Feature engineering is one of the most important and time consuming tasks in predictive analytics projects. It involves understanding domain knowledge and data exploration to discover relevant hand-crafted features from raw data. In this paper, we introduce a system called One Button Machine, or OneBM for short, which automates feature discovery in relational databases. OneBM automatically performs a key activity of data scientists, namely, joining of database tables and applying advanced data transformations to extract useful features from data. We validated OneBM in Kaggle competitions in which OneBM achieved performance as good as top 16 to 24 data scientists in three Kaggle competitions. More importantly, OneBM outperformed the state-of-the-art system in a Kaggle competition in terms of prediction accuracy and ranking on Kaggle leaderboard. The results show that OneBM can be useful for both data scientists and non-experts. It helps data scientists reduce data exploration time allowing them to try and error many ideas in short time. On the other hand, it enables non-experts, who are not familiar with data science, to quickly extract value from their data with a little effort, time and cost.
Data Science Machine (DSM) @cite_10 is the first system that automates feature engineering from a database of multiple tables. This feature engineering approach is based on an assumption that, for a given relational database, data scientists usually search for features via: 1. generating SQL queries to collect data for each example in the training set and 2. transforming the data into features. DSM automates the given two steps via creating an entity graph and performing automatic SQL query generation to join the tables along different paths of the entity graph. It converts the collected results into features using a predefined set of simple aggregation functions.
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In this paper, we develop the Data Science Machine, which is able to derive predictive models from raw data automatically. To achieve this automation, we first propose and develop the Deep Feature Synthesis algorithm for automatically generating features for relational datasets. The algorithm follows relationships in the data to a base field, and then sequentially applies mathematical functions along that path to create the final feature. Second, we implement a generalizable machine learning pipeline and tune it using a novel Gaussian Copula process based approach. We entered the Data Science Machine in 3 data science competitions that featured 906 other data science teams. Our approach beats 615 teams in these data science competitions. In 2 of the 3 competitions we beat a majority of competitors, and in the third, we achieved 94 of the best competitor's score. In the best case, with an ongoing competition, we beat 85.6 of the teams and achieved 95.7 of the top submissions score. Data Stream Management Systems (DSMS) have attracted much interest from the database community, and extensions of relational database languages were proposed for expressing continuous queries on data streams. However, while relational databases were built on the solid bedrock of logic, the same cannot be said for DSMS. Thus, a logic-based reconstruction of DSMS languages and their unique computational model is long overdue. Indeed, the banning of blocking queries and the fact that stream data are ordered by their arrival timestamps represent major new aspects that have yet to be characterized by simple theories. In this paper, we show that these new requirements can be modeled using the familiar deductive database concepts of closed-world assumption and explicit local stratification. Besides its obvious theoretical interest, this approach leads to the design of a powerful version of Datalog for data streams. This language is called Streamlog and takes the query and application languages of DSMS to new levels of expressive power, by removing the unnecessary limitations that severely impair current commercial systems and research prototypes. Populating large-scale structured databases from unstructured sources is a critical and challenging task in data analytics. As automated feature engineering methods grow increasingly prevalent, constructing sufficiently large labeled training sets has become the primary hurdle in building machine learning information extraction systems. In light of this, we have taken a new approach called data programming [7]. Rather than hand-labeling data, in the data programming paradigm, users generate large amounts of noisy training labels by programmatically encoding domain heuristics as simple rules. Using this approach over more traditional distant supervision methods and fully supervised approaches using labeled data, we have been able to construct knowledge base systems more rapidly and with higher quality. Since the ability to quickly prototype, evaluate, and debug these rules is a key component of this paradigm, we introduce DDLite, an interactive development framework for data programming. This paper reports feedback collected from DDLite users across a diverse set of entity extraction tasks. We share observations from several DDLite hackathons in which 10 biomedical researchers prototyped information extraction pipelines for chemicals, diseases, and anatomical named entities. Initial results were promising, with the disease tagging team obtaining an F1 score within 10 points of the state-of-the-art in only a single day-long hackathon's work. Our key insights concern the challenges of writing diverse rule sets for generating labels, and exploring training data. These findings motivate several areas of