The popularity of automated machine learning (AutoML) tools in different domains has increased over the past few years. Machine learning (ML) practitioners use AutoML tools to automate and optimize the process of feature engineering, model training, and hyperparameter optimization and so on. Recent work performed qualitative studies on practitioners' experiences of using AutoML tools and compared different AutoML tools based on their performance and provided features, but none of the existing work studied the practices of using AutoML tools in real-world projects at a large scale. Therefore, we conducted an empirical study to understand how ML practitioners use AutoML tools in their projects. To this end, we examined the top 10 most used AutoML tools and their respective usages in a large number of open-source project repositories hosted on GitHub. The results of our study show 1) which AutoML tools are mostly used by ML practitioners and 2) the characteristics of the repositories that use these AutoML tools. Also, we identified the purpose of using AutoML tools (e.g. model parameter sampling, search space management, model evaluation/error-analysis, Data/ feature transformation, and data labeling) and the stages of the ML pipeline (e.g. feature engineering) where AutoML tools are used. Finally, we report how often AutoML tools are used together in the same source code files. We hope our results can help ML practitioners learn about different AutoML tools and their usages, so that they can pick the right tool for their purposes. Besides, AutoML tool developers can benefit from our findings to gain insight into the usages of their tools and improve their tools to better fit the users' usages and needs.
Fatal diseases, as Critical Health Episodes (CHEs), represent real dangers for patients hospitalized in Intensive Care Units. These episodes can lead to irreversible organ damage and death. Nevertheless, diagnosing them in time would greatly reduce their inconvenience. This study therefore focused on building a highly effective early warning system for CHEs such as Acute Hypotensive Episodes and Tachycardia Episodes. To facilitate the precocity of the prediction, a gap of one hour was considered between the observation periods (Observation Windows) and the periods during which a critical event can occur (Target Windows). The MIMIC II dataset was used to evaluate the performance of the proposed system. This system first includes extracting additional features using three different modes. Then, the feature selection process allowing the selection of the most relevant features was performed using the Mutual Information Gain feature importance. Finally, the high-performance predictive model LightGBM was used to perform episode classification. This approach called MIG-LightGBM was evaluated using five different metrics: Event Recall (ER), Reduced Precision (RP), average Anticipation Time (aveAT), average False Alarms (aveFA), and Event F1-score (EF1-score). A method is therefore considered highly efficient for the early prediction of CHEs if it exhibits not only a large aveAT but also a large EF1-score and a low aveFA. Compared to systems using Extreme Gradient Boosting, Support Vector Classification or Naive Bayes as a predictive model, the proposed system was found to be highly dominant. It also confirmed its superiority over the Layered Learning approach.
Despite the remarkable progress in the development of predictive models for healthcare, applying these algorithms on a large scale has been challenging. Algorithms trained on a particular task, based on specific data formats available in a set of medical records, tend to not generalize well to other tasks or databases in which the data fields may differ. To address this challenge, we propose General Healthcare Predictive Framework (GenHPF), which is applicable to any EHR with minimal preprocessing for multiple prediction tasks. GenHPF resolves heterogeneity in medical codes and schemas by converting EHRs into a hierarchical textual representation while incorporating as many features as possible. To evaluate the efficacy of GenHPF, we conduct multi-task learning experiments with single-source and multi-source settings, on three publicly available EHR datasets with different schemas for 12 clinically meaningful prediction tasks. Our framework significantly outperforms baseline models that utilize domain knowledge in multi-source learning, improving average AUROC by 1.2%P in pooled learning and 2.6%P in transfer learning while also showing comparable results when trained on a single EHR dataset. Furthermore, we demonstrate that self-supervised pretraining using multi-source datasets is effective when combined with GenHPF, resulting in a 0.6%P AUROC improvement compared to models without pretraining. By eliminating the need for preprocessing and feature engineering, we believe that this work offers a solid framework for multi-task and multi-source learning that can be leveraged to speed up the scaling and usage of predictive algorithms in healthcare.
