Developing modern systems software is a complex task that combines business logic programming and Software Performance Engineering (SPE). The later is an experimental and labor-intensive activity focused on optimizing the system for a given hardware, software, and workload (hw/sw/wl) context. Today's SPE is performed during build/release phases by specialized teams, and cursed by: 1) lack of standardized and automated tools, 2) significant repeated work as hw/sw/wl context changes, 3) fragility induced by a "one-size-fit-all" tuning (where improvements on one workload or component may impact others). The net result: despite costly investments, system software is often outside its optimal operating point - anecdotally leaving 30% to 40% of performance on the table. The recent developments in Data Science (DS) hints at an opportunity: combining DS tooling and methodologies with a new developer experience to transform the practice of SPE. In this paper we present: MLOS, an ML-powered infrastructure and methodology to democratize and automate Software Performance Engineering. MLOS enables continuous, instance-level, robust, and trackable systems optimization. MLOS is being developed and employed within Microsoft to optimize SQL Server performance. Early results indicated that component-level optimizations can lead to 20%-90% improvements when custom-tuning for a specific hw/sw/wl, hinting at a significant opportunity. However, several research challenges remain that will require community involvement. To this end, we are in the process of open-sourcing the MLOS core infrastructure, and we are engaging with academic institutions to create an educational program around Software 2.0 and MLOS ideas.
The Coronavirus Disease (COVID-19) has affected 1.8 million people and resulted in more than 110,000 deaths as of April 12, 2020. Several studies have shown that tomographic patterns seen on chest Computed Tomography (CT), such as ground-glass opacities, consolidations, and crazy paving pattern, are correlated with the disease severity and progression. CT imaging can thus emerge as an important modality for the management of COVID-19 patients. AI-based solutions can be used to support CT based quantitative reporting and make reading efficient and reproducible if quantitative biomarkers, such as the Percentage of Opacity (PO), can be automatically computed. However, COVID-19 has posed unique challenges to the development of AI, specifically concerning the availability of appropriate image data and annotations at scale. In this paper, we propose to use synthetic datasets to augment an existing COVID-19 database to tackle these challenges. We train a Generative Adversarial Network (GAN) to inpaint COVID-19 related tomographic patterns on chest CTs from patients without infectious diseases. Additionally, we leverage location priors derived from manually labeled COVID-19 chest CTs patients to generate appropriate abnormality distributions. Synthetic data are used to improve both lung segmentation and segmentation of COVID-19 patterns by adding 20% of synthetic data to the real COVID-19 training data. We collected 2143 chest CTs, containing 327 COVID-19 positive cases, acquired from 12 sites across 7 countries. By testing on 100 COVID-19 positive and 100 control cases, we show that synthetic data can help improve both lung segmentation (+6.02% lesion inclusion rate) and abnormality segmentation (+2.78% dice coefficient), leading to an overall more accurate PO computation (+2.82% Pearson coefficient).
Purpose: To present a method that automatically detects and quantifies abnormal tomographic patterns commonly present in COVID-19, namely Ground Glass Opacities (GGO) and consolidations. Given that high opacity abnormalities (i.e., consolidations) were shown to correlate with severe disease, the paper introduces two combined severity measures (Percentage of Opacity, Percentage of High Opacity) and (Lung Severity Score, Lung High Opacity Score). They quantify the extent of overall COVID-19 abnormalities and the presence of high opacity abnormalities, global and lobe-wise, respectively, being computed based on 3D segmentations of lesions, lungs, and lobes. Materials and Methods: The proposed method takes as input a non-contrasted Chest CT and segments the lesions, lungs, and lobes in 3D. It outputs two combined measures of the severity of lung/lobe involvement, quantifying both the extent of COVID-19 abnormalities and presence of high opacities, based on deep learning and deep reinforcement learning. The first measure (POO, POHO) is global, while the second (LSS, LHOS) is lobe-wise. Evaluation is reported on CTs of 100 subjects (50 COVID-19 confirmed and 50 controls) from institutions from Canada, Europe and US. Ground truth is established by manual annotations of lesions, lungs, and lobes. Results: Pearson Correlation Coefficient between method prediction and ground truth is 0.97 (POO), 0.98 (POHO), 0.96 (LSS), 0.96 (LHOS). Automated processing time to compute the severity scores is 10 seconds/case vs 30 mins needed for manual annotations. Conclusion: A new method identifies regions of abnormalities seen in COVID-19 non-contrasted Chest CT and computes (POO, POHO) and (LSS, LHOS) severity scores.
We use over 350,000 Yelp reviews on 5,000 restaurants to perform an ablation study on text preprocessing techniques. We also compare the effectiveness of several machine learning and deep learning models on predicting user sentiment (negative, neutral, or positive). For machine learning models, we find that using binary bag-of-word representation, adding bi-grams, imposing minimum frequency constraints and normalizing texts have positive effects on model performance. For deep learning models, we find that using pre-trained word embeddings and capping maximum length often boost model performance. Finally, using macro F1 score as our comparison metric, we find simpler models such as Logistic Regression and Support Vector Machine to be more effective at predicting sentiments than more complex models such as Gradient Boosting, LSTM and BERT.