active data programming research. Big data bring new opportunities for methods that efficiently summarize and automatically extract knowledge from such compendia. While both supervised learning algorithms and unsupervised clustering algorithms have been successfully applied to biological data, they are either dependent on known biology or limited to discerning the most significant signals in the data. Here we present denoising autoencoders (DAs), which employ a data-defined learning objective independent of known biology, as a method to identify and extract complex patterns from genomic data. We evaluate the performance of DAs by applying them to a large collection of breast cancer gene expression data. Results show that DAs successfully construct features that contain both clinical and molecular information. There are features that represent tumor or normal samples, estrogen receptor (ER) status, and molecular subtypes. Features constructed by the autoencoder generalize to an independent dataset collected using a distinct experimental platform. By integrating data from ENCODE for feature interpretation, we discover a feature representing ER status through association with key transcription factors in breast cancer. We also identify a feature highly predictive of patient survival and it is enriched by FOXM1 signaling pathway. The features constructed by DAs are often bimodally distributed with one peak near zero and another near one, which facilitates discretization. In summary, we demonstrate that DAs effectively extract key biological principles from gene expression data and summarize them into constructed features with convenient properties. We improved wordification methodology and provide a formal framework and pseudo code.We statistically evaluated comparable algorithms on multiple relational databases.Experiments show favorable results in terms of accuracy and efficiency.Feature simplicity is compensated by n-gram construction and by feature weighting.We implemented the full experimental workflow in a data mining platform ClowdFlows. Inductive Logic Programming (ILP) and Relational Data Mining (RDM) address the task of inducing models or patterns from multi-relational data. One of the established approaches to RDM is propositionalization, characterized by transforming a relational database into a single-table representation. This paper presents a propositionalization technique called wordification which can be seen as a transformation of a relational database into a corpus of text documents. Wordification constructs simple, easy to understand features, acting as words in the transformed Bag-Of-Words representation. This paper presents the wordification methodology, together with an experimental comparison of several propositionalization approaches on seven relational datasets. The main advantages of the approach are: simple implementation, accuracy comparable to competitive methods, and greater scalability, as it performs several times faster on all experimental databases. Furthermore, the wordification methodology and the evaluation procedure are implemented as executable workflows in the web-based data mining platform ClowdFlows. The implemented workflows include also several other ILP and RDM algorithms, as well as the utility components that were added to the platform to enable access to these techniques to a wider research audience. Enterprise data analytics is a booming area in the data management industry. Many companies are racing to develop toolkits that closely integrate statistical and machine learning techniques with data management systems. Almost all such toolkits assume that the input to a learning algorithm is a single table. However, most relational datasets are not stored as single tables due to normalization. Thus, analysts often perform key-foreign key joins before learning on the join output. This strategy of learning after joins introduces redundancy avoided by normalization, which could lead to poorer end-to-end performance and maintenance overheads due to data duplication. In this work, we take a step towards enabling and optimizing learning over joins for a common class of machine learning techniques called generalized linear models that are solved using gradient descent algorithms in an RDBMS setting. We present alternative approaches to learn over a join that are easy to implement over existing RDBMSs. We introduce a new approach named factorized learning that pushes ML computations through joins and avoids redundancy in both I O and computations. We study the tradeoff space for all our approaches both analytically and empirically. Our results show that factorized learning is often substantially faster than the alternatives, but is not always the fastest, necessitating a cost-based approach. We also discuss extensions of all our approaches to multi-table joins as well as to Hive. There is an arms race in the data management industry to support analytics, in which one critical step is feature selection, the process of selecting a feature set that will be used to build a statistical model. Analytics is one of the biggest topics in data management, and feature selection is widely regarded as the most critical step of analytics; thus, we argue that managing the feature selection process is a pressing data management challenge. We study this challenge by describing a feature-selection language and a supporting prototype system that builds on top of current industrial, R-integration layers. From our interactions with analysts, we learned that feature selection is an interactive, human-in-the-loop process, which means that feature selection workloads are rife with reuse opportunities. Thus, we