OpenRaiser/Intern-Atlas huggingface dataset:
Enhancing speed and scalability of the ParFlow simulation code
Venue: arXiv cs.MS 2017
Year: 2017

Regional hydrology studies are often supported by high resolution simulations of subsurface flow that require expensive and extensive computations. Efficient usage of the latest high performance parallel computing systems becomes a necessity. The simulation software ParFlow has been demonstrated to meet this requirement and shown to have excellent solver scalability for up to 16,384 processes. In the present work we show that the code requires further enhancements in order to fully take advantage of current petascale machines. We identify ParFlow's way of parallelization of the computational mesh as a central bottleneck. We propose to reorganize this subsystem using fast mesh partition algorithms provided by the parallel adaptive mesh refinement library p4est. We realize this in a minimally invasive manner by modifying selected parts of the code to reinterpret the existing mesh data structures. We evaluate the scaling performance of the modified version of ParFlow, demonstrating good weak and strong scaling up to 458k cores of the Juqueen supercomputer, and test an example application at large scale.
Scaling Deep Learning-based Decoding of Polar Codes via Partitioning
Venue: arXiv cs.IT 2017
Year: 2017

The training complexity of deep learning-based channel decoders scales exponentially with the codebook size and therefore with the number of information bits. Thus, neural network decoding (NND) is currently only feasible for very short block lengths. In this work, we show that the conventional iterative decoding algorithm for polar codes can be enhanced when sub-blocks of the decoder are replaced by neural network (NN) based components. Thus, we partition the encoding graph into smaller sub-blocks and train them individually, closely approaching maximum a posteriori (MAP) performance per sub-block. These blocks are then connected via the remaining conventional belief propagation decoding stage(s). The resulting decoding algorithm is non-iterative and inherently enables a high-level of parallelization, while showing a competitive bit error rate (BER) performance. We examine the degradation through partitioning and compare the resulting decoder to state-of-the-art polar decoders such as successive cancellation list and belief propagation decoding.
Approximating Unique Games Using Low Diameter Graph Decomposition
Venue: arXiv cs.DS 2017
Year: 2017

We design approximation algorithms for Unique Games when the constraint graph admits good low diameter graph decomposition. For the ${\sf Max2Lin}_k$ problem in $K_r$-minor free graphs, when there is an assignment satisfying $1-\varepsilon$ fraction of constraints, we present an algorithm that produces an assignment satisfying $1-O(r\varepsilon)$ fraction of constraints, with the approximation ratio independent of the alphabet size. A corollary is an improved approximation algorithm for the ${\sf MaxCut}$ problem for $K_r$-minor free graphs. For general Unique Games in $K_r$-minor free graphs, we provide another algorithm that produces an assignment satisfying $1-O(r \sqrt{\varepsilon})$ fraction of constraints. Our approach is to round a linear programming relaxation to find a minimum subset of edges that intersects all the inconsistent cycles. We show that it is possible to apply the low diameter graph decomposition technique on the constraint graph directly, rather than to work on the label extended graph as in previous algorithms for Unique Games. The same approach applies when the constraint graph is of genus $g$, and we get similar results with $r$ replaced by $\log g$ in the ${\sf Max2Lin}_k$ problem and by $\sqrt{\log g}$ in the general problem. The former result generalizes the result of Gupta-Talwar for Unique Games in the ${\sf Max2Lin}_k$ case, and the latter result generalizes the result of Trevisan for general Unique Games.
Convolutional Neural Network Committees for Melanoma Classification with Classical And Expert Knowledge Based Image Transforms Data Augmentation
Venue: arXiv cs.CV 2017
Year: 2017

Skin cancer is a major public health problem, as is the most common type of cancer and represents more than half of cancer diagnoses worldwide. Early detection influences the outcome of the disease and motivates our work. We investigate the composition of CNN committees and data augmentation for the the ISBI 2017 Melanoma Classification Challenge (named Skin Lesion Analysis towards Melanoma Detection) facing the peculiarities of dealing with such a small, unbalanced, biological database. For that, we explore committees of Convolutional Neural Networks trained over the ISBI challenge training dataset artificially augmented by both classical image processing transforms and image warping guided by specialist knowledge about the lesion axis and improve the final classifier invariance to common melanoma variations.
Learning Chained Deep Features and Classifiers for Cascade in Object Detection
Venue: arXiv cs.CV 2017
Year: 2017