With the injection of contrast material into blood vessels, multi-phase contrasted CT images can enhance the visibility of vessel networks in the human body. Reconstructing the 3D geometric morphology of liver vessels from the contrasted CT images can enable multiple liver preoperative surgical planning applications. Automatic reconstruction of liver vessel morphology remains a challenging problem due to the morphological complexity of liver vessels and the inconsistent vessel intensities among different multi-phase contrasted CT images. On the other side, high integrity is required for the 3D reconstruction to avoid decision making biases. In this paper, we propose a framework for liver vessel morphology reconstruction using both a fully convolutional neural network and a graph attention network. A fully convolutional neural network is first trained to produce the liver vessel centerline heatmap. An over-reconstructed liver vessel graph model is then traced based on the heatmap using an image processing based algorithm. We use a graph attention network to prune the false-positive branches by predicting the presence probability of each segmented branch in the initial reconstruction using the aggregated CNN features. We evaluated the proposed framework on an in-house dataset consisting of 418 multi-phase abdomen CT images with contrast. The proposed graph network pruning improves the overall reconstruction F1 score by 6.4% over the baseline. It also outperformed the other state-of-the-art curvilinear structure reconstruction algorithms.
Detecting malignant pulmonary nodules at an early stage can allow medical interventions which increases the survival rate of lung cancer patients. Using computer vision techniques to detect nodules can improve the sensitivity and the speed of interpreting chest CT for lung cancer screening. Many studies have used CNNs to detect nodule candidates. Though such approaches have been shown to outperform the conventional image processing based methods regarding the detection accuracy, CNNs are also known to be limited to generalize on under-represented samples in the training set and prone to imperceptible noise perturbations. Such limitations can not be easily addressed by scaling up the dataset or the models. In this work, we propose to add adversarial synthetic nodules and adversarial attack samples to the training data to improve the generalization and the robustness of the lung nodule detection systems. In order to generate hard examples of nodules from a differentiable nodule synthesizer, we use projected gradient descent (PGD) to search the latent code within a bounded neighbourhood that would generate nodules to decrease the detector response. To make the network more robust to unanticipated noise perturbations, we use PGD to search for noise patterns that can trigger the network to give over-confident mistakes. By evaluating on two different benchmark datasets containing consensus annotations from three radiologists, we show that the proposed techniques can improve the detection performance on real CT data. To understand the limitations of both the conventional networks and the proposed augmented networks, we also perform stress-tests on the false positive reduction networks by feeding different types of artificially produced patches. We show that the augmented networks are more robust to both under-represented nodules as well as resistant to noise perturbations.
Continuous-time event sequences represent discrete events occurring in continuous time. Such sequences arise frequently in real-life and cover a wide variety of natural events, such as earthquakes, or events corresponding to human actions, such as medical administrations. Usually we expect the event sequences to follow some regular pattern over time. However, sometimes these regular patterns may be interrupted by unexpected absence or unexpected occurrences of events. Identification of these unexpected cases can be very important as they may point to abnormal situations that need human attention. In this work, we study and develop methods for detecting outliers in continuous-time event sequences, including unexpected absence and unexpected occurrences of events. Since the patterns that event sequences tend to follow may change in different contexts, we develop outlier detection methods based on point processes that take into account different contexts. Our outlier scoring methods are based on Bayesian decision theory and hypothesis testing with theoretical guarantees. To test the performance of the methods, we conduct experiments on both synthetic data and real-world clinical data and show the effectiveness of the proposed methods.
This paper investigates a population-based training regime based on game-theoretic principles called Policy-Spaced Response Oracles (PSRO). PSRO is general in the sense that it (1) encompasses well-known algorithms such as fictitious play and double oracle as special cases, and (2) in principle applies to general-sum, many-player games. Despite this, prior studies of PSRO have been focused on two-player zero-sum games, a regime wherein Nash equilibria are tractably computable. In moving from two-player zero-sum games to more general settings, computation of Nash equilibria quickly becomes infeasible. Here, we extend the theoretical underpinnings of PSRO by considering an alternative solution concept, {\alpha}-Rank, which is unique (thus faces no equilibrium selection issues, unlike Nash) and tractable to compute in general-sum, many-player settings. We establish convergence guarantees in several games classes, and identify links between Nash equilibria and {\alpha}-Rank. We demonstrate the competitive performance of {\alpha}-Rank-based PSRO against an exact Nash solver-based PSRO in 2-player Kuhn and Leduc Poker. We then go beyond the reach of prior PSRO applications by considering 3- to 5-player poker games, yielding instances where {\alpha}-Rank achieves faster convergence than approximate Nash solvers, thus establishing it as a favorable general games solver. We also carry out an initial empirical validation in MuJoCo soccer, illustrating the feasibility of the proposed approach in another complex domain.