study how to materialize portions of this computation using not only classical database materialization optimizations but also methods that have not previously been used in database optimization, including structural decomposition methods (like QR factorization) and warmstart. These new methods have no analog in traditional SQL systems, but they may be interesting for array and scientific database applications. On a diverse set of data sets and programs, we find that traditional database-style approaches that ignore these new opportunities are more than two orders of magnitude slower than an optimal plan in this new tradeoff space across multiple R-backends. Furthermore, we show that it is possible to build a simple cost-based optimizer to automatically select a near-optimal execution plan for feature selection. We present a novel probabilistic approach for fitting a statistical model to an image. A 3D Morphable Model (3DMM) of faces is interpreted as a generative (Top-Down) Bayesian model. Random Forests are used as noisy detectors (Bottom-Up) for the face and facial landmark positions. The Top-Down and Bottom-Up parts are then combined using a Data-Driven Markov Chain Monte Carlo Method (DDMCMC). As core of the integration, we use the Metropolis-Hastings algorithm which has two main advantages. First, the algorithm can handle unreliable detections and therefore does not need the detectors to take an early and possible wrong hard decision before fitting. Second, it is open for integration of various cues to guide the fitting process. Based on the proposed approach, we implemented a completely automatic, pose and illumination invariant face recognition application. We are able to train and test the building blocks of our application on different databases. The system is evaluated on the Multi-PIE database and reaches state of the art performance. We introduce a type of Deep Boltzmann Machine (DBM) that is suitable for extracting distributed semantic representations from a large unstructured collection of documents. We overcome the apparent difficulty of training a DBM with judicious parameter tying. This enables an efficient pretraining algorithm and a state initialization scheme for fast inference. The model can be trained just as efficiently as a standard Restricted Boltzmann Machine. Our experiments show that the model assigns better log probability to unseen data than the Replicated Softmax model. Features extracted from our model outperform LDA, Replicated Softmax, and DocNADE models on document retrieval and document classification tasks. Objective A system that translates narrative text in the medical domain into structured representation is in great demand. The system performs three sub-tasks: concept extraction, assertion classification, and relation identification. @PARASPLIT Design The overall system consists of five steps: (1) pre-processing sentences, (2) marking noun phrases (NPs) and adjective phrases (APs), (3) extracting concepts that use a dosage-unit dictionary to dynamically switch two models based on Conditional Random Fields (CRF), (4) classifying assertions based on voting of five classifiers, and (5) identifying relations using normalized sentences with a set of effective discriminating features. @PARASPLIT Measurements Macro-averaged and micro-averaged precision, recall and F-measure were used to evaluate results. @PARASPLIT Results The performance is competitive with the state-of-the-art systems with micro-averaged F-measure of 0.8489 for concept extraction, 0.9392 for assertion classification and 0.7326 for relation identification. @PARASPLIT Conclusions The system exploits an array of common features and achieves state-of-the-art performance. Prudent feature engineering sets the foundation of our systems. In concept extraction, we demonstrated that switching models, one of which is especially designed for telegraphic sentences, improved extraction of the treatment concept significantly. In assertion classification, a set of features derived from a rule-based classifier were proven to be effective for the classes such as conditional and possible. These classes would suffer from data scarcity in conventional machine-learning methods. In relation identification, we use two-staged architecture, the second of which applies pairwise classifiers to possible candidate classes. This architecture significantly improves performance. Selection of the right space parts is an essential step during the design of complex engineering systems and requires information that is typically embedded in unstructured documents like datasheets, Interface Control Documents (ICDs) and technical manuals. Satsearch (https: satsearch.co) aims to consolidate global space supply chain information within a single platform, by converting unstructured datasheets into machine-readable, human-readable, electronic datasheets (EDS). After satsearch’s initial, manual efforts at generating EDS from source datasheets for space parts, they realized that the process is not scalable. A possible solution is to employ knowledge base information extraction systems. The Design Engineering Assistant (DEA) team from the University of Strathclyde is currently working on the automation of the extraction of information from unstructured documents (e.g. textbooks, reports, datasheets, research papers, etc.) through the development of an expert system. This paper summarizes the approach and outcomes of a feasibility study for the DEA, assessing benefits and obstacles for the implementation of a fully-automated information extraction process, focusing at this stage only on datasheets for space parts for preliminary mission design. We introduce