Cascade is a widely used approach that rejects obvious negative samples at early stages for learning better classifier and faster inference. This paper presents chained cascade network (CC-Net). In this CC-Net, the cascaded classifier at a stage is aided by the classification scores in previous stages. Feature chaining is further proposed so that the feature learning for the current cascade stage uses the features in previous stages as the prior information. The chained ConvNet features and classifiers of multiple stages are jointly learned in an end-to-end network. In this way, features and classifiers at latter stages handle more difficult samples with the help of features and classifiers in previous stages. It yields consistent boost in detection performance on benchmarks like PASCAL VOC 2007 and ImageNet. Combined with better region proposal, CC-Net leads to state-of-the-art result of 81.1% mAP on PASCAL VOC 2007.
Algorithm for computing semi-Fourier sequences of expressions involving exponentiations and integrations
Venue: arXiv cs.SC 2017
Year: 2017

We provide an algorithm for computing semi-Fourier sequences for expressions constructed from arithmetic operations, exponentiations and integrations. The semi-Fourier sequence is a relaxed version of Fourier sequence for polynomials (expressions made of additions and multiplications).
Pronunciation recognition of English phonemes /\textipa{@}/, /æ/, /\textipa{A}:/ and /\textipa{2}/ using Formants and Mel Frequency Cepstral Coefficients
Venue: arXiv cs.CL 2017
Year: 2017

The Vocal Joystick Vowel Corpus, by Washington University, was used to study monophthongs pronounced by native English speakers. The objective of this study was to quantitatively measure the extent at which speech recognition methods can distinguish between similar sounding vowels. In particular, the phonemes /\textipa{@}/, /æ/, /\textipa{A}:/ and /\textipa{2}/ were analysed. 748 sound files from the corpus were used and subjected to Linear Predictive Coding (LPC) to compute their formants, and to Mel Frequency Cepstral Coefficients (MFCC) algorithm, to compute the cepstral coefficients. A Decision Tree Classifier was used to build a predictive model that learnt the patterns of the two first formants measured in the data set, as well as the patterns of the 13 cepstral coefficients. An accuracy of 70\% was achieved using formants for the mentioned phonemes. For the MFCC analysis an accuracy of 52 \% was achieved and an accuracy of 71\% when /\textipa{@}/ was ignored. The results obtained show that the studied algorithms are far from mimicking the ability of distinguishing subtle differences in sounds like human hearing does.
A Neural Attention Model for Categorizing Patient Safety Events
Venue: arXiv cs.CL 2017
Year: 2017

Medical errors are leading causes of death in the US and as such, prevention of these errors is paramount to promoting health care. Patient Safety Event reports are narratives describing potential adverse events to the patients and are important in identifying and preventing medical errors. We present a neural network architecture for identifying the type of safety events which is the first step in understanding these narratives. Our proposed model is based on a soft neural attention model to improve the effectiveness of encoding long sequences. Empirical results on two large-scale real-world datasets of patient safety reports demonstrate the effectiveness of our method with significant improvements over existing methods.
LTSG: Latent Topical Skip-Gram for Mutually Learning Topic Model and Vector Representations
Venue: arXiv cs.CL 2017
Year: 2017

Topic models have been widely used in discovering latent topics which are shared across documents in text mining. Vector representations, word embeddings and topic embeddings, map words and topics into a low-dimensional and dense real-value vector space, which have obtained high performance in NLP tasks. However, most of the existing models assume the result trained by one of them are perfect correct and used as prior knowledge for improving the other model. Some other models use the information trained from external large corpus to help improving smaller corpus. In this paper, we aim to build such an algorithm framework that makes topic models and vector representations mutually improve each other within the same corpus. An EM-style algorithm framework is employed to iteratively optimize both topic model and vector representations. Experimental results show that our model outperforms state-of-art methods on various NLP tasks.
Microservices: How To Make Your Application Scale
Venue: arXiv cs.SE 2017
Year: 2017

