccurate prediction of the solubility of chemical substances in solvents remains a challenge. The sparsity of high-quality solubility data is recognized as the biggest hurdle in the development of robust data-driven methods for practical use. Nonetheless, the effects of the quality and quantity of data on aqueous solubility predictions have not yet been scrutinized. In this study, the roles of the size and the quality of data sets on the performances of the solubility prediction models are unraveled, and the concepts of actual and observed performances are introduced. In an effort to curtail the gap between actual and observed performances, a quality-oriented data selection method, which evaluates the quality of data and extracts the most accurate part of it through statistical validation, is designed. Applying this method on the largest publicly available solubility database and using a consensus machine learning approach, a top-performing solubility prediction model is achieved.

Study question Can a machine learning (ML) model, developed using modern neural network architecture produce comparable annotation data; utilisable for algorithmic outcome prediction, to manual time-lapse annotations? Summary answer The model automatically annotated unseen embryos with comparable results to manual methods, generating morphokinetic data to enable comparably predictive outputs from an embryo selection algorithm. What is known already The application of artificial intelligence across healthcare industries, including fertility, is increasing. Several ML models are available that seek to generate or analyse embryo images and morphokinetic data, and to determine embryo viability potential. Along with photographic images, the use of time-lapse in IVF laboratories has amassed numeric data, resulting predominantly from annotated manual assessment of images over time. Embryo annotation practice is variable in quality, can be subjective and is time-consuming; commonly taking several minutes per embryo. The development of rapid, accurate automatic annotation would represent a significant time-saving as well as an increase in reproducibility and accuracy. Study design, size, duration Multicentre quality assured annotation data from 63,383 time-lapse monitored embryos (EmbryoScope®), comprising over 400 million individual images, were used to train a ML model to automatically generate morphokinetic annotations. Data was derived from 8 UK clinics within a cohesive group between 2012-2021. Accuracy was assessed using 900 unseen embryos (with live birth outcome) by comparing the output of an established in-house, prospectively validated embryo selection model when the input was either ML-automated, or manual annotations. Participants/materials, setting, methods Multi-focal plane images were processed on the Azure cloud (Microsoft) and resampled to 300x300 pixels. A Laplacian-based focal stacking algorithm merged frames into a single image. The model consisted of an EfficientNetB4 Convolutional Neural Network classifier to extract features and classify the stage of embryo images. A Temporal Convolutional Network interpreted a time-series of image features; producing annotations from pronuclear fading through to blastocyst. Soft localisation loss function used QA data to integrate annotation subjectivities. Main results and the role of chance The ML model rapidly and automatically generated annotations. Efficacy and comparability of the ML model to automate reliable, utilisable annotations was demonstrated by comparison with manual annotation data and the ML model’s ability to auto-generate annotations which could be used to predict live birth by providing annotation data to an established, validated in house embryo selection model. Live birth-predictive capability was measured, and benchmarked against manual annotation, using the area under the receiver operating characteristic curve (AUC). When tested on time-lapse images, collected from pronuclear fading to full blastulation, representing 900 previously unseen, transferred blastocysts where live birth outcomes were blinded, the in-house developed auto-annotation ML model resulted in an AUC of 0.686 compared with 0.661 for manual annotations, for live birth prediction. Auto annotation using the developed model took only milliseconds to complete per embryo. The developed auto-annotation model, built and tested on large data, is considered suitable for productionisation with the aim of being validated and integrated into an application to support IVF laboratory practice. Limitations, reasons for caution Whilst this model was trained to recognise key morphokinetic events, there are other morphokinetic variables that may be useful in the prediction of live birth and further improve embryo selection, or deselection, ability. Akin to manual interpretation, some embryos may fail to be annotated or need second opinion. Wider implications of the findings There is increasing evidence supporting the application of ML to utilise big data from time-lapse imaging and fertility care generally. Whilst promising benefits to IVF clinics and patients, responsible use of data is required alongside large high-quality datasets, and rigorous validation, to ensure safe and robust applications. Trial registration number N/A

Many pharmacologic studies record data as binary, yes-or-no, variables with analysis using logistic regression. In a previous study, it was shown that estimates of C50, the drug concentration associated with a 50% probability of drug effect, were unbiased, whereas estimates of gamma, the term describing the steepness of the concentration-effect relationship, were biased when sparse data were naively pooled for analysis. In this study, it was determined whether mixed-effects analysis improved the accuracy of parameter estimation. Pharmacodynamic studies with binary, yes-or-no, responses were simulated and analyzed with NONMEM. The bias and coefficient of variation of C50 and gamma estimates were determined as a function of numbers of patients in the simulated study, the number of simulated data points per patient, and the "true" value of gamma. In addition, 100 sparse binary human data sets were generated from an evaluation of midazolam for postoperative sedation of adult patients undergoing cardiac surgery by random selection of a single data point (sedation score vs. midazolam plasma concentration) from each of the 30 patients in the study. C50 and gamma were estimated for each of these data sets by using NONMEM and were compared with the estimates from the complete data set of 656 observations. Estimates of C50 were unbiased, even for sparse data (one data point per patient) with coefficients of variation of 30-50%. Estimates of gamma were highly biased for sparse data for all values of gamma greater than 1, and the value of gamma was overestimated. Unbiased estimation of gamma required 10 data points per patient. The coefficient of variation of gamma estimates was greater than that of the C50 estimates. Clinical data for sedation with midazolam confirmed the simulation results, showing an overestimate of gamma with sparse data. Although accurate estimations of C50 from sparse binary data are possible, estimates of gamma are biased. Data with 10 or more observations per patient is necessary for accurate estimations of gamma.