a Deep Boltzmann Machine model suitable for modeling and extracting latent semantic representations from a large unstructured collection of documents. We overcome the apparent difficulty of training a DBM with judicious parameter tying. This parameter tying enables an efficient pretraining algorithm and a state initialization scheme that aids inference. The model can be trained just as efficiently as a standard Restricted Boltzmann Machine. Our experiments show that the model assigns better log probability to unseen data than the Replicated Softmax model. Features extracted from our model outperform LDA, Replicated Softmax, and DocNADE models on document retrieval and document classification tasks. A methodical procedure for organization of fault detection experiments for synchronous sequential machines possessing distinguishing sequences (DS) is given. The organization is based on the transition checking approach. The checking experiment is considered in three concatenative parts: 1) the initial sequence which brings the machine under test into a specific state, 2) the α-sequence to recognize all the states and to establish the information about the next states under the input DS, and 3) the β-sequence to check all the individual transitions in the state table. Designing computer programs to automatically categorize images using low-level features is a challenging research topic in computer vision. In this paper, we present a new learning technique, which extends Multiple-Instance Learning (MIL), and its application to the problem of region-based image categorization. Images are viewed as bags, each of which contains a number of instances corresponding to regions obtained from image segmentation. The standard MIL problem assumes that a bag is labeled positive if at least one of its instances is positive; otherwise, the bag is negative. In the proposed MIL framework, DD-SVM, a bag label is determined by some number of instances satisfying various properties. DD-SVM first learns a collection of instance prototypes according to a Diverse Density (DD) function. Each instance prototype represents a class of instances that is more likely to appear in bags with the specific label than in the other bags. A nonlinear mapping is then defined using the instance prototypes and maps every bag to a point in a new feature space, named the bag feature space. Finally, standard support vector machines are trained in the bag feature space. We provide experimental results on an image categorization problem and a drug activity prediction problem. Science applications are accumulating an ever-increasing amount of multidimensional data. Although some of it can be processed in a relational database, much of it is better suited to array-based engines. As such, it is important to optimize the query processing of these systems. This paper focuses on efficient query processing of join operations within an array database. These engines invariably chunk'' their data into multidimensional tiles that they use to efficiently process spatial queries. As such, traditional relational algorithms need to be substantially modified to take advantage of array tiles. Moreover, most n-dimensional science data is unevenly distributed in array space because its underlying observations rarely follow a uniform pattern. It is crucial that the optimization of array joins be skew-aware. In addition, owing to the scale of science applications, their query processing usually spans multiple nodes. This further complicates the planning of array joins. In this paper, we introduce a join optimization framework that is skew-aware for distributed joins. This optimization consists of two phases. In the first, a logical planner selects the query's algorithm (e.g., merge join), the granularity of the its tiles, and the reorganization operations needed to align the data. The second phase implements this logical plan by assigning tiles to cluster nodes using an analytical cost model. Our experimental results, on both synthetic and real-world data, demonstrate that this optimization framework speeds up array joins by up to 2.5X in comparison to the baseline. Scientific experiments and large-scale simulations produce massive amounts of data. Many of these scientific datasets are arrays, and are stored in file formats such as HDF5 and NetCDF. Although scientific data management systems, such as SciDB, are designed to manipulate arrays, there are challenges in integrating these systems into existing analysis workflows. Major barriers include the expensive task of preparing and loading data before querying, and converting the final results to a format that is understood by the existing post-processing and visualization tools. As a consequence, integrating a data management system into an existing scientific data analysis workflow is time-consuming and requires extensive user involvement. In this paper, we present the design of a new scientific data analysis system that efficiently processes queries directly over data stored in the HDF5 file format. This design choice eliminates the tedious and error-prone data loading process, and makes the query results readily available to the next processing steps of the analysis workflow. Our design leverages the increasing main memory capacities found in supercomputers through bitmap indexing and in-memory query execution. In addition, query processing over the HDF5 data format can be effortlessly parallelized to utilize the ample concurrency available in large-scale supercomputers and modern parallel file systems. We evaluate the performance of our system on a large supercomputing system and experiment with both a synthetic dataset and a