The microservice architecture is a style inspired by service-oriented computing that has recently started gaining popularity and that promises to change the way in which software is perceived, conceived and designed. In this paper, we describe the main features of microservices and highlight how these features improve scalability.
Next Basket Prediction using Recurring Sequential Patterns
Venue: arXiv cs.DB 2017
Year: 2017

Nowadays, a hot challenge for supermarket chains is to offer personalized services for their customers. Next basket prediction, i.e., supplying the customer a shopping list for the next purchase according to her current needs, is one of these services. Current approaches are not capable to capture at the same time the different factors influencing the customer's decision process: co-occurrency, sequentuality, periodicity and recurrency of the purchased items. To this aim, we define a pattern Temporal Annotated Recurring Sequence (TARS) able to capture simultaneously and adaptively all these factors. We define the method to extract TARS and develop a predictor for next basket named TBP (TARS Based Predictor) that, on top of TARS, is able to to understand the level of the customer's stocks and recommend the set of most necessary items. By adopting the TBP the supermarket chains could crop tailored suggestions for each individual customer which in turn could effectively speed up their shopping sessions. A deep experimentation shows that TARS are able to explain the customer purchase behavior, and that TBP outperforms the state-of-the-art competitors.
Space-Time Channel Modulation
Venue: arXiv cs.IT 2017
Year: 2017

In this paper, we introduce the concept of space-time channel modulation (STCM), which extends the classical space-time block codes into a new third dimension: channel states (transmission media) dimension. Three novel STCM schemes, which provide interesting trade-offs among decoding complexity, error performance and data rate, are proposed. It is shown via computer simulations that the proposed STCM schemes achieve considerably better error performance than the existing media-based modulation (MBM) and classical systems.
Small hitting-sets for tiny arithmetic circuits or: How to turn bad designs into good
Venue: arXiv cs.CC 2017
Year: 2017

We show that if we can design poly($s$)-time hitting-sets for $Σ\wedge^aΣΠ^{O(\log s)}$ circuits of size $s$, where $a=ω(1)$ is arbitrarily small and the number of variables, or arity $n$, is $O(\log s)$, then we can derandomize blackbox PIT for general circuits in quasipolynomial time. This also establishes that either E$\not\subseteq$\#P/poly or that VP$\ne$VNP. In fact, we show that one only needs a poly($s$)-time hitting-set against individual-degree $a'=ω(1)$ polynomials that are computable by a size-$s$ arity-$(\log s)$ $ΣΠΣ$ circuit (note: $Π$ fanin may be $s$). Alternatively, we claim that, to understand VP one only needs to find hitting-sets, for depth-$3$, that have a small parameterized complexity. Another tiny family of interest is when we restrict the arity $n=ω(1)$ to be arbitrarily small. We show that if we can design poly($s,μ(n)$)-time hitting-sets for size-$s$ arity-$n$ $ΣΠΣ\wedge$ circuits (resp.~$Σ\wedge^aΣΠ$), where function $μ$ is arbitrary, then we can solve PIT for VP in quasipoly-time, and prove the corresponding lower bounds. Our methods are strong enough to prove a surprising {\em arity reduction} for PIT-- to solve the general problem completely it suffices to find a blackbox PIT with time-complexity $sd2^{O(n)}$. We give several examples of ($\log s$)-variate circuits where a new measure (called cone-size) helps in devising poly-time hitting-sets, but the same question for their $s$-variate versions is open till date: For eg., diagonal depth-$3$ circuits, and in general, models that have a {\em small} partial derivative space. We also introduce a new concept, called cone-closed basis isolation, and provide example models where it occurs, or can be achieved by a small shift.
Ontologies in System Engineering: a Field Report
Venue: arXiv cs.AI 2017
Year: 2017

