Breast Cancer is the most prevalent cancer in the world. The World Health Organization reports that the disease still affects a significant portion of the developing world citing increased mortality rates in the majority of low to middle income countries. The most popular protocol pathologists use for diagnosing breast cancer is the Nottingham grading system which grades the proliferation of tumors based on 3 major criteria, the most important of them being mitotic cell count. The way in which pathologists evaluate mitotic cell count is to subjectively and qualitatively analyze cells present in stained slides of tissue and make a decision on its mitotic state i.e. is it mitotic or not?This process is extremely inefficient and tiring for pathologists and so an efficient, accurate, and fully automated tool to aid with the diagnosis is extremely desirable. Fortunately, creating such a tool is made significantly easier with the AutoML tool available from Microsoft Azure, however to the best of our knowledge the AutoML tool has never been formally evaluated for use in mitotic cell detection in histopathology images. This paper serves as an evaluation of the AutoML tool for this purpose and will provide a first look on how the tool handles this challenging problem. All code is available athttps://github.com/WaltAFWilliams/AMDet
Analyzing better time series with limited human effort is of interest to academia and industry. Driven by business scenarios, we organized the first Automated Time Series Regression challenge (AutoSeries) for the WSDM Cup 2020. We present its design, analysis, and post-hoc experiments. The code submission requirement precluded participants from any manual intervention, testing automated machine learning capabilities of solutions, across many datasets, under hardware and time limitations. We prepared 10 datasets from diverse application domains (sales, power consumption, air quality, traffic, and parking), featuring missing data, mixed continuous and categorical variables, and various sampling rates. Each dataset was split into a training and a test sequence (which was streamed, allowing models to continuously adapt). The setting of time series regression, differs from classical forecasting in that covariates at the present time are known. Great strides were made by participants to tackle this AutoSeries problem, as demonstrated by the jump in performance from the sample submission, and post-hoc comparisons with AutoGluon. Simple yet effective methods were used, based on feature engineering, LightGBM, and random search hyper-parameter tuning, addressing all aspects of the challenge. Our post-hoc analyses revealed that providing additional time did not yield significant improvements. The winners' code was open-sourced https://www.4paradigm.com/competition/autoseries2020.
We ascertain and compare the performances of AutoML tools on large, highly imbalanced healthcare datasets. We generated a large dataset using historical administrative claims including demographic information and flags for disease codes in four different time windows prior to 2019. We then trained three AutoML tools on this dataset to predict six different disease outcomes in 2019 and evaluated model performances on several metrics. The AutoML tools showed improvement from the baseline random forest model but did not differ significantly from each other. All models recorded low area under the precision-recall curve and failed to predict true positives while keeping the true negative rate high. Model performance was not directly related to prevalence. We provide a specific use-case to illustrate how to select a threshold that gives the best balance between true and false positive rates, as this is an important consideration in medical applications. Healthcare datasets present several challenges for AutoML tools, including large sample size, high imbalance, and limitations in the available features types. Improvements in scalability, combinations of imbalance-learning resampling and ensemble approaches, and curated feature selection are possible next steps to achieve better performance. Among the three explored, no AutoML tool consistently outperforms the rest in terms of predictive performance. The performances of the models in this study suggest that there may be room for improvement in handling medical claims data. Finally, selection of the optimal prediction threshold should be guided by the specific practical application.
Many AutoML problems involve optimizing discrete objects under a black-box reward. Neural-guided search provides a flexible means of searching these combinatorial spaces using an autoregressive recurrent neural network. A major benefit of this approach is that builds up objects sequentially--this provides an opportunity to incorporate domain knowledge into the search by directly modifying the logits emitted during sampling. In this work, we formalize a framework for incorporating such in situ priors and constraints into neural-guided search, and provide sufficient conditions for enforcing constraints. We integrate several priors and constraints from existing works into this framework, propose several new ones, and demonstrate their efficacy in informing the task of symbolic regression.
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.