Feature engineering has become one of the most important steps to improve model prediction performance, and to produce quality datasets. However, this process requires non-trivial domain-knowledge which involves a time-consuming process. Thereby, automating such process has become an active area of research and of interest in industrial applications. In this paper, a novel method, called Meta-learning and Causality Based Feature Engineering (MACFE), is proposed; our method is based on the use of meta-learning, feature distribution encoding, and causality feature selection. In MACFE, meta-learning is used to find the best transformations, then the search is accelerated by pre-selecting "original" features given their causal relevance. Experimental evaluations on popular classification datasets show that MACFE can improve the prediction performance across eight classifiers, outperforms the current state-of-the-art methods in average by at least 6.54%, and obtains an improvement of 2.71% over the best previous works.
End-to-end AutoML has attracted intensive interests from both academia and industry which automatically searches for ML pipelines in a space induced by feature engineering, algorithm/model selection, and hyper-parameter tuning. Existing AutoML systems, however, suffer from scalability issues when applying to application domains with large, high-dimensional search spaces. We present VolcanoML, a scalable and extensible framework that facilitates systematic exploration of large AutoML search spaces. VolcanoML introduces and implements basic building blocks that decompose a large search space into smaller ones, and allows users to utilize these building blocks to compose an execution plan for the AutoML problem at hand. VolcanoML further supports a Volcano-style execution model -- akin to the one supported by modern database systems -- to execute the plan constructed. Our evaluation demonstrates that, not only does VolcanoML raise the level of expressiveness for search space decomposition in AutoML, it also leads to actual findings of decomposition strategies that are significantly more efficient than the ones employed by state-of-the-art AutoML systems such as auto-sklearn. This paper is the extended version of the initial VolcanoML paper appeared in VLDB 2021.
Automated machine learning (AutoML) frameworks have become important tools in the data scientists' arsenal, as they dramatically reduce the manual work devoted to the construction of ML pipelines. Such frameworks intelligently search among millions of possible ML pipelines - typically containing feature engineering, model selection and hyper parameters tuning steps - and finally output an optimal pipeline in terms of predictive accuracy. However, when the dataset is large, each individual configuration takes longer to execute, therefore the overall AutoML running times become increasingly high. To this end, we present SubStrat, an AutoML optimization strategy that tackles the data size, rather than configuration space. It wraps existing AutoML tools, and instead of executing them directly on the entire dataset, SubStrat uses a genetic-based algorithm to find a small yet representative data subset which preserves a particular characteristic of the full data. It then employs the AutoML tool on the small subset, and finally, it refines the resulted pipeline by executing a restricted, much shorter, AutoML process on the large dataset. Our experimental results, performed on two popular AutoML frameworks, Auto-Sklearn and TPOT, show that SubStrat reduces their running times by 79% (on average), with less than 2% average loss in the accuracy of the resulted ML pipeline.
We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the progress of deep learning in this field. In this paper, we propose such a benchmark called PEER, a comprehensive and multi-task benchmark for Protein sEquence undERstanding. PEER provides a set of diverse protein understanding tasks including protein function prediction, protein localization prediction, protein structure prediction, protein-protein interaction prediction, and protein-ligand interaction prediction. We evaluate different types of sequence-based methods for each task including traditional feature engineering approaches, different sequence encoding methods as well as large-scale pre-trained protein language models. In addition, we also investigate the performance of these methods under the multi-task learning setting. Experimental results show that large-scale pre-trained protein language models achieve the best performance for most individual tasks, and jointly training multiple tasks further boosts the performance. The datasets and source codes of this benchmark are all available at https://github.com/DeepGraphLearning/PEER_Benchmark
We introduce OmniXAI (short for Omni eXplainable AI), an open-source Python library of eXplainable AI (XAI), which offers omni-way explainable AI capabilities and various interpretable machine learning techniques to address the pain points of understanding and interpreting the decisions made by machine learning (ML) in practice. OmniXAI aims to be a one-stop comprehensive library that makes explainable AI easy for data scientists, ML researchers and practitioners who need explanation for various types of data, models and explanation methods at different stages of ML process (data exploration, feature engineering, model development, evaluation, and decision-making, etc). In particular, our library includes a rich family of explanation methods integrated in a unified interface, which supports multiple data types (tabular data, images, texts, time-series), multiple types of ML models (traditional ML in Scikit-learn and deep learning models in PyTorch/TensorFlow), and a range of diverse explanation methods including "model-specific" and "model-agnostic" ones (such as feature-attribution explanation, counterfactual explanation, gradient-based explanation, etc). For practitioners, the library provides an easy-to-use unified interface to generate the explanations for their applications by only writing a few lines of codes, and also a GUI dashboard for visualization of different explanations for more insights about decisions. In this technical report, we present OmniXAI's design principles, system architectures, and major functionalities, and also demonstrate several example use cases across different types of data, tasks, and models.