In recent years ontologies enjoyed a growing popularity outside specialized AI communities. System engineering is no exception to this trend, with ontologies being proposed as a basis for several tasks in complex industrial implements, including system design, monitoring and diagnosis. In this paper, we consider four different contributions to system engineering wherein ontologies are instrumental to provide enhancements over traditional ad-hoc techniques. For each application, we briefly report the methodologies, the tools and the results obtained with the goal to provide an assessment of merits and limits of ontologies in such domains.
Triangular Decomposition of Matrices in a Domain
Venue: arXiv cs.SC 2017
Year: 2017

Deterministic recursive algorithms for the computation of matrix triangular decompositions with permutations like LU and Bruhat decomposition are presented for the case of commutative domains. This decomposition can be considered as a generalization of LU and Bruhat decompositions, because they both may be easily obtained from this triangular decomposition. Algorithms have the same complexity as the algorithm of matrix multiplication.
k-Means Clustering and Ensemble of Regressions: An Algorithm for the ISIC 2017 Skin Lesion Segmentation Challenge
Venue: arXiv cs.CV 2017
Year: 2017

This abstract briefly describes a segmentation algorithm developed for the ISIC 2017 Skin Lesion Detection Competition hosted at [ref]. The objective of the competition is to perform a segmentation (in the form of a binary mask image) of skin lesions in dermoscopic images as close as possible to a segmentation performed by trained clinicians, which is taken as ground truth. This project only takes part in the segmentation phase of the challenge. The other phases of the competition (feature extraction and lesion identification) are not considered. The proposed algorithm consists of 4 steps: (1) lesion image preprocessing, (2) image segmentation using k-means clustering of pixel colors, (3) calculation of a set of features describing the properties of each segmented region, and (4) calculation of a final score for each region, representing the likelihood of corresponding to a suitable lesion segmentation. The scores in step (4) are obtained by averaging the results of 2 different regression models using the scores of each region as input. Before using the algorithm these regression models must be trained using the training set of images and ground truth masks provided by the Competition. Steps 2 to 4 are repeated with an increasing number of clusters (and therefore the image is segmented into more regions) until there is no further improvement of the calculated scores.
WaterGAN: Unsupervised Generative Network to Enable Real-time Color Correction of Monocular Underwater Images
Venue: arXiv cs.CV 2017
Year: 2017

This paper reports on WaterGAN, a generative adversarial network (GAN) for generating realistic underwater images from in-air image and depth pairings in an unsupervised pipeline used for color correction of monocular underwater images. Cameras onboard autonomous and remotely operated vehicles can capture high resolution images to map the seafloor, however, underwater image formation is subject to the complex process of light propagation through the water column. The raw images retrieved are characteristically different than images taken in air due to effects such as absorption and scattering, which cause attenuation of light at different rates for different wavelengths. While this physical process is well described theoretically, the model depends on many parameters intrinsic to the water column as well as the objects in the scene. These factors make recovery of these parameters difficult without simplifying assumptions or field calibration, hence, restoration of underwater images is a non-trivial problem. Deep learning has demonstrated great success in modeling complex nonlinear systems but requires a large amount of training data, which is difficult to compile in deep sea environments. Using WaterGAN, we generate a large training dataset of paired imagery, both raw underwater and true color in-air, as well as depth data. This data serves as input to a novel end-to-end network for color correction of monocular underwater images. Due to the depth-dependent water column effects inherent to underwater environments, we show that our end-to-end network implicitly learns a coarse depth estimate of the underwater scene from monocular underwater images. Our proposed pipeline is validated with testing on real data collected from both a pure water tank and from underwater surveys in field testing. Source code is made publicly available with sample datasets and pretrained models.
Capacitated Center Problems with Two-Sided Bounds and Outliers
Venue: arXiv cs.DS 2017
Year: 2017

In recent years, the capacitated center problems have attracted a lot of research interest. Given a set of vertices $V$, we want to find a subset of vertices $S$, called centers, such that the maximum cluster radius is minimized. Moreover, each center in $S$ should satisfy some capacity constraint, which could be an upper or lower bound on the number of vertices it can serve. Capacitated $k$-center problems with one-sided bounds (upper or lower) have been well studied in previous work, and a constant factor approximation was obtained. We are the first to study the capacitated center problem with both capacity lower and upper bounds (with or without outliers). We assume each vertex has a uniform lower bound and a non-uniform upper bound. For the case of opening exactly $k$ centers, we note that a generalization of a recent LP approach can achieve constant factor approximation algorithms for our problems. Our main contribution is a simple combinatorial algorithm for the case where there is no cardinality constraint on the number of open centers. Our combinatorial algorithm is simpler and achieves better constant approximation factor compared to the LP approach.
Viewpoint Adaptation for Rigid Object Detection
Venue: arXiv cs.CV 2017
Year: 2017

