A System for Real-Time Interactive Analysis of Deep Learning Training

Performing diagnosis or exploratory analysis during the training of deep learning models is challenging but often necessary for making a sequence of decisions guided by the incremental observations. Currently available systems for this purpose are limited to monitoring only the logged data that must be specified before the training process starts. Each time a new information is desired, a cycle of stop-change-restart is required in the training process. These limitations make interactive exploration and diagnosis tasks difficult, imposing long tedious iterations during the model development. We present a new system that enables users to perform interactive queries on live processes generating real-time information that can be rendered in multiple formats on multiple surfaces in the form of several desired visualizations simultaneously. To achieve this, we model various exploratory inspection and diagnostic tasks for deep learning training processes as specifications for streams using a map-reduce paradigm with which many data scientists are already familiar. Our design achieves generality and extensibility by defining composable primitives which is a fundamentally different approach than is used by currently available systems. The open source implementation of our system is available as TensorWatch project at https://github.com/microsoft/tensorwatch.Comment: Accepted at ACM SIGCHI Symposium on Engineering Interactive Computing Systems (EICS 2019). Code available as TensorWatch project at https://github.com/microsoft/tensorwatc

What Makes a Top-Performing Precision Medicine Search Engine? Tracing Main System Features in a Systematic Way

From 2017 to 2019 the Text REtrieval Conference (TREC) held a challenge task on precision medicine using documents from medical publications (PubMed) and clinical trials. Despite lots of performance measurements carried out in these evaluation campaigns, the scientific community is still pretty unsure about the impact individual system features and their weights have on the overall system performance. In order to overcome this explanatory gap, we first determined optimal feature configurations using the Sequential Model-based Algorithm Configuration (SMAC) program and applied its output to a BM25-based search engine. We then ran an ablation study to systematically assess the individual contributions of relevant system features: BM25 parameters, query type and weighting schema, query expansion, stop word filtering, and keyword boosting. For evaluation, we employed the gold standard data from the three TREC-PM installments to evaluate the effectiveness of different features using the commonly shared infNDCG metric.Comment: Accepted for SIGIR2020, 10 page

Big-Data Science in Porous Materials: Materials Genomics and Machine Learning

By combining metal nodes with organic linkers we can potentially synthesize millions of possible metal organic frameworks (MOFs). At present, we have libraries of over ten thousand synthesized materials and millions of in-silico predicted materials. The fact that we have so many materials opens many exciting avenues to tailor make a material that is optimal for a given application. However, from an experimental and computational point of view we simply have too many materials to screen using brute-force techniques. In this review, we show that having so many materials allows us to use big-data methods as a powerful technique to study these materials and to discover complex correlations. The first part of the review gives an introduction to the principles of big-data science. We emphasize the importance of data collection, methods to augment small data sets, how to select appropriate training sets. An important part of this review are the different approaches that are used to represent these materials in feature space. The review also includes a general overview of the different ML techniques, but as most applications in porous materials use supervised ML our review is focused on the different approaches for supervised ML. In particular, we review the different method to optimize the ML process and how to quantify the performance of the different methods. In the second part, we review how the different approaches of ML have been applied to porous materials. In particular, we discuss applications in the field of gas storage and separation, the stability of these materials, their electronic properties, and their synthesis. The range of topics illustrates the large variety of topics that can be studied with big-data science. Given the increasing interest of the scientific community in ML, we expect this list to rapidly expand in the coming years.Comment: Editorial changes (typos fixed, minor adjustments to figures

Machine learning for genetic prediction of psychiatric disorders: a systematic review

