arXiv subjects

Siqi Liu

Publications and source records attributed to Siqi Liu.

At least 109 records · Page 6Linked to original sources

arXiv2020

No Surprises: Training Robust Lung Nodule Detection for Low-Dose CT Scans by Augmenting with Adversarial Attacks

Detecting malignant pulmonary nodules at an early stage can allow medical interventions which may increase 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. 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.

eess.IV↗

arXiv2020

dm_control: Software and Tasks for Continuous Control

The dm_control software package is a collection of Python libraries and task suites for reinforcement learning agents in an articulated-body simulation. A MuJoCo wrapper provides convenient bindings to functions and data structures. The PyMJCF and Composer libraries enable procedural model manipulation and task authoring. The Control Suite is a fixed set of tasks with standardised structure, intended to serve as performance benchmarks. The Locomotion framework provides high-level abstractions and examples of locomotion tasks. A set of configurable manipulation tasks with a robot arm and snap-together bricks is also included. dm_control is publicly available at https://www.github.com/deepmind/dm_control

cs.RO↗

arXiv2020

Automated detection and quantification of COVID-19 airspace disease on chest radiographs: A novel approach achieving radiologist-level performance using a CNN trained on digital reconstructed radiographs (DRRs) from CT-based ground-truth

Purpose: To leverage volumetric quantification of airspace disease (AD) derived from a superior modality (CT) serving as ground truth, projected onto digitally reconstructed radiographs (DRRs) to: 1) train a convolutional neural network to quantify airspace disease on paired CXRs; and 2) compare the DRR-trained CNN to expert human readers in the CXR evaluation of patients with confirmed COVID-19. Materials and Methods: We retrospectively selected a cohort of 86 COVID-19 patients (with positive RT-PCR), from March-May 2020 at a tertiary hospital in the northeastern USA, who underwent chest CT and CXR within 48 hrs. The ground truth volumetric percentage of COVID-19 related AD (POv) was established by manual AD segmentation on CT. The resulting 3D masks were projected into 2D anterior-posterior digitally reconstructed radiographs (DRR) to compute area-based AD percentage (POa). A convolutional neural network (CNN) was trained with DRR images generated from a larger-scale CT dataset of COVID-19 and non-COVID-19 patients, automatically segmenting lungs, AD and quantifying POa on CXR. CNN POa results were compared to POa quantified on CXR by two expert readers and to the POv ground-truth, by computing correlations and mean absolute errors. Results: Bootstrap mean absolute error (MAE) and correlations between POa and POv were 11.98% [11.05%-12.47%] and 0.77 [0.70-0.82] for average of expert readers, and 9.56%-9.78% [8.83%-10.22%] and 0.78-0.81 [0.73-0.85] for the CNN, respectively. Conclusion: Our CNN trained with DRR using CT-derived airspace quantification achieved expert radiologist level of accuracy in the quantification of airspace disease on CXR, in patients with positive RT-PCR for COVID-19.

eess.IV↗

arXiv2020

MLOS: An Infrastructure for Automated Software Performance Engineering

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.

cs.DC↗

arXiv2020

3D Tomographic Pattern Synthesis for Enhancing the Quantification of COVID-19

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).

eess.IV↗

arXiv2020

Sentiment Analysis of Yelp Reviews: A Comparison of Techniques and Models

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.

cs.CL↗

arXiv2020

Graph Attention Network based Pruning for Reconstructing 3D Liver Vessel Morphology from Contrasted CT Images

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.

eess.IV↗

arXiv2020

A Generalized Training Approach for Multiagent Learning

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, $α$-Rank, which is unique (thus faces no equilibrium selection issues, unlike Nash) and applies readily to general-sum, many-player settings. We establish convergence guarantees in several games classes, and identify links between Nash equilibria and $α$-Rank. We demonstrate the competitive performance of $α$-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 $α$-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.

cs.MA↗

arXiv2019

High-Dimensional Expanders from Expanders

We present an elementary way to transform an expander graph into a simplicial complex where all high order random walks have a constant spectral gap, i.e., they converge rapidly to the stationary distribution. As an upshot, we obtain new constructions, as well as a natural probabilistic model to sample constant degree high-dimensional expanders. In particular, we show that given an expander graph $G$, adding self loops to $G$ and taking the tensor product of the modified graph with a high-dimensional expander produces a new high-dimensional expander. Our proof of rapid mixing of high order random walks is based on the decomposable Markov chains framework introduced by Jerrum et al.

