OpenRaiser/Intern-Atlas huggingface dataset:
Semantic Segmentation of highly class imbalanced fully labelled 3D volumetric biomedical images and unsupervised Domain Adaptation of the pre-trained Segmentation Network to segment another fully unlabelled Biomedical 3D Image stack
Venue: arXiv cs.CV 2020
Year: 2020

The goal of our work is to perform pixel label semantic segmentation on 3D biomedical volumetric data. Manual annotation is always difficult for a large bio-medical dataset. So, we consider two cases where one dataset is fully labeled and the other dataset is assumed to be fully unlabelled. We first perform Semantic Segmentation on the fully labeled isotropic biomedical source data (FIBSEM) and try to incorporate the the trained model for segmenting the target unlabelled dataset(SNEMI3D)which shares some similarities with the source dataset in the context of different types of cellular bodies and other cellular components. Although, the cellular components vary in size and shape. So in this paper, we have proposed a novel approach in the context of unsupervised domain adaptation while classifying each pixel of the target volumetric data into cell boundary and cell body. Also, we have proposed a novel approach to giving non-uniform weights to different pixels in the training images while performing the pixel-level semantic segmentation in the presence of the corresponding pixel-wise label map along with the training original images in the source domain. We have used the Entropy Map or a Distance Transform matrix retrieved from the given ground truth label map which has helped to overcome the class imbalance problem in the medical image data where the cell boundaries are extremely thin and hence, extremely prone to be misclassified as non-boundary.
Online Hyperparameter Search Interleaved with Proximal Parameter Updates
Venue: arXiv cs.LG 2020
Year: 2020

There is a clear need for efficient algorithms to tune hyperparameters for statistical learning schemes, since the commonly applied search methods (such as grid search with N-fold cross-validation) are inefficient and/or approximate. Previously existing algorithms that efficiently search for hyperparameters relying on the smoothness of the cost function cannot be applied in problems such as Lasso regression. In this contribution, we develop a hyperparameter optimization method that relies on the structure of proximal gradient methods and does not require a smooth cost function. Such a method is applied to Leave-one-out (LOO)-validated Lasso and Group Lasso to yield efficient, data-driven, hyperparameter optimization algorithms. Numerical experiments corroborate the convergence of the proposed method to a local optimum of the LOO validation error curve, and the efficiency of its approximations.
A Survey of Convolutional Neural Networks: Analysis, Applications, and Prospects
Venue: arXiv cs.CV 2020
Year: 2020

Convolutional Neural Network (CNN) is one of the most significant networks in the deep learning field. Since CNN made impressive achievements in many areas, including but not limited to computer vision and natural language processing, it attracted much attention both of industry and academia in the past few years. The existing reviews mainly focus on the applications of CNN in different scenarios without considering CNN from a general perspective, and some novel ideas proposed recently are not covered. In this review, we aim to provide novel ideas and prospects in this fast-growing field as much as possible. Besides, not only two-dimensional convolution but also one-dimensional and multi-dimensional ones are involved. First, this review starts with a brief introduction to the history of CNN. Second, we provide an overview of CNN. Third, classic and advanced CNN models are introduced, especially those key points making them reach state-of-the-art results. Fourth, through experimental analysis, we draw some conclusions and provide several rules of thumb for function selection. Fifth, the applications of one-dimensional, two-dimensional, and multi-dimensional convolution are covered. Finally, some open issues and promising directions for CNN are discussed to serve as guidelines for future work.
Rethinking Spatially-Adaptive Normalization
Venue: arXiv cs.CV 2020
Year: 2020

