OpenRaiser/Intern-Atlas huggingface dataset:
Leveraging OpenStack and Ceph for a Controlled-Access Data Cloud
Venue: arXiv cs.DC 2018
Year: 2018

While traditional HPC has and continues to satisfy most workflows, a new generation of researchers has emerged looking for sophisticated, scalable, on-demand, and self-service control of compute infrastructure in a cloud-like environment. Many also seek safe harbors to operate on or store sensitive and/or controlled-access data in a high capacity environment. To cater to these modern users, the Minnesota Supercomputing Institute designed and deployed Stratus, a locally-hosted cloud environment powered by the OpenStack platform, and backed by Ceph storage. The subscription-based service complements existing HPC systems by satisfying the following unmet needs of our users: a) on-demand availability of compute resources, b) long-running jobs (i.e., $> 30$ days), c) container-based computing with Docker, and d) adequate security controls to comply with controlled-access data requirements. This document provides an in-depth look at the design of Stratus with respect to security and compliance with the NIH's controlled-access data policy. Emphasis is placed on lessons learned while integrating OpenStack and Ceph features into a so-called "walled garden", and how those technologies influenced the security design. Many features of Stratus, including tiered secure storage with the introduction of a controlled-access data "cache", fault-tolerant live-migrations, and fully integrated two-factor authentication, depend on recent OpenStack and Ceph features.
Automatic Speech Recognition for Humanitarian Applications in Somali
Venue: arXiv cs.CL 2018
Year: 2018

We present our first efforts in building an automatic speech recognition system for Somali, an under-resourced language, using 1.57 hrs of annotated speech for acoustic model training. The system is part of an ongoing effort by the United Nations (UN) to implement keyword spotting systems supporting humanitarian relief programmes in parts of Africa where languages are severely under-resourced. We evaluate several types of acoustic model, including recent neural architectures. Language model data augmentation using a combination of recurrent neural networks (RNN) and long short-term memory neural networks (LSTMs) as well as the perturbation of acoustic data are also considered. We find that both types of data augmentation are beneficial to performance, with our best system using a combination of convolutional neural networks (CNNs), time-delay neural networks (TDNNs) and bi-directional long short term memory (BLSTMs) to achieve a word error rate of 53.75%.
Submodular Function Maximization in Parallel via the Multilinear Relaxation
Venue: arXiv cs.DS 2018
Year: 2018

Balkanski and Singer [5] recently initiated the study of adaptivity (or parallelism) for constrained submodular function maximization, and studied the setting of a cardinality constraint. Very recent improvements for this problem by Balkanski, Rubinstein, and Singer [6] and Ene and Nguyen [21] resulted in a near-optimal $(1-1/e-ε)$-approximation in $O(\log n/ε^2)$ rounds of adaptivity. Partly motivated by the goal of extending these results to more general constraints, we describe parallel algorithms for approximately maximizing the multilinear relaxation of a monotone submodular function subject to packing constraints. Formally our problem is to maximize $F(x)$ over $x \in [0,1]^{n}$ subject to $Ax \le 1$ where $F$ is the multilinear relaxation of a monotone submodular function. Our algorithm achieves a near-optimal $(1-1/e-ε)$-approximation in $O(\log^2 m \log n/ε^4)$ rounds where $n$ is the cardinality of the ground set and $m$ is the number of packing constraints. For many constraints of interest, the resulting fractional solution can be rounded via known randomized rounding schemes that are oblivious to the specific submodular function. We thus derive randomized algorithms with poly-logarithmic adaptivity for a number of constraints including partition and laminar matroids, matchings, knapsack constraints, and their intersections.
SETH Says: Weak Fréchet Distance is Faster, but only if it is Continuous and in One Dimension
Venue: arXiv cs.CG 2018
Year: 2018

We show by reduction from the Orthogonal Vectors problem that algorithms with strongly subquadratic running time cannot approximate the Fréchet distance between curves better than a factor $3$ unless SETH fails. We show that similar reductions cannot achieve a lower bound with a factor better than $3$. Our lower bound holds for the continuous, the discrete, and the weak discrete Fréchet distance even for curves in one dimension. Interestingly, the continuous weak Fréchet distance behaves differently. Our lower bound still holds for curves in two dimensions and higher. However, for curves in one dimension, we provide an exact algorithm to compute the weak Fréchet distance in linear time.
Contrastive Explanations for Reinforcement Learning in terms of Expected Consequences
Venue: arXiv cs.LG 2018
Year: 2018