Computational methods to accelerate natural disaster response include change detection, map alignment, and vision-aided navigation. Current software functions optimally only on near-nadir images, though off-nadir images are often the first sources of information following a natural disaster. The use of off-nadir images for the aforementioned tasks requires the computation of geocentric pose, which is an aerial vehicle's spatial orientation with respect to gravity. This study proposes a deep learning ensemble framework to predict geocentric pose using 5,923 near-nadir and off-nadir RGB satellite images of cities worldwide. First, a U-Net Fully Convolutional Neural Network predicts the pixel-wise above-ground elevation mask of the RGB images. Then, the elevation masks are concatenated with the RGB images to form four-channel inputs fed into a second convolutional model, which predicts orientation angle and magnification scale. A performance accuracy of R2=0.917 significantly outperforms previous methodologies. In addition, outlier removal is performed through supervised interpolation, and a sensitivity analysis of elevation masks is conducted to gauge the usefulness of data features, motivating future avenues of feature engineering. The high-accuracy software built in this study contributes to mapping and navigation procedures for effective disaster response to save lives.
Experience has shown that trading in stock and cryptocurrency markets has the potential to be highly profitable. In this light, considerable effort has been recently devoted to investigate how to apply machine learning and deep learning to interpret and predict market behavior. This research introduces a new deep neural network architecture and a novel idea of how to prepare financial data before feeding them to the model. In the data preparation part, the first step is to generate many features using technical indicators and then apply the XGBoost model for feature engineering. Splitting data into three categories and using separate autoencoders, we extract high-level mixed features at the second step. This data preprocessing is introduced to predict price movements. Regarding modeling, different convolutional layers, an long short-term memory unit, and several fully-connected layers have been designed to perform binary classification. This research also introduces a trading strategy to exploit the trained model outputs. Three different datasets are used to evaluate this method, where results indicate that this framework can provide us with profitable and robust predictions.
Collaborative filtering models generally perform better than content-based filtering models and do not require careful feature engineering. However, in the cold-start scenario collaborative information may be scarce or even unavailable, whereas the content information may be abundant, but also noisy and expensive to acquire. Thus, selection of particular features that improve cold-start recommendations becomes an important and non-trivial task. In the recent approach by Nembrini et al., the feature selection is driven by the correlational compatibility between collaborative and content-based models. The problem is formulated as a Quadratic Unconstrained Binary Optimization (QUBO) which, due to its NP-hard complexity, is solved using Quantum Annealing on a quantum computer provided by D-Wave. Inspired by the reported results, we contend the idea that current quantum annealers are superior for this problem and instead focus on classical algorithms. In particular, we tackle QUBO via TTOpt, a recently proposed black-box optimizer based on tensor networks and multilinear algebra. We show the computational feasibility of this method for large problems with thousands of features, and empirically demonstrate that the solutions found are comparable to the ones obtained with D-Wave across all examined datasets.