real cosmology observation dataset. Our system frequently outperforms the relational database system that the cosmology team currently uses, and is more than 10X faster than Hive when processing data in parallel. Overall, by eliminating the data loading step, our query processing system is more effective in supporting in situ scientific analysis workflows. Extracting automatically the complex set of features composing real high-dimensional data is crucial for achieving high performance in machine--learning tasks. Restricted Boltzmann Machines (RBM) are empirically known to be efficient for this purpose, and to be able to generate distributed and graded representations of the data. We characterize the structural conditions (sparsity of the weights, low effective temperature, nonlinearities in the activation functions of hidden units, and adaptation of fields maintaining the activity in the visible layer) allowing RBM to operate in such a compositional phase. Evidence is provided by the replica analysis of an adequate statistical ensemble of random RBMs and by RBM trained on the handwritten digits dataset MNIST. Continued reliance on human operators for managing data centers is a major impediment for them from ever reaching extreme dimensions. Large computer systems in general, and data centers in particular, will ultimately be managed using predictive computational and executable models obtained through data-science tools, and at that point, the intervention of humans will be limited to setting high-level goals and policies rather than performing low-level operations. Data-driven autonomics, where management and control are based on holistic predictive models that are built and updated using generated data, opens one possible path towards limiting the role of operators in data centers. In this paper, we present a data-science study of a public Google dataset collected in a 12K-node cluster with the goal of building and evaluating a predictive model for node failures. We use BigQuery, the big data SQL platform from the Google Cloud suite, to process massive amounts of data and generate a rich feature set characterizing machine state over time. We describe how an ensemble classifier can be built out of many Random Forest classifiers each trained on these features, to predict if machines will fail in a future 24-hour window. Our evaluation reveals that if we limit false positive rates to 5 , we can achieve true positive rates between 27 and 88 with precision varying between 50 and 72 . We discuss the practicality of including our predictive model as the central component of a data-driven autonomic manager and operating it on-line with live data streams (rather than off-line on data logs). All of the scripts used for BigQuery and classification analyses are publicly available from the authors' website. Continued reliance on human operators for managing data centers is a major impediment for them from ever reaching extreme dimensions. Large computer systems in general, and data centers in particular, will ultimately be managed using predictive computational and executable models obtained through data-science tools, and at that point, the intervention of humans will be limited to setting high-level goals and policies rather than performing low-level operations. Data-driven autonomics, where management and control are based on holistic predictive models that are built and updated using generated data, opens one possible path towards limiting the role of operators in data centers. In this paper, we present a data-science study of a public Google dataset collected in a 12K-node cluster with the goal of building and evaluating a predictive model for node failures. We use BigQuery, the big data SQL platform from the Google Cloud suite, to process massive amounts of data and generate a rich feature set characterizing machine state over time. We describe how an ensemble classifier can be built out of many Random Forest classifiers each trained on these features, to predict if machines will fail in a future 24-hour window. Our evaluation reveals that if we limit false positive rates to 5 , we can achieve true positive rates between 27 and 88 with precision varying between 50 and 72 . We discuss the practicality of including our predictive model as the central component of a data-driven autonomic manager and operating it on-line with live data streams (rather than off-line on data logs). All of the scripts used for BigQuery and classification analyses are publicly available from the authors' website. In this paper, a novel automatic image annotation system is proposed, which integrates two sets of support vector machines (SVMs), namely the multiple instance learning (MIL)-based and global-feature-based SVMs, for annotation. The MIL-based bag features are obtained by applying MIL on the image blocks, where the enhanced diversity density (DD) algorithm and a faster searching algorithm are applied to improve the efficiency and accuracy. They are further input to a set of SVMs for finding the optimum hyperplanes to annotate training images. Similarly, global color and texture features, including color histogram and modified edge histogram, are fed into another set of SVMs for categorizing training images. Consequently, two sets of image features are constructed for each test image and are, respectively, sent to the two sets of SVMs, whose outputs are incorporated by an automatic weight estimation method to obtain the final annotation results. Our proposed annotation approach demonstrates a promising performance for an image database of 12000 general-purpose images from COREL, as compared with some current peer systems in the literature.