Building robust deep learning-based models requires diverse training data, ideally from several sources. However, these datasets cannot be combined easily because of patient privacy concerns or regulatory hurdles, especially if medical data is involved. Federated learning (FL) is a way to train machine learning models without the need for centralized datasets. Each FL client trains on their local data while only sharing model parameters with a global server that aggregates the parameters from all clients. At the same time, each client's data can exhibit differences and inconsistencies due to the local variation in the patient population, imaging equipment, and acquisition protocols. Hence, the federated learned models should be able to adapt to the local particularities of a client's data. In this work, we combine FL with an AutoML technique based on local neural architecture search by training a "supernet". Furthermore, we propose an adaptation scheme to allow for personalized model architectures at each FL client's site. The proposed method is evaluated on four different datasets from 3D prostate MRI and shown to improve the local models' performance after adaptation through selecting an optimal path through the AutoML supernet.
Deep learning models for medical image segmentation are primarily data-driven. Models trained with more data lead to improved performance and generalizability. However, training is a computationally expensive process because multiple hyper-parameters need to be tested to find the optimal setting for best performance. In this work, we focus on accelerating the estimation of hyper-parameters by proposing two novel methodologies: proxy data and proxy networks. Both can be useful for estimating hyper-parameters more efficiently. We test the proposed techniques on CT and MR imaging modalities using well-known public datasets. In both cases using one dataset for building proxy data and another data source for external evaluation. For CT, the approach is tested on spleen segmentation with two datasets. The first dataset is from the medical segmentation decathlon (MSD), where the proxy data is constructed, the secondary dataset is utilized as an external validation dataset. Similarly, for MR, the approach is evaluated on prostate segmentation where the first dataset is from MSD and the second dataset is PROSTATEx. First, we show higher correlation to using full data for training when testing on the external validation set using smaller proxy data than a random selection of the proxy data. Second, we show that a high correlation exists for proxy networks when compared with the full network on validation Dice score. Third, we show that the proposed approach of utilizing a proxy network can speed up an AutoML framework for hyper-parameter search by 3.3x, and by 4.4x if proxy data and proxy network are utilized together.
The pipeline optimization problem in machine learning requires simultaneous optimization of pipeline structures and parameter adaptation of their elements. Having an elegant way to express these structures can help lessen the complexity in the management and analysis of their performances together with the different choices of optimization strategies. With these issues in mind, we created the AutoMLPipeline (AMLP) toolkit which facilitates the creation and evaluation of complex machine learning pipeline structures using simple expressions. We use AMLP to find optimal pipeline signatures, datamine them, and use these datamined features to speed-up learning and prediction. We formulated a two-stage pipeline optimization with surrogate modeling in AMLP which outperforms other AutoML approaches with a 4-hour time budget in less than 5 minutes of AMLP computation time.
Recently, pure transformer-based models have shown great potentials for vision tasks such as image classification and detection. However, the design of transformer networks is challenging. It has been observed that the depth, embedding dimension, and number of heads can largely affect the performance of vision transformers. Previous models configure these dimensions based upon manual crafting. In this work, we propose a new one-shot architecture search framework, namely AutoFormer, dedicated to vision transformer search. AutoFormer entangles the weights of different blocks in the same layers during supernet training. Benefiting from the strategy, the trained supernet allows thousands of subnets to be very well-trained. Specifically, the performance of these subnets with weights inherited from the supernet is comparable to those retrained from scratch. Besides, the searched models, which we refer to AutoFormers, surpass the recent state-of-the-arts such as ViT and DeiT. In particular, AutoFormer-tiny/small/base achieve 74.7%/81.7%/82.4% top-1 accuracy on ImageNet with 5.7M/22.9M/53.7M parameters, respectively. Lastly, we verify the transferability of AutoFormer by providing the performance on downstream benchmarks and distillation experiments. Code and models are available at https://github.com/microsoft/AutoML.
Learning embeddings for entities and relations in knowledge graph (KG) have benefited many downstream tasks. In recent years, scoring functions, the crux of KG learning, have been human-designed to measure the plausibility of triples and capture different kinds of relations in KGs. However, as relations exhibit intricate patterns that are hard to infer before training, none of them consistently perform the best on benchmark tasks. In this paper, inspired by the recent success of automated machine learning (AutoML), we search bilinear scoring functions for different KG tasks through the AutoML techniques. However, it is non-trivial to explore domain-specific information here. We first set up a search space for AutoBLM by analyzing existing scoring functions. Then, we propose a progressive algorithm (AutoBLM) and an evolutionary algorithm (AutoBLM+), which are further accelerated by filter and predictor to deal with the domain-specific properties for KG learning. Finally, we perform extensive experiments on benchmarks in KG completion, multi-hop query, and entity classification tasks. Empirical results show that the searched scoring functions are KG dependent, new to the literature, and outperform the existing scoring functions. AutoBLM+ is better than AutoBLM as the evolutionary algorithm can flexibly explore better structures in the same budget.