Spatially-adaptive normalization is remarkably successful recently in conditional semantic image synthesis, which modulates the normalized activation with spatially-varying transformations learned from semantic layouts, to preserve the semantic information from being washed away. Despite its impressive performance, a more thorough understanding of the true advantages inside the box is still highly demanded, to help reduce the significant computation and parameter overheads introduced by these new structures. In this paper, from a return-on-investment point of view, we present a deep analysis of the effectiveness of SPADE and observe that its advantages actually come mainly from its semantic-awareness rather than the spatial-adaptiveness. Inspired by this point, we propose class-adaptive normalization (CLADE), a lightweight variant that is not adaptive to spatial positions or layouts. Benefited from this design, CLADE greatly reduces the computation cost while still being able to preserve the semantic information during the generation. Extensive experiments on multiple challenging datasets demonstrate that while the resulting fidelity is on par with SPADE, its overhead is much cheaper than SPADE. Take the generator for ADE20k dataset as an example, the extra parameter and computation cost introduced by CLADE are only 4.57% and 0.07% while that of SPADE are 39.21% and 234.73% respectively.
Empirical Upper Bound, Error Diagnosis and Invariance Analysis of Modern Object Detectors
Venue: arXiv cs.CV 2020
Year: 2020

Object detection remains as one of the most notorious open problems in computer vision. Despite large strides in accuracy in recent years, modern object detectors have started to saturate on popular benchmarks raising the question of how far we can reach with deep learning tools and tricks. Here, by employing 2 state-of-the-art object detection benchmarks, and analyzing more than 15 models over 4 large scale datasets, we I) carefully determine the upper bound in AP, which is 91.6% on VOC (test2007), 78.2% on COCO (val2017), and 58.9% on OpenImages V4 (validation), regardless of the IOU threshold. These numbers are much better than the mAP of the best model (47.9% on VOC, and 46.9% on COCO; IOUs=.5:.05:.95), II) characterize the sources of errors in object detectors, in a novel and intuitive way, and find that classification error (confusion with other classes and misses) explains the largest fraction of errors and weighs more than localization and duplicate errors, and III) analyze the invariance properties of models when surrounding context of an object is removed, when an object is placed in an incongruent background, and when images are blurred or flipped vertically. We find that models generate a lot of boxes on empty regions and that context is more important for detecting small objects than larger ones. Our work taps into the tight relationship between object detection and object recognition and offers insights for building better models. Our code is publicly available at https://github.com/aliborji/Deetctionupper bound.git.
Efficient Scale Estimation Methods using Lightweight Deep Convolutional Neural Networks for Visual Tracking
Venue: arXiv cs.CV 2020
Year: 2020

In recent years, visual tracking methods that are based on discriminative correlation filters (DCF) have been very promising. However, most of these methods suffer from a lack of robust scale estimation skills. Although a wide range of recent DCF-based methods exploit the features that are extracted from deep convolutional neural networks (CNNs) in their translation model, the scale of the visual target is still estimated by hand-crafted features. Whereas the exploitation of CNNs imposes a high computational burden, this paper exploits pre-trained lightweight CNNs models to propose two efficient scale estimation methods, which not only improve the visual tracking performance but also provide acceptable tracking speeds. The proposed methods are formulated based on either holistic or region representation of convolutional feature maps to efficiently integrate into DCF formulations to learn a robust scale model in the frequency domain. Moreover, against the conventional scale estimation methods with iterative feature extraction of different target regions, the proposed methods exploit proposed one-pass feature extraction processes that significantly improve the computational efficiency. Comprehensive experimental results on the OTB-50, OTB-100, TC-128 and VOT-2018 visual tracking datasets demonstrate that the proposed visual tracking methods outperform the state-of-the-art methods, effectively.
Gender-specific behavior change following terror attacks
Venue: arXiv cs.SI 2020
Year: 2020

Terrorists use violence in pursuit of political goals. While terror often has severe consequences for victims, it remains an open question how terror attacks affect the general population. We study the behavioral response of citizens of cities affected by $7$ different terror attacks. We compare real-time mobile communication patterns in the first $24$ hours following a terror attack to the corresponding patterns on days with no terror attack. On ordinary days, the group of female and male participants have different activity patterns. Following a terror attack, however, we observe a significant increase of the gender differences. Knowledge about citizens' behavior response patterns following terror attacks may have important implications for the public response during and after an attack.
Swarm robotics and complex behaviour of continuum material
Venue: arXiv cs.CE 2020
Year: 2020

