Learning-based Single-step Quantitative Susceptibility Mapping Reconstruction Without Brain Extraction

Quantitative susceptibility mapping (QSM) estimates the underlying tissue magnetic susceptibility from MRI gradient-echo phase signal and typically requires several processing steps. These steps involve phase unwrapping, brain volume extraction, background phase removal and solving an ill-posed inverse problem. The resulting susceptibility map is known to suffer from inaccuracy near the edges of the brain tissues, in part due to imperfect brain extraction, edge erosion of the brain tissue and the lack of phase measurement outside the brain. This inaccuracy has thus hindered the application of QSM for measuring the susceptibility of tissues near the brain edges, e.g., quantifying cortical layers and generating superficial venography. To address these challenges, we propose a learning-based QSM reconstruction method that directly estimates the magnetic susceptibility from total phase images without the need for brain extraction and background phase removal, referred to as autoQSM. The neural network has a modified U-net structure and is trained using QSM maps computed by a two-step QSM method. 209 healthy subjects with ages ranging from 11 to 82 years were employed for patch-wise network training. The network was validated on data dissimilar to the training data, e.g. in vivo mouse brain data and brains with lesions, which suggests that the network has generalized and learned the underlying mathematical relationship between magnetic field perturbation and magnetic susceptibility. AutoQSM was able to recover magnetic susceptibility of anatomical structures near the edges of the brain including the veins covering the cortical surface, spinal cord and nerve tracts near the mouse brain boundaries. The advantages of high-quality maps, no need for brain volume extraction and high reconstruction speed demonstrate its potential for future applications.Comment: 26 page

Image Matters: Scalable Detection of Offensive and Non-Compliant Content / Logo in Product Images

In e-commerce, product content, especially product images have a significant influence on a customer's journey from product discovery to evaluation and finally, purchase decision. Since many e-commerce retailers sell items from other third-party marketplace sellers besides their own, the content published by both internal and external content creators needs to be monitored and enriched, wherever possible. Despite guidelines and warnings, product listings that contain offensive and non-compliant images continue to enter catalogs. Offensive and non-compliant content can include a wide range of objects, logos, and banners conveying violent, sexually explicit, racist, or promotional messages. Such images can severely damage the customer experience, lead to legal issues, and erode the company brand. In this paper, we present a computer vision driven offensive and non-compliant image detection system for extremely large image datasets. This paper delves into the unique challenges of applying deep learning to real-world product image data from retail world. We demonstrate how we resolve a number of technical challenges such as lack of training data, severe class imbalance, fine-grained class definitions etc. using a number of practical yet unique technical strategies. Our system combines state-of-the-art image classification and object detection techniques with budgeted crowdsourcing to develop a solution customized for a massive, diverse, and constantly evolving product catalog.Comment: 10 page

signSGD with Majority Vote is Communication Efficient And Fault Tolerant

Training neural networks on large datasets can be accelerated by distributing the workload over a network of machines. As datasets grow ever larger, networks of hundreds or thousands of machines become economically viable. The time cost of communicating gradients limits the effectiveness of using such large machine counts, as may the increased chance of network faults. We explore a particularly simple algorithm for robust, communication-efficient learning---signSGD. Workers transmit only the sign of their gradient vector to a server, and the overall update is decided by a majority vote. This algorithm uses $32\times$ less communication per iteration than full-precision, distributed SGD. Under natural conditions verified by experiment, we prove that signSGD converges in the large and mini-batch settings, establishing convergence for a parameter regime of Adam as a byproduct. Aggregating sign gradients by majority vote means that no individual worker has too much power. We prove that unlike SGD, majority vote is robust when up to 50% of workers behave adversarially. The class of adversaries we consider includes as special cases those that invert or randomise their gradient estimate. On the practical side, we built our distributed training system in Pytorch. Benchmarking against the state of the art collective communications library (NCCL), our framework---with the parameter server housed entirely on one machine---led to a 25% reduction in time for training resnet50 on Imagenet when using 15 AWS p3.2xlarge machines

On Deep Set Learning and the Choice of Aggregations

Recently, it has been shown that many functions on sets can be represented by sum decompositions. These decompositons easily lend themselves to neural approximations, extending the applicability of neural nets to set-valued inputs---Deep Set learning. This work investigates a core component of Deep Set architecture: aggregation functions. We suggest and examine alternatives to commonly used aggregation functions, including learnable recurrent aggregation functions. Empirically, we show that the Deep Set networks are highly sensitive to the choice of aggregation functions: beyond improved performance, we find that learnable aggregations lower hyper-parameter sensitivity and generalize better to out-of-distribution input size