Land Carbon verification has long been a challenge in the carbon credit market. Carbon verification methods currently available are expensive, and may generate low-quality credit. Scalable and accurate remote sensing techniques enable new approaches to monitor changes in Above Ground Biomass (AGB) and Soil Organic Carbon (SOC). The majority of state-of-the-art research employs remote sensing on AGB and SOC separately, although some studies indicate a positive correlation between the two. We intend to combine the two domains in our research to improve state-of-the-art total carbon estimation and to provide insight into the voluntary carbon trading market. We begin by establishing baseline model in our study area in Scotland, using state-of-the-art methodologies in the SOC and AGB domains. The effects of feature engineering techniques such as variance inflation factor and feature selection on machine learning models are then investigated. This is extended by combining predictor variables from the two domains. Finally, we leverage the possible correlation between AGB and SOC to establish a relationship between the two and propose novel models in an attempt outperform the state-of-the-art results. We compared three machine learning techniques, boosted regression tree, random forest, and xgboost. These techniques have been demonstrated to be the most effective in both domains.
Surrogate models are data-based approximations of computationally expensive simulations that enable efficient exploration of the model's design space and informed decision-making in many physical domains. The usage of surrogate models in the vibroacoustic domain, however, is challenging due to the non-smooth, complex behavior of wave phenomena. This paper investigates four Machine Learning (ML) approaches in the modelling of surrogates of Sound Transmission Loss (STL). Feature importance and feature engineering are used to improve the models' accuracy while increasing their interpretability and physical consistency. The transfer of the proposed techniques to other problems in the vibroacoustic domain and possible limitations of the models are discussed.
Input features play a crucial role in DNN-based recommender systems with thousands of categorical and continuous fields from users, items, contexts, and interactions. Noisy features and inappropriate embedding dimension assignments can deteriorate the performance of recommender systems and introduce unnecessary complexity in model training and online serving. Optimizing the input configuration of DNN models, including feature selection and embedding dimension assignment, has become one of the essential topics in feature engineering. However, in existing industrial practices, feature selection and dimension search are optimized sequentially, i.e., feature selection is performed first, followed by dimension search to determine the optimal dimension size for each selected feature. Such a sequential optimization mechanism increases training costs and risks generating suboptimal input configurations. To address this problem, we propose a differentiable neural input razor (i-Razor) that enables joint optimization of feature selection and dimension search. Concretely, we introduce an end-to-end differentiable model to learn the relative importance of different embedding regions of each feature. Furthermore, a flexible pruning algorithm is proposed to achieve feature filtering and dimension derivation simultaneously. Extensive experiments on two large-scale public datasets in the Click-Through-Rate (CTR) prediction task demonstrate the efficacy and superiority of i-Razor in balancing model complexity and performance.
We present a study of the potential for Convolutional Neural Networks (CNNs) to enable separation of astrophysical transients from image artifacts, a task known as "real-bogus" classification without requiring a template subtracted (or difference) image which requires a computationally expensive process to generate, involving image matching on small spatial scales in large volumes of data. Using data from the Dark Energy Survey, we explore the use of CNNs to (1) automate the "real-bogus" classification, (2) reduce the computational costs of transient discovery. We compare the efficiency of two CNNs with similar architectures, one that uses "image triplets" (templates, search, and difference image) and one that takes as input the template and search only. We measure the decrease in efficiency associated with the loss of information in input finding that the testing accuracy is reduced from 96% to 91.1%. We further investigate how the latter model learns the required information from the template and search by exploring the saliency maps. Our work (1) confirms that CNNs are excellent models for "real-bogus" classification that rely exclusively on the imaging data and require no feature engineering task; (2) demonstrates that high-accuracy (> 90%) models can be built without the need to construct difference images, but some accuracy is lost. Since once trained, neural networks can generate predictions at minimal computational costs, we argue that future implementations of this methodology could dramatically reduce the computational costs in the detection of transients in synoptic surveys like Rubin Observatory's Legacy Survey of Space and Time by bypassing the Difference Image Analysis entirely.