Machine Learning models become increasingly proficient in complex tasks. However, even for experts in the field, it can be difficult to understand what the model learned. This hampers trust and acceptance, and it obstructs the possibility to correct the model. There is therefore a need for transparency of machine learning models. The development of transparent classification models has received much attention, but there are few developments for achieving transparent Reinforcement Learning (RL) models. In this study we propose a method that enables a RL agent to explain its behavior in terms of the expected consequences of state transitions and outcomes. First, we define a translation of states and actions to a description that is easier to understand for human users. Second, we developed a procedure that enables the agent to obtain the consequences of a single action, as well as its entire policy. The method calculates contrasts between the consequences of a policy derived from a user query, and of the learned policy of the agent. Third, a format for generating explanations was constructed. A pilot survey study was conducted to explore preferences of users for different explanation properties. Results indicate that human users tend to favor explanations about policy rather than about single actions.
Effective Reformulation of Query for Code Search using Crowdsourced Knowledge and Extra-Large Data Analytics
Venue: arXiv cs.SE 2018
Year: 2018

Software developers frequently issue generic natural language queries for code search while using code search engines (e.g., GitHub native search, Krugle). Such queries often do not lead to any relevant results due to vocabulary mismatch problems. In this paper, we propose a novel technique that automatically identifies relevant and specific API classes from Stack Overflow Q & A site for a programming task written as a natural language query, and then reformulates the query for improved code search. We first collect candidate API classes from Stack Overflow using pseudo-relevance feedback and two term weighting algorithms, and then rank the candidates using Borda count and semantic proximity between query keywords and the API classes. The semantic proximity has been determined by an analysis of 1.3 million questions and answers of Stack Overflow. Experiments using 310 code search queries report that our technique suggests relevant API classes with 48% precision and 58% recall which are 32% and 48% higher respectively than those of the state-of-the-art. Comparisons with two state-of-the-art studies and three popular search engines (e.g., Google, Stack Overflow, and GitHub native search) report that our reformulated queries (1) outperform the queries of the state-of-the-art, and (2) significantly improve the code search results provided by these contemporary search engines.
Hierarchical Classification using Binary Data
Venue: arXiv cs.LG 2018
Year: 2018

In classification problems, especially those that categorize data into a large number of classes, the classes often naturally follow a hierarchical structure. That is, some classes are likely to share similar structures and features. Those characteristics can be captured by considering a hierarchical relationship among the class labels. Here, we extend a recent simple classification approach on binary data in order to efficiently classify hierarchical data. In certain settings, specifically, when some classes are significantly easier to identify than others, we showcase computational and accuracy advantages.
Lesion segmentation using U-Net network
Venue: arXiv cs.CV 2018
Year: 2018

This paper explains the method used in the segmentation challenge (Task 1) in the International Skin Imaging Collaboration's (ISIC) Skin Lesion Analysis Towards Melanoma Detection challenge held in 2018. We have trained a U-Net network to perform the segmentation. The key elements for the training were first to adjust the loss function to incorporate unbalanced proportion of background and second to perform post-processing operation to adjust the contour of the prediction.
Toward a language-theoretic foundation for planning and filtering
Venue: arXiv cs.AI 2018
Year: 2018

We address problems underlying the algorithmic question of automating the co-design of robot hardware in tandem with its apposite software. Specifically, we consider the impact that degradations of a robot's sensor and actuation suites may have on the ability of that robot to complete its tasks. We introduce a new formal structure that generalizes and consolidates a variety of well-known structures including many forms of plans, planning problems, and filters, into a single data structure called a procrustean graph, and give these graph structures semantics in terms of ideas based in formal language theory. We describe a collection of operations on procrustean graphs (both semantics-preserving and semantics-mutating), and show how a family of questions about the destructiveness of a change to the robot hardware can be answered by applying these operations. We also highlight the connections between this new approach and existing threads of research, including combinatorial filtering, Erdmann's strategy complexes, and hybrid automata.
Combining Heterogeneously Labeled Datasets For Training Segmentation Networks
Venue: arXiv cs.CV 2018
Year: 2018

Accurate segmentation of medical images is an important step towards analyzing and tracking disease related morphological alterations in the anatomy. Convolutional neural networks (CNNs) have recently emerged as a powerful tool for many segmentation tasks in medical imaging. The performance of CNNs strongly depends on the size of the training data and combining data from different sources is an effective strategy for obtaining larger training datasets. However, this is often challenged by heterogeneous labeling of the datasets. For instance, one of the dataset may be missing labels or a number of labels may have been combined into a super label. In this work we propose a cost function which allows integration of multiple datasets with heterogeneous label subsets into a joint training. We evaluated the performance of this strategy on thigh MR and a cardiac MR datasets in which we artificially merged labels for half of the data. We found the proposed cost function substantially outperforms a naive masking approach, obtaining results very close to using the full annotations.
A Temporal Difference Reinforcement Learning Theory of Emotion: unifying emotion, cognition and adaptive behavior
Venue: arXiv cs.AI 2018
Year: 2018