Notes on Deep Learning for NLP

My notes on Deep Learning for NLP.Comment: work in progres

Implementation Matters in Deep Policy Gradients: A Case Study on PPO and TRPO

We study the roots of algorithmic progress in deep policy gradient algorithms through a case study on two popular algorithms: Proximal Policy Optimization (PPO) and Trust Region Policy Optimization (TRPO). Specifically, we investigate the consequences of "code-level optimizations:" algorithm augmentations found only in implementations or described as auxiliary details to the core algorithm. Seemingly of secondary importance, such optimizations turn out to have a major impact on agent behavior. Our results show that they (a) are responsible for most of PPO's gain in cumulative reward over TRPO, and (b) fundamentally change how RL methods function. These insights show the difficulty and importance of attributing performance gains in deep reinforcement learning. Code for reproducing our results is available at https://github.com/MadryLab/implementation-matters .Comment: ICLR 2020 version. arXiv admin note: text overlap with arXiv:1811.0255

Deep Learning: Generalization Requires Deep Compositional Feature Space Design

Generalization error defines the discriminability and the representation power of a deep model. In this work, we claim that feature space design using deep compositional function plays a significant role in generalization along with explicit and implicit regularizations. Our claims are being established with several image classification experiments. We show that the information loss due to convolution and max pooling can be marginalized with the compositional design, improving generalization performance. Also, we will show that learning rate decay acts as an implicit regularizer in deep model training.Comment: fig added, with minor typo correction

Automatic Liver Lesion Segmentation Using A Deep Convolutional Neural Network Method

Liver lesion segmentation is an important step for liver cancer diagnosis, treatment planning and treatment evaluation. LiTS (Liver Tumor Segmentation Challenge) provides a common testbed for comparing different automatic liver lesion segmentation methods. We participate in this challenge by developing a deep convolutional neural network (DCNN) method. The particular DCNN model works in 2.5D in that it takes a stack of adjacent slices as input and produces the segmentation map corresponding to the center slice. The model has 32 layers in total and makes use of both long range concatenation connections of U-Net [1] and short-range residual connections from ResNet [2]. The model was trained using the 130 LiTS training datasets and achieved an average Dice score of 0.67 when evaluated on the 70 test CT scans, which ranked first for the LiTS challenge at the time of the ISBI 2017 conference.Comment: Submission for ISBI'2017 LiTS Challenge ISIC201

Experiments on Parallel Training of Deep Neural Network using Model Averaging

In this work we apply model averaging to parallel training of deep neural network (DNN). Parallelization is done in a model averaging manner. Data is partitioned and distributed to different nodes for local model updates, and model averaging across nodes is done every few minibatches. We use multiple GPUs for data parallelization, and Message Passing Interface (MPI) for communication between nodes, which allows us to perform model averaging frequently without losing much time on communication. We investigate the effectiveness of Natural Gradient Stochastic Gradient Descent (NG-SGD) and Restricted Boltzmann Machine (RBM) pretraining for parallel training in model-averaging framework, and explore the best setups in term of different learning rate schedules, averaging frequencies and minibatch sizes. It is shown that NG-SGD and RBM pretraining benefits parameter-averaging based model training. On the 300h Switchboard dataset, a 9.3 times speedup is achieved using 16 GPUs and 17 times speedup using 32 GPUs with limited decoding accuracy loss

STAIR Actions: A Video Dataset of Everyday Home Actions

A new large-scale video dataset for human action recognition, called STAIR Actions is introduced. STAIR Actions contains 100 categories of action labels representing fine-grained everyday home actions so that it can be applied to research in various home tasks such as nursing, caring, and security. In STAIR Actions, each video has a single action label. Moreover, for each action category, there are around 1,000 videos that were obtained from YouTube or produced by crowdsource workers. The duration of each video is mostly five to six seconds. The total number of videos is 102,462. We explain how we constructed STAIR Actions and show the characteristics of STAIR Actions compared to existing datasets for human action recognition. Experiments with three major models for action recognition show that STAIR Actions can train large models and achieve good performance. STAIR Actions can be downloaded from http://actions.stair.centerComment: STAIR Actions dataset can be downloaded from http://actions.stair.cente