cs.DM↗

arXiv2019

Multi-Sensor 3D Object Box Refinement for Autonomous Driving

We propose a 3D object detection system with multi-sensor refinement in the context of autonomous driving. In our framework, the monocular camera serves as the fundamental sensor for 2D object proposal and initial 3D bounding box prediction. While the stereo cameras and LiDAR are treated as adaptive plug-in sensors to refine the 3D box localization performance. For each observed element in the raw measurement domain (e.g., pixels for stereo, 3D points for LiDAR), we model the local geometry as an instance vector representation, which indicates the 3D coordinate of each element respecting to the object frame. Using this unified geometric representation, the 3D object location can be unified refined by the stereo photometric alignment or point cloud alignment. We demonstrate superior 3D detection and localization performance compared to state-of-the-art monocular, stereo methods and competitive performance compared with the baseline LiDAR method on the KITTI object benchmark.

cs.CV↗

arXiv2019

V-MPO: On-Policy Maximum a Posteriori Policy Optimization for Discrete and Continuous Control

Some of the most successful applications of deep reinforcement learning to challenging domains in discrete and continuous control have used policy gradient methods in the on-policy setting. However, policy gradients can suffer from large variance that may limit performance, and in practice require carefully tuned entropy regularization to prevent policy collapse. As an alternative to policy gradient algorithms, we introduce V-MPO, an on-policy adaptation of Maximum a Posteriori Policy Optimization (MPO) that performs policy iteration based on a learned state-value function. We show that V-MPO surpasses previously reported scores for both the Atari-57 and DMLab-30 benchmark suites in the multi-task setting, and does so reliably without importance weighting, entropy regularization, or population-based tuning of hyperparameters. On individual DMLab and Atari levels, the proposed algorithm can achieve scores that are substantially higher than has previously been reported. V-MPO is also applicable to problems with high-dimensional, continuous action spaces, which we demonstrate in the context of learning to control simulated humanoids with 22 degrees of freedom from full state observations and 56 degrees of freedom from pixel observations, as well as example OpenAI Gym tasks where V-MPO achieves substantially higher asymptotic scores than previously reported.

cs.AI↗

arXiv2019

Griffon: Reasoning about Job Anomalies with Unlabeled Data in Cloud-based Platforms

Microsoft's internal big data analytics platform is comprised of hundreds of thousands of machines, serving over half a million jobs daily, from thousands of users. The majority of these jobs are recurring and are crucial for the company's operation. Although administrators spend significant effort tuning system performance, some jobs inevitably experience slowdowns, i.e., their execution time degrades over previous runs. Currently, the investigation of such slowdowns is a labor-intensive and error-prone process, which costs Microsoft significant human and machine resources, and negatively impacts several lines of businesses. In this work, we present Griffin, a system we built and have deployed in production last year to automatically discover the root cause of job slowdowns. Existing solutions either rely on labeled data (i.e., resolved incidents with labeled reasons for job slowdowns), which is in most cases non-existent or non-trivial to acquire, or on time-series analysis of individual metrics that do not target specific jobs holistically. In contrast, in Griffin we cast the problem to a corresponding regression one that predicts the runtime of a job, and show how the relative contributions of the features used to train our interpretable model can be exploited to rank the potential causes of job slowdowns. Evaluated over historical incidents, we show that Griffin discovers slowdown causes that are consistent with the ones validated by domain-expert engineers, in a fraction of the time required by them.

cs.LG↗

arXiv2019

Deep Reinforcement Learning for Clinical Decision Support: A Brief Survey

Owe to the recent advancements in Artificial Intelligence especially deep learning, many data-driven decision support systems have been implemented to facilitate medical doctors in delivering personalized care. We focus on the deep reinforcement learning (DRL) models in this paper. DRL models have demonstrated human-level or even superior performance in the tasks of computer vision and game playings, such as Go and Atari game. However, the adoption of deep reinforcement learning techniques in clinical decision optimization is still rare. We present the first survey that summarizes reinforcement learning algorithms with Deep Neural Networks (DNN) on clinical decision support. We also discuss some case studies, where different DRL algorithms were applied to address various clinical challenges. We further compare and contrast the advantages and limitations of various DRL algorithms and present a preliminary guide on how to choose the appropriate DRL algorithm for particular clinical applications.