The architectures of deep artificial neural networks (DANNs) are routinely studied to improve their predictive performance. However, the relationship between the architecture of a DANN and its robustness to noise and adversarial attacks is less explored. We investigate how the robustness of DANNs relates to their underlying graph architectures or structures. This study: (1) starts by exploring the design space of architectures of DANNs using graph-theoretic robustness measures; (2) transforms the graphs to DANN architectures to train/validate/test on various image classification tasks; (3) explores the relationship between the robustness of trained DANNs against noise and adversarial attacks and the robustness of their underlying architectures estimated via graph-theoretic measures. We show that the topological entropy and Olivier-Ricci curvature of the underlying graphs can quantify the robustness performance of DANNs. The said relationship is stronger for complex tasks and large DANNs. Our work will allow autoML and neural architecture search community to explore design spaces of robust and accurate DANNs.
This work improves the quality of automated machine learning (AutoML) systems by using dataset and function descriptions while significantly decreasing computation time from minutes to milliseconds by using a zero-shot approach. Given a new dataset and a well-defined machine learning task, humans begin by reading a description of the dataset and documentation for the algorithms to be used. This work is the first to use these textual descriptions, which we call privileged information, for AutoML. We use a pre-trained Transformer model to process the privileged text and demonstrate that using this information improves AutoML performance. Thus, our approach leverages the progress of unsupervised representation learning in natural language processing to provide a significant boost to AutoML. We demonstrate that using only textual descriptions of the data and functions achieves reasonable classification performance, and adding textual descriptions to data meta-features improves classification across tabular datasets. To achieve zero-shot AutoML we train a graph neural network with these description embeddings and the data meta-features. Each node represents a training dataset, which we use to predict the best machine learning pipeline for a new test dataset in a zero-shot fashion. Our zero-shot approach rapidly predicts a high-quality pipeline for a supervised learning task and dataset. In contrast, most AutoML systems require tens or hundreds of pipeline evaluations. We show that zero-shot AutoML reduces running and prediction times from minutes to milliseconds, consistently across datasets. By speeding up AutoML by orders of magnitude this work demonstrates real-time AutoML.
Automated Machine Learning (AutoML) has gained increasing success on tabular data in recent years. However, processing unstructured data like text is a challenge and not widely supported by open-source AutoML tools. This work compares three manually created text representations and text embeddings automatically created by AutoML tools. Our benchmark includes four popular open-source AutoML tools and eight datasets for text classification purposes. The results show that straightforward text representations perform better than AutoML tools with automatically created text embeddings.
In this paper, we present a novel neuroevolutionary method to identify the architecture and hyperparameters of convolutional autoencoders. Remarkably, we used a hypervolume indicator in the context of neural architecture search for autoencoders, for the first time to our current knowledge. Results show that images were compressed by a factor of more than 10, while still retaining enough information to achieve image classification for the majority of the tasks. Thus, this new approach can be used to speed up the AutoML pipeline for image compression.
Short Message Service (SMS) is a very popular service used for communication by mobile users. However, this popular service can be abused by executing illegal activities and influencing security risks. Nowadays, many automatic machine learning (AutoML) tools exist which can help domain experts and lay users to build high-quality ML models with little or no machine learning knowledge. In this work, a classification performance comparison was conducted between three automatic ML tools for SMS spam message filtering. These tools are mljar-supervised AutoML, H2O AutoML, and Tree-based Pipeline Optimization Tool (TPOT) AutoML. Experimental results showed that ensemble models achieved the best classification performance. The Stacked Ensemble model, which was built using H2O AutoML, achieved the best performance in terms of Log Loss (0.8370), true positive (1088/1116), and true negative (281/287) metrics. There is a 19.05\% improvement in Log Loss with respect to TPOT AutoML and 5.56\% improvement with respect to mljar-supervised AutoML. The satisfactory filtering performance achieved with AutoML tools provides a potential application for AutoML tools to automatically determine the best ML model that can perform best for SMS spam message filtering.