Emotions are intimately tied to motivation and the adaptation of behavior, and many animal species show evidence of emotions in their behavior. Therefore, emotions must be related to powerful mechanisms that aid survival, and, emotions must be evolutionary continuous phenomena. How and why did emotions evolve in nature, how do events get emotionally appraised, how do emotions relate to cognitive complexity, and, how do they impact behavior and learning? In this article I propose that all emotions are manifestations of reward processing, in particular Temporal Difference (TD) error assessment. Reinforcement Learning (RL) is a powerful computational model for the learning of goal oriented tasks by exploration and feedback. Evidence indicates that RL-like processes exist in many animal species. Key in the processing of feedback in RL is the notion of TD error, the assessment of how much better or worse a situation just became, compared to what was previously expected (or, the estimated gain or loss of utility - or well-being - resulting from new evidence). I propose a TDRL Theory of Emotion and discuss its ramifications for our understanding of emotions in humans, animals and machines, and present psychological, neurobiological and computational evidence in its support.
On critical and maximal digraphs
Venue: arXiv cs.DM 2018
Year: 2018

This paper is devoted to the study of directed graphs with extremal properties relative to certain metric functionals. We characterize up to isomorphism critical digraphs with infinite values of diameter, quasi-diameter, radius and quasi-radius. Moreover, maximal digraphs with finite values of radius and quasi-diameter are studied.
Creating e-learning means of free software
Venue: arXiv cs.CY 2018
Year: 2018

Informatization of education enriches traditional teaching methods with new forms and methods, which are based on the broad and harmonious use of ICT. Electronic pedagogy acquires the status of one of the most popular trends in the development of pedagogy of our time, in which such a tool as e-learning courses is the result of the accumulation of modern information and communication technologies with the theory and practice of e-learning. The article examines the standards of information exchange between learning systems and free software used to create e-learning courses. It is noted that electronic training courses are part of distance learning systems, as well as an independent tool. The considered systems of creation of electronic training courses allow creating electronic educational resources independently or partially, relying on the modern vision of the object model of information representation.
Real-Time Online Re-Planning for Grasping Under Clutter and Uncertainty
Venue: arXiv cs.RO 2018
Year: 2018

We consider the problem of grasping in clutter. While there have been motion planners developed to address this problem in recent years, these planners are mostly tailored for open-loop execution. Open-loop execution in this domain, however, is likely to fail, since it is not possible to model the dynamics of the multi-body multi-contact physical system with enough accuracy, neither is it reasonable to expect robots to know the exact physical properties of objects, such as frictional, inertial, and geometrical. Therefore, we propose an online re-planning approach for grasping through clutter. The main challenge is the long planning times this domain requires, which makes fast re-planning and fluent execution difficult to realize. In order to address this, we propose an easily parallelizable stochastic trajectory optimization based algorithm that generates a sequence of optimal controls. We show that by running this optimizer only for a small number of iterations, it is possible to perform real time re-planning cycles to achieve reactive manipulation under clutter and uncertainty.
On complexity of post-processing in analyzing GATE-driven X-ray spectrum
Venue: arXiv cs.ET 2018
Year: 2018

Computed Tomography (CT) imaging is one of the most influential diagnostic methods. In clinical reconstruction, an effective energy is used instead of total X-ray spectrum. This approximation causes an accuracy decline. To increase the contrast, single source or dual source dual energy CT can be used to reach optimal values of tissue differentiation. However, these infrastructures are still at the laboratory level, and their safeties for patients are still yet to mature. Therefore, computer modelling of DECT could be used. We propose a novel post-processing approach for converting a total X-ray spectrum into irregular intervals of quantized energy. We simulate a phantom in GATE/GEANT4 and irradiate it based on CT configuration. Inverse Radon transform is applied to the acquired sinogram to construct the Pixel-based Attenuation Matrix (PAM). To construct images represented by each interval, water attenuation coefficient of the interval is extracted from NIST and used in the Hounsfield unit (HU) scale in conjunction with PAM. The CT image is modified by using of an associated normalized photon flux and calculated HU corresponding to the interval. We demonstrate the proposed method efficiency via complexity analysis, using absolute and relative complexities, entropy measures, Kolmogorov complexity, morphological richness, and quantitative segmentation criteria associated with standard fuzzy C-means. The irregularity of the modified CT images decreases over the simulated ones.
Learning Human Poses from Actions
Venue: arXiv cs.CV 2018
Year: 2018