This paper describes our submission to SemEval-2022 Task 6 on sarcasm detection and its five subtasks for English and Arabic. Sarcasm conveys a meaning which contradicts the literal meaning, and it is mainly found on social networks. It has a significant role in understanding the intention of the user. For detecting sarcasm, we used deep learning techniques based on transformers due to its success in the field of Natural Language Processing (NLP) without the need for feature engineering. The datasets were taken from tweets. We created new datasets by augmenting with external data or by using word embeddings and repetition of instances. Experiments were done on the datasets with different types of preprocessing because it is crucial in this task. The rank of our team was consistent across four subtasks (fourth rank in three subtasks and sixth rank in one subtask); whereas other teams might be in the top ranks for some subtasks but rank drastically less in other subtasks. This implies the robustness and stability of the models and the techniques we used.
The Automunge open source python library platform for tabular data pre-processing automates feature engineering data transformations of numerical encoding and missing data infill to received tidy data on bases fit to properties of columns in a designated train set for consistent and efficient application to subsequent data pipelines such as for inference, where transformations may be applied to distinct columns in "family tree" sets with generations and branches of derivations. Included in the library of transformations are methods to extract structure from bounded categorical string sets by way of automated string parsing, in which comparisons between entries in the set of unique values are parsed to identify character subset overlaps which may be encoded by appended columns of boolean overlap detection activations or by replacing string entries with identified overlap partitions. Further string parsing options, which may also be applied to unbounded categoric sets, include extraction of numeric substring partitions from entries or search functions to identify presence of specified substring partitions. The aggregation of these methods into "family tree" sets of transformations are demonstrated for use to automatically extract structure from categoric string compositions in relation to the set of entries in a column, such as may be applied to prepare categoric string set encodings for machine learning without human intervention.
Mainstream practice in machine learning with tabular data may take for granted that any feature engineering beyond scaling for numeric sets is superfluous in context of deep neural networks. This paper will offer arguments for potential benefits of extended encodings of numeric streams in deep learning by way of a survey of options for numeric transformations as available in the Automunge open source python library platform for tabular data pipelines, where transformations may be applied to distinct columns in "family tree" sets with generations and branches of derivations. Automunge transformation options include normalization, binning, noise injection, derivatives, and more. The aggregation of these methods into family tree sets of transformations are demonstrated for use to present numeric features to machine learning in multiple configurations of varying information content, as may be applied to encode numeric sets of unknown interpretation. Experiments demonstrate the realization of a novel generalized solution to data augmentation by noise injection for tabular learning, as may materially benefit model performance in applications with underserved training data.
In this work, we focus on low-resource dependency parsing for multiple languages. Several strategies are tailored to enhance performance in low-resource scenarios. While these are well-known to the community, it is not trivial to select the best-performing combination of these strategies for a low-resource language that we are interested in, and not much attention has been given to measuring the efficacy of these strategies. We experiment with 5 low-resource strategies for our ensembled approach on 7 Universal Dependency (UD) low-resource languages. Our exhaustive experimentation on these languages supports the effective improvements for languages not covered in pretrained models. We show a successful application of the ensembled system on a truly low-resource language Sanskrit. The code and data are available at: https://github.com/Jivnesh/SanDP
We present our submission to the Extreme Value Analysis 2021 Data Challenge in which teams were asked to accurately predict distributions of wildfire frequency and size within spatio-temporal regions of missing data. For the purpose of this competition we developed a variant of the powerful variational autoencoder models dubbed the Conditional Missing data Importance-Weighted Autoencoder (CMIWAE). Our deep latent variable generative model requires little to no feature engineering and does not necessarily rely on the specifics of scoring in the Data Challenge. It is fully trained on incomplete data, with the single objective to maximize log-likelihood of the observed wildfire information. We mitigate the effects of the relatively low number of training samples by stochastic sampling from a variational latent variable distribution, as well as by ensembling a set of CMIWAE models trained and validated on different splits of the provided data. The presented approach is not domain-specific and is amenable to application in other missing data recovery tasks with tabular or image-like information conditioned on auxiliary information.