cs.LG↗

arXiv2019

Emergent Coordination Through Competition

We study the emergence of cooperative behaviors in reinforcement learning agents by introducing a challenging competitive multi-agent soccer environment with continuous simulated physics. We demonstrate that decentralized, population-based training with co-play can lead to a progression in agents' behaviors: from random, to simple ball chasing, and finally showing evidence of cooperation. Our study highlights several of the challenges encountered in large scale multi-agent training in continuous control. In particular, we demonstrate that the automatic optimization of simple shaping rewards, not themselves conducive to co-operative behavior, can lead to long-horizon team behavior. We further apply an evaluation scheme, grounded by game theoretic principals, that can assess agent performance in the absence of pre-defined evaluation tasks or human baselines.

cs.AI↗

arXiv2019

Decompose to manipulate: Manipulable Object Synthesis in 3D Medical Images with Structured Image Decomposition

The performance of medical image analysis systems is constrained by the quantity of high-quality image annotations. Such systems require data to be annotated by experts with years of training, especially when diagnostic decisions are involved. Such datasets are thus hard to scale up. In this context, it is hard for supervised learning systems to generalize to the cases that are rare in the training set but would be present in real-world clinical practices. We believe that the synthetic image samples generated by a system trained on the real data can be useful for improving the supervised learning tasks in the medical image analysis applications. Allowing the image synthesis to be manipulable could help synthetic images provide complementary information to the training data rather than simply duplicating the real-data manifold. In this paper, we propose a framework for synthesizing 3D objects, such as pulmonary nodules, in 3D medical images with manipulable properties. The manipulation is enabled by decomposing of the object of interests into its segmentation mask and a 1D vector containing the residual information. The synthetic object is refined and blended into the image context with two adversarial discriminators. We evaluate the proposed framework on lung nodules in 3D chest CT images and show that the proposed framework could generate realistic nodules with manipulable shapes, textures and locations, etc. By sampling from both the synthetic nodules and the real nodules from 2800 3D CT volumes during the classifier training, we show the synthetic patches could improve the overall nodule detection performance by average 8.44% competition performance metric (CPM) score.

cs.CV↗

arXiv2019

Hierarchical visuomotor control of humanoids

We aim to build complex humanoid agents that integrate perception, motor control, and memory. In this work, we partly factor this problem into low-level motor control from proprioception and high-level coordination of the low-level skills informed by vision. We develop an architecture capable of surprisingly flexible, task-directed motor control of a relatively high-DoF humanoid body by combining pre-training of low-level motor controllers with a high-level, task-focused controller that switches among low-level sub-policies. The resulting system is able to control a physically-simulated humanoid body to solve tasks that require coupling visual perception from an unstabilized egocentric RGB camera during locomotion in the environment. For a supplementary video link, see https://youtu.be/7GISvfbykLE .

cs.AI↗

arXiv2018

Class-Aware Adversarial Lung Nodule Synthesis in CT Images

Though large-scale datasets are essential for training deep learning systems, it is expensive to scale up the collection of medical imaging datasets. Synthesizing the objects of interests, such as lung nodules, in medical images based on the distribution of annotated datasets can be helpful for improving the supervised learning tasks, especially when the datasets are limited by size and class balance. In this paper, we propose the class-aware adversarial synthesis framework to synthesize lung nodules in CT images. The framework is built with a coarse-to-fine patch in-painter (generator) and two class-aware discriminators. By conditioning on the random latent variables and the target nodule labels, the trained networks are able to generate diverse nodules given the same context. By evaluating on the public LIDC-IDRI dataset, we demonstrate an example application of the proposed framework for improving the accuracy of the lung nodule malignancy estimation as a binary classification problem, which is important in the lung screening scenario. We show that combining the real image patches and the synthetic lung nodules in the training set can improve the mean AUC classification score across different network architectures by 2%.

cs.CV↗

arXiv2018

Line Artist: A Multiple Style Sketch to Painting Synthesis Scheme

Drawing a beautiful painting is a dream of many people since childhood. In this paper, we propose a novel scheme, Line Artist, to synthesize artistic style paintings with freehand sketch images, leveraging the power of deep learning and advanced algorithms. Our scheme includes three models. The Sketch Image Extraction (SIE) model is applied to generate the training data. It includes smoothing reality images and pencil sketch extraction. The Detailed Image Synthesis (DIS) model trains a conditional generative adversarial network to generate detailed real-world information. The Adaptively Weighted Artistic Style Transfer (AWAST) model is capable to combine multiple style images with a content with the VGG19 network and PageRank algorithm. The appealing artistic images are then generated by optimization iterations. Experiments are operated on the Kaggle Cats dataset and The Oxford Buildings Dataset. Our synthesis results are proved to be artistic, beautiful and robust.

cs.CV↗