An object detector performs suboptimally when applied to image data taken from a viewpoint different from the one with which it was trained. In this paper, we present a viewpoint adaptation algorithm that allows a trained single-view object detector to be adapted to a new, distinct viewpoint. We first illustrate how a feature space transformation can be inferred from a known homography between the source and target viewpoints. Second, we show that a variety of trained classifiers can be modified to behave as if that transformation were applied to each testing instance. The proposed algorithm is evaluated on a person detection task using images from the PETS 2007 and CAVIAR datasets, as well as from a new synthetic multi-view person detection dataset. It yields substantial performance improvements when adapting single-view person detectors to new viewpoints, and simultaneously reduces computational complexity. This work has the potential to improve detection performance for cameras viewing objects from arbitrary viewpoints, while simplifying data collection and feature extraction.
Small-space encoding LCE data structure with constant-time queries
Venue: arXiv cs.DS 2017
Year: 2017

The \emph{longest common extension} (\emph{LCE}) problem is to preprocess a given string $w$ of length $n$ so that the length of the longest common prefix between suffixes of $w$ that start at any two given positions is answered quickly. In this paper, we present a data structure of $O(z τ^2 + \frac{n}τ)$ words of space which answers LCE queries in $O(1)$ time and can be built in $O(n \log σ)$ time, where $1 \leq τ\leq \sqrt{n}$ is a parameter, $z$ is the size of the Lempel-Ziv 77 factorization of $w$ and $σ$ is the alphabet size. This is an \emph{encoding} data structure, i.e., it does not access the input string $w$ when answering queries and thus $w$ can be deleted after preprocessing. On top of this main result, we obtain further results using (variants of) our LCE data structure, which include the following: - For highly repetitive strings where the $zτ^2$ term is dominated by $\frac{n}τ$, we obtain a \emph{constant-time and sub-linear space} LCE query data structure. - Even when the input string is not well compressible via Lempel-Ziv 77 factorization, we still can obtain a \emph{constant-time and sub-linear space} LCE data structure for suitable $τ$ and for $σ\leq 2^{o(\log n)}$. - The time-space trade-off lower bounds for the LCE problem by Bille et al. [J. Discrete Algorithms, 25:42-50, 2014] and by Kosolobov [CoRR, abs/1611.02891, 2016] can be "surpassed" in some cases with our LCE data structure.
Hidden Community Detection in Social Networks
Venue: arXiv cs.SI 2017
Year: 2017

We introduce a new paradigm that is important for community detection in the realm of network analysis. Networks contain a set of strong, dominant communities, which interfere with the detection of weak, natural community structure. When most of the members of the weak communities also belong to stronger communities, they are extremely hard to be uncovered. We call the weak communities the hidden community structure. We present a novel approach called HICODE (HIdden COmmunity DEtection) that identifies the hidden community structure as well as the dominant community structure. By weakening the strength of the dominant structure, one can uncover the hidden structure beneath. Likewise, by reducing the strength of the hidden structure, one can more accurately identify the dominant structure. In this way, HICODE tackles both tasks simultaneously. Extensive experiments on real-world networks demonstrate that HICODE outperforms several state-of-the-art community detection methods in uncovering both the dominant and the hidden structure. In the Facebook university social networks, we find multiple non-redundant sets of communities that are strongly associated with residential hall, year of registration or career position of the faculties or students, while the state-of-the-art algorithms mainly locate the dominant ground truth category. In the Due to the difficulty of labeling all ground truth communities in real-world datasets, HICODE provides a promising approach to pinpoint the existing latent communities and uncover communities for which there is no ground truth. Finding this unknown structure is an extremely important community detection problem.