Frequent Itemset Mining is one of the most investigated fields of data mining. It is expensive to mine frequent itemsets for a large scale data set. Especially when some data is added into the data set, it is still time-consuming from the scratch to re-compute the complete data set to update the frequent itemsets of the data set. Aiming to improve the performance of frequent itemset mining for large scale and dynamic data set, we propose a new incremental Apriori algorithm based on Spark. It reuses existing results from previous computation to modify the frequent itemsets according to the newly added data, which avoid massive recomputation. The newly proposed algorithm also takes full advantage of distributed resources with the support of Spark. Analysis in theory ensures that the newly proposed algorithm is correct. Experiments on the real-world data set demonstrate that the newly proposed algorithm effectively avoids reduplicated computation and improves the performance of frequent itemset mining with no additional storage overhead.

Improving autocoding performance of rare categories in injury classification: Is more training data or filtering the solution?

The advent of modern genotyping technologies has revolutionized genomic selection in animal breeding. Large marker datasets have shown several drawbacks for traditional genomic prediction methods in terms of flexibility, accuracy, and computational power. Recently, the application of machine learning models in animal breeding has gained a lot of interest due to their tremendous flexibility and their ability to capture patterns in large noisy datasets. Here, we present a general overview of a handful of machine learning algorithms and their application in genomic prediction to provide a meta-picture of their performance in genomic estimated breeding values estimation, genotype imputation, and feature selection. Finally, we discuss a potential adoption of machine learning models in genomic prediction in developing countries. The results of the reviewed studies showed that machine learning models have indeed performed well in fitting large noisy data sets and modeling minor nonadditive effects in some of the studies. However, sometimes conventional methods outperformed machine learning models, which confirms that there's no universal method for genomic prediction. In summary, machine learning models have great potential for extracting patterns from single nucleotide polymorphism datasets. Nonetheless, the level of their adoption in animal breeding is still low due to data limitations, complex genetic interactions, a lack of standardization and reproducibility, and the lack of interpretability of machine learning models when trained with biological data. Consequently, there is no remarkable outperformance of machine learning methods compared to traditional methods in genomic prediction. Therefore, more research should be conducted to discover new insights that could enhance livestock breeding programs.

Modelling sparse and large data sets is highly in demand yet challenging in recommender systems. With the computation only on the non-zero ratings, Poisson Factorization (PF) enabled by variational inference has shown its high efficiency in scalable recommendation, e.g., modeling millions of ratings. However, as PF learns the ratings by individual users on items with the Gamma distribution, it cannot capture the coupling relations between users (items) and the rating popularity (i.e., favorable rating scores that are given to one item) and rating sparsity (i.e., those users (items) with many zero ratings) for one item (user). This work proposes Coupled Poisson Factorization (CPF) to learn the couplings between users (items), and the user/item attributes (i.e., metadata) are integrated into CPF to form the Metadata-integrated CPF (mCPF) to not only handle sparse but also popular ratings in very large-scale data. Our empirical results show that the proposed models significantly outperform PF and address the key limitations in PF for scalable recommendation.

This paper introduces a hidden topic-based framework for processing short and sparse documents (e.g., search result snippets, product descriptions, book/movie summaries, and advertising messages) on the Web. The framework focuses on solving two main challenges posed by these kinds of documents: 1) data sparseness and 2) synonyms/homonyms. The former leads to the lack of shared words and contexts among documents while the latter are big linguistic obstacles in natural language processing (NLP) and information retrieval (IR). The underlying idea of the framework is that common hidden topics discovered from large external data sets (universal data sets), when included, can make short documents less sparse and more topic-oriented. Furthermore, hidden topics from universal data sets help handle unseen data better. The proposed framework can also be applied for different natural languages and data domains. We carefully evaluated the framework by carrying out two experiments for two important online applications (Web search result classification and matching/ranking for contextual advertising) with large-scale universal data sets and we achieved significant results.