In swarm robotics, just as for an animal swarm in Nature, one of the aims is to reach and maintain a desired configuration. One of the possibilities for the team, to reach this aim, is to see what its neighbours are doing. This approach generates a rules system governing the movement of the single robot just by reference to neighbour's motion. The same approach is used in position based dynamics to simulate behaviour of complex continuum materials under deformation. Therefore, in some previous works, we have considered a two-dimensional lattice of particles and calculated its time evolution by using a rules system derived from our experience in swarm robotics. The new position of a particle, like the element of a swarm, is determined by the spatial position of the other particles. No dynamic is considered, but it can be thought as being hidden in the behaviour rules. This method has given good results in some simple situations reproducing the behaviour of deformable bodies under imposed strain. In this paper we try to stress our model to highlight its limits and how they can be improved. Some other, more complex, examples are computed and discussed. Shear test, different lattice, different fracture mechanism and ASTM shape sample behaviour have been investigated by the software tool we have developed.
MobileBERT: a Compact Task-Agnostic BERT for Resource-Limited Devices
Venue: arXiv cs.CL 2020
Year: 2020

Natural Language Processing (NLP) has recently achieved great success by using huge pre-trained models with hundreds of millions of parameters. However, these models suffer from heavy model sizes and high latency such that they cannot be deployed to resource-limited mobile devices. In this paper, we propose MobileBERT for compressing and accelerating the popular BERT model. Like the original BERT, MobileBERT is task-agnostic, that is, it can be generically applied to various downstream NLP tasks via simple fine-tuning. Basically, MobileBERT is a thin version of BERT_LARGE, while equipped with bottleneck structures and a carefully designed balance between self-attentions and feed-forward networks. To train MobileBERT, we first train a specially designed teacher model, an inverted-bottleneck incorporated BERT_LARGE model. Then, we conduct knowledge transfer from this teacher to MobileBERT. Empirical studies show that MobileBERT is 4.3x smaller and 5.5x faster than BERT_BASE while achieving competitive results on well-known benchmarks. On the natural language inference tasks of GLUE, MobileBERT achieves a GLUEscore o 77.7 (0.6 lower than BERT_BASE), and 62 ms latency on a Pixel 4 phone. On the SQuAD v1.1/v2.0 question answering task, MobileBERT achieves a dev F1 score of 90.0/79.2 (1.5/2.1 higher than BERT_BASE).
Can Two Walk Together: Privacy Enhancing Methods and Preventing Tracking of Users
Venue: arXiv cs.CR 2020
Year: 2020

We present a new concern when collecting data from individuals that arises from the attempt to mitigate privacy leakage in multiple reporting: tracking of users participating in the data collection via the mechanisms added to provide privacy. We present several definitions for untrackable mechanisms, inspired by the differential privacy framework. Specifically, we define the trackable parameter as the log of the maximum ratio between the probability that a set of reports originated from a single user and the probability that the same set of reports originated from two users (with the same private value). We explore the implications of this new definition. We show how differentially private and untrackable mechanisms can be combined to achieve a bound for the problem of detecting when a certain user changed their private value. Examining Google's deployed solution for everlasting privacy, we show that RAPPOR (Erlingsson et al. ACM CCS, 2014) is trackable in our framework for the parameters presented in their paper. We analyze a variant of randomized response for collecting statistics of single bits, Bitwise Everlasting Privacy, that achieves good accuracy and everlasting privacy, while only being reasonably untrackable, specifically grows linearly in the number of reports. For collecting statistics about data from larger domains (for histograms and heavy hitters) we present a mechanism that prevents tracking for a limited number of responses. We also present the concept of Mechanism Chaining, using the output of one mechanism as the input of another, in the scope of Differential Privacy, and show that the chaining of an $\varepsilon_1$-LDP mechanism with an $\varepsilon_2$-LDP mechanism is $\ln\frac{e^{\varepsilon_1+\varepsilon_2}+1}{e^{\varepsilon_1}+e^{\varepsilon_2}}$-LDP and that this bound is tight.
Graph Distances and Clustering
Venue: arXiv cs.DM 2020
Year: 2020