Collaborative filtering (CF), as a fundamental approach for recommender systems, is usually built on the latent factor model with learnable parameters to predict users' preferences towards items. However, designing a proper CF model for a given data is not easy, since the properties of datasets are highly diverse. In this paper, motivated by the recent advances in automated machine learning (AutoML), we propose to design a data-specific CF model by AutoML techniques. The key here is a new framework that unifies state-of-the-art (SOTA) CF methods and splits them into disjoint stages of input encoding, embedding function, interaction function, and prediction function. We further develop an easy-to-use, robust, and efficient search strategy, which utilizes random search and a performance predictor for efficient searching within the above framework. In this way, we can combinatorially generalize data-specific CF models, which have not been visited in the literature, from SOTA ones. Extensive experiments on five real-world datasets demonstrate that our method can consistently outperform SOTA ones for various CF tasks. Further experiments verify the rationality of the proposed framework and the efficiency of the search strategy. The searched CF models can also provide insights for exploring more effective methods in the future
Automated machine learning techniques benefited from tremendous research progress in recently. These developments and the continuous-growing demand for machine learning experts led to the development of numerous AutoML tools. However, these tools assume that the entire training dataset is available upfront and that the underlying distribution does not change over time. These assumptions do not hold in a data stream mining setting where an unbounded stream of data cannot be stored and is likely to manifest concept drift. Industry applications of machine learning on streaming data become more popular due to the increasing adoption of real-time streaming patterns in IoT, microservices architectures, web analytics, and other fields. The research summarized in this paper surveys the state-of-the-art open-source AutoML tools, applies them to data collected from streams, and measures how their performance changes over time. For comparative purposes, batch, batch incremental and instance incremental estimators are applied and compared. Moreover, a meta-learning technique for online algorithm selection based on meta-feature extraction is proposed and compared while model replacement and continual AutoML techniques are discussed. The results show that off-the-shelf AutoML tools can provide satisfactory results but in the presence of concept drift, detection or adaptation techniques have to be applied to maintain the predictive accuracy over time.
In addition to the best model architecture and hyperparameters, a full AutoML solution requires selecting appropriate hardware automatically. This can be framed as a multi-objective optimization problem: there is not a single best hardware configuration but a set of optimal ones achieving different trade-offs between cost and runtime. In practice, some choices may be overly costly or take days to train. To lift this burden, we adopt a multi-objective approach that selects and adapts the hardware configuration automatically alongside neural architectures and their hyperparameters. Our method builds on Hyperband and extends it in two ways. First, we replace the stopping rule used in Hyperband by a non-dominated sorting rule to preemptively stop unpromising configurations. Second, we leverage hyperparameter evaluations from related tasks via transfer learning by building a probabilistic estimate of the Pareto front that finds promising configurations more efficiently than random search. We show in extensive NAS and HPO experiments that both ingredients bring significant speed-ups and cost savings, with little to no impact on accuracy. In three benchmarks where hardware is selected in addition to hyperparameters, we obtain runtime and cost reductions of at least 5.8x and 8.8x, respectively. Furthermore, when applying our multi-objective method to the tuning of hyperparameters only, we obtain a 10\% improvement in runtime while maintaining the same accuracy on two popular NAS benchmarks.
We propose the ChaCha (Champion-Challengers) algorithm for making an online choice of hyperparameters in online learning settings. ChaCha handles the process of determining a champion and scheduling a set of `live' challengers over time based on sample complexity bounds. It is guaranteed to have sublinear regret after the optimal configuration is added into consideration by an application-dependent oracle based on the champions. Empirically, we show that ChaCha provides good performance across a wide array of datasets when optimizing over featurization and hyperparameter decisions.
A key element in solving real-life data science problems is selecting the types of models to use. Tree ensemble models (such as XGBoost) are usually recommended for classification and regression problems with tabular data. However, several deep learning models for tabular data have recently been proposed, claiming to outperform XGBoost for some use cases. This paper explores whether these deep models should be a recommended option for tabular data by rigorously comparing the new deep models to XGBoost on various datasets. In addition to systematically comparing their performance, we consider the tuning and computation they require. Our study shows that XGBoost outperforms these deep models across the datasets, including the datasets used in the papers that proposed the deep models. We also demonstrate that XGBoost requires much less tuning. On the positive side, we show that an ensemble of deep models and XGBoost performs better on these datasets than XGBoost alone.