Machine learning methods have been employed to make predictions in psychiatry from genotypes, with the potential to bring improved prediction of outcomes in psychiatric genetics; however, their current performance is unclear. We aim to systematically review machine learning methods for predicting psychiatric disorders from genetics alone and evaluate their discrimination, bias and implementation. Medline, PsycInfo, Web of Science and Scopus were searched for terms relating to genetics, psychiatric disorders and machine learning, including neural networks, random forests, support vector machines and boosting, on 10 September 2019. Following PRISMA guidelines, articles were screened for inclusion independently by two authors, extracted, and assessed for risk of bias. Overall, 63 full texts were assessed from a pool of 652 abstracts. Data were extracted for 77 models of schizophrenia, bipolar, autism or anorexia across 13 studies. Performance of machine learning methods was highly varied (0.48–0.95 AUC) and differed between schizophrenia (0.54–0.95 AUC), bipolar (0.48–0.65 AUC), autism (0.52–0.81 AUC) and anorexia (0.62–0.69 AUC). This is likely due to the high risk of bias identified in the study designs and analysis for reported results. Choices for predictor selection, hyperparameter search and validation methodology, and viewing of the test set during training were common causes of high risk of bias in analysis. Key steps in model development and validation were frequently not performed or unreported. Comparison of discrimination across studies was constrained by heterogeneity of predictors, outcome and measurement, in addition to sample overlap within and across studies. Given widespread high risk of bias and the small number of studies identified, it is important to ensure established analysis methods are adopted. We emphasise best practices in methodology and reporting for improving future studies

Accelerating hyperparameter optimisation with PyCOMPSs

Machine Learning applications now span across multiple domains due to the increase in computational power of modern systems. There has been a recent surge in Machine Learning applications in High Performance Computing (HPC) in an attempt to speed up training. However, besides training, hyperparameters optimisation(HPO) is one of the most time consuming and resource intensive parts in a Machine Learning Workflow. Numerous algorithms and tools exist to accelerate the process of finding the right parameters for a model. Most of these tools do not utilize the parallelism provided by modern systems and are serial or limited to a single node. The few ones that are offer distributed execution require a serious amount of programming effort. There is, therefore, a need for a tool/scheme that can scale and leverage HPC infrastructures such as supercomputers, with minimum programmers effort and little or no overhead in performance. We present a HPO scheme built on top of PyCOMPSs, a programming model and runtime which aims to ease the development of parallel applications for distributed infrastructures. We show that PyCOMPSs is a powerful framework that can accelerate the process of Hyperparameter Optimisation across multiple devices and computing units. We also show that PyCOMPSs provides easy programmability, seamless distribution and scalability, key features missing in existing tools. Furthermore, we perform a detailed performance analysis showing different configurations to demonstrate the effectiveness our approach.Peer Reviewe

Design Space Exploration of Heterogeneous-Accelerator SoCs with Hyperparameter Optimization

International audienceModern SoC systems consist of general-purpose processor cores augmented with large numbers of specialized accelerators. Building such systems requires a design flow allowing the design space to be explored at the system level with an appropriate strategy. In this paper, we describe a methodology allowing to explore the design space of power-performance heterogeneous SoCs by combining an architecture simulator (gem5-Aladdin) and a hyperparameteroptimization method (Hyperopt). This methodology allows different types of parallelism with loop unrolling strategies and memory coherency interfaces to be swept. The flow has been applied to a convolutional neural network algorithm. We show that the most energy efficient architecture achieves a 2x to 4x improvement in energy-delay-product compared to an architecture without parallelism. Furthermore, the obtained solution is more efficient than commonly implemented architectures (Systolic, 2D-mapping, and Tiling). We also applied the methodology to find the optimal architecture including its coherency interface for a complex SoC made up of six accelerated-workloads.We show that a hybrid interface appears to be the most efficient; it reaches 22% and 12% improvement in energy-delay-product compared to just only using non-coherent and only LLC-coherent models, respectively

A Dynamic Early Stopping Criterion for Random Search in SVM Hyperparameter Optimization

We introduce a dynamic early stopping condition for Random Search optimization algorithms. We test our algorithm for SVM hyperparameter optimization for classification tasks, on six commonly used datasets. According to the experimental results, we reduce significantly the number of trials used. Since each trial requires a re-training of the SVM model, our method accelerates the RS optimization. The code runs on a multi-core system and we analyze the achieved scalability for an increasing number of cores