With a view on graph clustering, we present a definition of vertex-to-vertex distance which is based on shared connectivity. We argue that vertices sharing more connections are closer to each other than vertices sharing fewer connections. Our thesis is centered on the widely accepted notion that strong clusters are formed by high levels of induced subgraph density, where subgraphs represent clusters. We argue these clusters are formed by grouping vertices deemed to be similar in their connectivity. At the cluster level (induced subgraph level), our thesis translates into low mean intra-cluster distances. Our definition differs from the usual shortest-path geodesic distance. In this article, we compare three distance measures from the literature. Our benchmark is the accuracy of each measure's reflection of intra-cluster density, when aggregated (averaged) at the cluster level. We conduct our tests on synthetic graphs generated using the planted partition model, where clusters and intra-cluster density are known in advance. We examine correlations between mean intra-cluster distances and intra-cluster densities. Our numerical experiments show that Jaccard and Otsuka-Ochiai offer very accurate measures of density, when averaged over vertex pairs within clusters.
SOPanG 2: online searching over a pan-genome without false positives
Venue: arXiv cs.DS 2020
Year: 2020

Motivation: The pan-genome can be stored as elastic-degenerate (ED) string, a recently introduced compact representation of multiple overlapping sequences. However, a search over the ED string does not indicate which individuals (if any) match the entire query. Results: We augment the ED string with sources (individuals' indexes) and propose an extension of the SOPanG (Shift-Or for Pan-Genome) tool to report only true positive matches, omitting those not occurring in any of the haplotypes. The additional stage for checking the matches yields a penalty of less than 3.5% relative speed in practice, which means that SOPanG 2 is able to report pattern matches in a pan-genome, mapping them onto individuals, at the single-thread throughput of above 430 MB/s on real data. Availability and implementation: SOPanG 2 can be downloaded here: github.com/MrAlexSee/sopang
When, Where, and What? A New Dataset for Anomaly Detection in Driving Videos
Venue: arXiv cs.CV 2020
Year: 2020

Video anomaly detection (VAD) has been extensively studied. However, research on egocentric traffic videos with dynamic scenes lacks large-scale benchmark datasets as well as effective evaluation metrics. This paper proposes traffic anomaly detection with a \textit{when-where-what} pipeline to detect, localize, and recognize anomalous events from egocentric videos. We introduce a new dataset called Detection of Traffic Anomaly (DoTA) containing 4,677 videos with temporal, spatial, and categorical annotations. A new spatial-temporal area under curve (STAUC) evaluation metric is proposed and used with DoTA. State-of-the-art methods are benchmarked for two VAD-related tasks.Experimental results show STAUC is an effective VAD metric. To our knowledge, DoTA is the largest traffic anomaly dataset to-date and is the first supporting traffic anomaly studies across when-where-what perspectives. Our code and dataset can be found in: https://github.com/MoonBlvd/Detection-of-Traffic-Anomaly
A Method for Curation of Web-Scraped Face Image Datasets
Venue: arXiv cs.CV 2020
Year: 2020

Web-scraped, in-the-wild datasets have become the norm in face recognition research. The numbers of subjects and images acquired in web-scraped datasets are usually very large, with number of images on the millions scale. A variety of issues occur when collecting a dataset in-the-wild, including images with the wrong identity label, duplicate images, duplicate subjects and variation in quality. With the number of images being in the millions, a manual cleaning procedure is not feasible. But fully automated methods used to date result in a less-than-ideal level of clean dataset. We propose a semi-automated method, where the goal is to have a clean dataset for testing face recognition methods, with similar quality across men and women, to support comparison of accuracy across gender. Our approach removes near-duplicate images, merges duplicate subjects, corrects mislabeled images, and removes images outside a defined range of pose and quality. We conduct the curation on the Asian Face Dataset (AFD) and VGGFace2 test dataset. The experiments show that a state-of-the-art method achieves a much higher accuracy on the datasets after they are curated. Finally, we release our cleaned versions of both datasets to the research community.
Exemplar Auditing for Multi-Label Biomedical Text Classification
Venue: arXiv cs.CL 2020
Year: 2020