We consider the task of learning to estimate human pose in still images. In order to avoid the high cost of full supervision, we propose to use a diverse data set, which consists of two types of annotations: (i) a small number of images are labeled using the expensive ground-truth pose; and (ii) other images are labeled using the inexpensive action label. As action information helps narrow down the pose of a human, we argue that this approach can help reduce the cost of training without significantly affecting the accuracy. To demonstrate this we design a probabilistic framework that employs two distributions: (i) a conditional distribution to model the uncertainty over the human pose given the image and the action; and (ii) a prediction distribution, which provides the pose of an image without using any action information. We jointly estimate the parameters of the two aforementioned distributions by minimizing their dissimilarity coefficient, as measured by a task-specific loss function. During both training and testing, we only require an efficient sampling strategy for both the aforementioned distributions. This allows us to use deep probabilistic networks that are capable of providing accurate pose estimates for previously unseen images. Using the MPII data set, we show that our approach outperforms baseline methods that either do not use the diverse annotations or rely on pointwise estimates of the pose.
ISIC 2017 Skin Lesion Segmentation Using Deep Encoder-Decoder Network
Venue: arXiv cs.CV 2018
Year: 2018

This paper summarizes our method and validation results for part 1 of the ISBI Challenge 2018. Our algorithm makes use of deep encoder-decoder network and novel skin lesion data augmentation to segment the challenge objective. Besides, we also propose an effective testing strategy by applying multi-model comparison.
Algorithm Selection for Collaborative Filtering: the influence of graph metafeatures and multicriteria metatargets
Venue: arXiv cs.IR 2018
Year: 2018

To select the best algorithm for a new problem is an expensive and difficult task. However, there are automatic solutions to address this problem: using Metalearning, which takes advantage of problem characteristics (i.e. metafeatures), one is able to predict the relative performance of algorithms. In the Collaborative Filtering scope, recent works have proposed diverse metafeatures describing several dimensions of this problem. Despite interesting and effective findings, it is still unknown whether these are the most effective metafeatures. Hence, this work proposes a new set of graph metafeatures, which approach the Collaborative Filtering problem from a Graph Theory perspective. Furthermore, in order to understand whether metafeatures from multiple dimensions are a better fit, we investigate the effects of comprehensive metafeatures. These metafeatures are a selection of the best metafeatures from all existing Collaborative Filtering metafeatures. The impact of the most representative metafeatures is investigated in a controlled experimental setup. Another contribution we present is the use of a Pareto-Efficient ranking procedure to create multicriteria metatargets. These new rankings of algorithms, which take into account multiple evaluation measures, allow to explore the algorithm selection problem in a fairer and more detailed way. According to the experimental results, the graph metafeatures are a good alternative to related work metafeatures. However, the results have shown that the feature selection procedure used to create the comprehensive metafeatures is is not effective, since there is no gain in predictive performance. Finally, an extensive metaknowledge analysis was conducted to identify the most influential metafeatures.
On the computational analysis of the genetic algorithm for attitude control of a carrier system
Venue: arXiv cs.NE 2018
Year: 2018

This paper intends to cover three main topics. First, a fuzzy-PID controller is designed to control the thrust vector of a launch vehicle, accommodating a CanSat. Then, the genetic algorithm (GA) is employed to optimize the controller performance. Finally, through adjusting the algorithm parameters, their impact on the optimization process is examined. In this regard, the motion vector control is programmed based on the governing dynamic equations of motion for payload delivery in the desired altitude and flight-path angle. This utilizes one single input and one preferential fuzzy inference engine, where the latter acts to avoid the system instability in large angles for the thrust vector. The optimization objective functions include the deviations of the thrust vector and the system from the equilibrium state, which must be met simultaneously. Sensitivity analysis of the parameters of the genetic algorithm involves examining nine different cases and discussing their impact on the optimization results.
Multicolumn Networks for Face Recognition
Venue: arXiv cs.CV 2018
Year: 2018

The objective of this work is set-based face recognition, i.e. to decide if two sets of images of a face are of the same person or not. Conventionally, the set-wise feature descriptor is computed as an average of the descriptors from individual face images within the set. In this paper, we design a neural network architecture that learns to aggregate based on both "visual" quality (resolution, illumination), and "content" quality (relative importance for discriminative classification). To this end, we propose a Multicolumn Network (MN) that takes a set of images (the number in the set can vary) as input, and learns to compute a fix-sized feature descriptor for the entire set. To encourage high-quality representations, each individual input image is first weighted by its "visual" quality, determined by a self-quality assessment module, and followed by a dynamic recalibration based on "content" qualities relative to the other images within the set. Both of these qualities are learnt implicitly during training for set-wise classification. Comparing with the previous state-of-the-art architectures trained with the same dataset (VGGFace2), our Multicolumn Networks show an improvement of between 2-6% on the IARPA IJB face recognition benchmarks, and exceed the state of the art for all methods on these benchmarks.