Irregular computations over large-scale sparse data are prevalent in critical data applications and they have significant room for improvement on modern computer systems from the aspects of parallelism and data locality. We introduce new techniques to efficiently map large irregular computations onto modern multi-core systems with non-uniform memory access (NUMA) behavior. Our techniques are broadly applicable for irregular computations with multi-dimensional sparse arrays (or sparse tensors). We implement a static-cum-dynamic task scheduling scheme with low overhead for effective parallelization of sparse computations. We introduce locality-aware optimizations to the task scheduling mechanism that are driven by the sparse input data pattern. We evaluate our techniques using two popular sparse tensor decomposition methods that have wide applications in data mining, graph analysis, signal processing, and elsewhere. Our techniques not only improve parallel performance but also result in improved performance scalability with increasing number of cores. We achieve around 4–5x improvement in performance over existing parallel approaches and observe “scalable” parallel performance on modern multi-core systems with up to 32 processor cores. We take real sparse data sets as input to the sparse tensor computations and demonstrate the achieved improvements.

Advances in mass spectrometry-based proteomics have yielded a substantial mapping of the tyrosine phosphoproteome and thus provided an important step toward a systematic analysis of intracellular signaling networks in higher eukaryotes. In this study we decomposed an uncharacterized proteomics data set of 481 unique phosphotyrosine (Tyr(P)) peptides by sequence similarity to known ligands of the Src homology 2 (SH2) and the phosphotyrosine binding (PTB) domains. From 20 clusters we extracted 16 known and four new interaction motifs. Using quantitative mass spectrometry we pulled down Tyr(P)-specific binding partners for peptides corresponding to the extracted motifs. We confirmed numerous previously known interaction motifs and found 15 new interactions mediated by phosphosites not previously known to bind SH2 or PTB. Remarkably, a novel hydrophobic N-terminal motif ((L/V/I)(L/V/I)pY) was identified and validated as a binding motif for the SH2 domain-containing inositol phosphatase SHIP2. Our decomposition of the in vivo Tyr(P) proteome furthermore suggests that two-thirds of the Tyr(P) sites mediate interaction, whereas the remaining third govern processes such as enzyme activation and nucleic acid binding.

With the rapid growth of web technology and easy access of internet, online shopping has been increased. Now people express their opinions and share their experiences that greatly influence new buyers for purchasing products, thereby generating large data sets. This large data is very helpful for analyzing customer preference, needs and its behavior toward a product. Companies face the challenge of analyzing this sheer amount of data to extract customer opinion. To address this challenge, in this paper, we performed sentiment analysis on the customer review real-world data at phrase level to find out customer preference by analyzing subjective expressions. Then we calculated the strength of sentiment word to find out the intensity of each expression and applied clustering for placing the words in various clusters based on their intensity. We also compared the results of our technique with star-ranking given on the same dataset and found the drastic change in our results. We also provide a visual representation of our results to provide a clear insight of customer preference and behavior to help decision makers for better decision making.

Correlated anomaly detection (CAD) from streaming data is a type of group anomaly detection and an essential task in useful real-time data mining applications like botnet detection, financial event detection, industrial process monitor, etc. The primary approach for this type of detection in previous researches is based on principal score (PS) of divided batches or sliding windows by computing top eigenvalues of the correlation matrix, e.g. the Lanczos algorithm. However, this paper brings up the phenomenon of principal score degeneration for large data set, and then mathematically and practically prove current PS-based methods are likely to fail for CAD on large-scale streaming data even if the number of correlated anomalies grows with the data size at a reasonable rate; in reality, anomalies tend to be the minority of the data, and this issue can be more serious. We propose a framework with two novel randomized algorithms rPS and gPS for better detection of correlated anomalies from large streaming data of various correlation strength. The experiment shows high and balanced recall and estimated accuracy of our framework for anomaly detection from a large server log data set and a U.S. stock daily price data set in comparison to direct principal score evaluation and some other recent group anomaly detection algorithms. Moreover, our techniques significantly improve the computation efficiency and scalability for principal score calculation.

Chapter 20 - Query Suggestion with Large Scale Data

Individualized boosting learning for classification

Machine learning (ML) models based on a large data set of in-cylinder flow fields of an IC engine obtained by high-speed particle image velocimetry allow the identification of relevant flow structures underlying cycle-to-cycle variations of engine performance. To this end, deep feature learning is employed to train ML models that predict cycles of high and low in-cylinder maximum pressure. Deep convolutional autoencoders are self-supervised-trained to encode flow field features in low dimensional latent space. Without the limitations ascribable to manual feature engineering, ML models based on these learned features are able to classify high energy cycles already from the flow field during late intake and the compression stroke as early as 290 crank angle degrees before top dead center ([Formula: see text]) with a mean accuracy above chance level. The prediction accuracy from [Formula: see text] to [Formula: see text] is comparable to baseline ML approaches utilizing an extensive set of engineered features. Relevant flow structures in the compression stroke are revealed by feature analysis of ML models and are interpreted using conditional averaged flow quantities. This analysis unveils the importance of the horizontal velocity component of in-cylinder flows in predicting engine performance. Combining deep learning and conventional flow analysis techniques promises to be a powerful tool for ultimately revealing high-level flow features relevant to the prediction of cycle-to-cycle variations and further engine optimization.