Many practical applications of AI in medicine consist of semi-supervised discovery: The investigator aims to identify features of interest at a resolution more fine-grained than that of the available human labels. This is often the scenario faced in healthcare applications as coarse, high-level labels (e.g., billing codes) are often the only sources that are readily available. These challenges are compounded for modalities such as text, where the feature space is very high-dimensional, and often contains considerable amounts of noise. In this work, we generalize a recently proposed zero-shot sequence labeling method, "binary labeling via a convolutional decomposition", to the case where the available document-level human labels are themselves relatively high-dimensional. The approach yields classification with "introspection", relating the fine-grained features of an inference-time prediction to their nearest neighbors from the training set, under the model. The approach is effective, yet parsimonious, as demonstrated on a well-studied MIMIC-III multi-label classification task of electronic health record data, and is useful as a tool for organizing the analysis of neural model predictions and high-dimensional datasets. Our proposed approach yields both a competitively effective classification model and an interrogation mechanism to aid healthcare workers in understanding the salient features that drive the model's predictions.
Improved Bounds and Algorithms for Sparsity-Constrained Group Testing
Venue: arXiv cs.IT 2020
Year: 2020

In group testing, the goal is to identify a subset of defective items within a larger set of items based on tests whose outcomes indicate whether any defective item is present. This problem is relevant in areas such as medical testing, data science, communications, and many more. Motivated by physical considerations, we consider a sparsity-based constrained setting (Gandikota et al., 2019) in which the testing procedure is subject to one of the following two constraints: items are finitely divisible and thus may participate in at most $γ$ tests; or tests are size-constrained to pool no more than $ρ$ items per test. While information-theoretic limits and algorithms are known for the non-adaptive setting, relatively little is known in the adaptive setting. We address this gap by providing an information-theoretic converse that holds even in the adaptive setting, as well as a near-optimal noiseless adaptive algorithm for $γ$-divisible items. In broad scaling regimes, our upper and lower bounds asymptotically match up to a factor of $e$. We also present a simple asymptotically optimal adaptive algorithm for $ρ$-sized tests. In addition, in the non-adaptive setting with $γ$-divisible items, we use the Definite Defectives (DD) decoding algorithm and study bounds on the required number of tests for vanishing error probability under the random near-constant test-per-item design. We show that the number of tests required can be significantly less than the Combinatorial Orthogonal Matching Pursuit (COMP) decoding algorithm, and is asymptotically optimal in broad scaling regimes.
Human Motion Transfer from Poses in the Wild
Venue: arXiv cs.CV 2020
Year: 2020

In this paper, we tackle the problem of human motion transfer, where we synthesize novel motion video for a target person that imitates the movement from a reference video. It is a video-to-video translation task in which the estimated poses are used to bridge two domains. Despite substantial progress on the topic, there exist several problems with the previous methods. First, there is a domain gap between training and testing pose sequences--the model is tested on poses it has not seen during training, such as difficult dancing moves. Furthermore, pose detection errors are inevitable, making the job of the generator harder. Finally, generating realistic pixels from sparse poses is challenging in a single step. To address these challenges, we introduce a novel pose-to-video translation framework for generating high-quality videos that are temporally coherent even for in-the-wild pose sequences unseen during training. We propose a pose augmentation method to minimize the training-test gap, a unified paired and unpaired learning strategy to improve the robustness to detection errors, and two-stage network architecture to achieve superior texture quality. To further boost research on the topic, we build two human motion datasets. Finally, we show the superiority of our approach over the state-of-the-art studies through extensive experiments and evaluations on different datasets.