OpenRaiser/Intern-Atlas huggingface dataset:
DynaSOAr: A Parallel Memory Allocator for Object-oriented Programming on GPUs with Efficient Memory Access
Venue: arXiv cs.PL 2019
Year: 2019

Object-oriented programming has long been regarded as too inefficient for SIMD high-performance computing, despite the fact that many important HPC applications have an inherent object structure. On SIMD accelerators, including GPUs, this is mainly due to performance problems with memory allocation and memory access: There are a few libraries that support parallel memory allocation directly on accelerator devices, but all of them suffer from uncoalesed memory accesses. We discovered a broad class of object-oriented programs with many important real-world applications that can be implemented efficiently on massively parallel SIMD accelerators. We call this class Single-Method Multiple-Objects (SMMO), because parallelism is expressed by running a method on all objects of a type. To make fast GPU programming available to average programmers, we developed DynaSOAr, a CUDA framework for SMMO applications. DynaSOAr consists of (1) a fully-parallel, lock-free, dynamic memory allocator, (2) a data layout DSL and (3) an efficient, parallel do-all operation. DynaSOAr achieves performance superior to state-of-the-art GPU memory allocators by controlling both memory allocation and memory access. DynaSOAr improves the usage of allocated memory with a Structure of Arrays data layout and achieves low memory fragmentation through efficient management of free and allocated memory blocks with lock-free, hierarchical bitmaps. Contrary to other allocators, our design is heavily based on atomic operations, trading raw (de)allocation performance for better overall application performance. In our benchmarks, DynaSOAr achieves a speedup of application code of up to 3x over state-of-the-art allocators. Moreover, DynaSOAr manages heap memory more efficiently than other allocators, allowing programmers to run up to 2x larger problem sizes with the same amount of memory.
Learning with Analytical Models
Venue: arXiv cs.PF 2019
Year: 2019

To understand and predict the performance of scientific applications, several analytical and machine learning approaches have been proposed, each having its advantages and disadvantages. In this paper, we propose and validate a hybrid approach for performance modeling and prediction, which combines analytical and machine learning models. The proposed hybrid model aims to minimize prediction cost while providing reasonable prediction accuracy. Our validation results show that the hybrid model is able to learn and correct the analytical models to better match the actual performance. Furthermore, the proposed hybrid model improves the prediction accuracy in comparison to pure machine learning techniques while using small training datasets, thus making it suitable for hardware and workload changes.
Automatically Evolving CNN Architectures Based on Blocks
Venue: arXiv cs.NE 2019
Year: 2019

The performance of Convolutional Neural Networks (CNNs) highly relies on their architectures. In order to design a CNN with promising performance, extended expertise in both CNNs and the investigated problem is required, which is not necessarily held by every user interested in CNNs or the problem domain. In this paper, we propose to automatically evolve CNN architectures by using a genetic algorithm based on ResNet blocks and DenseNet blocks. The proposed algorithm is \textbf{completely} automatic in designing CNN architectures, particularly, neither pre-processing before it starts nor post-processing on the designed CNN is needed. Furthermore, the proposed algorithm does not require users with domain knowledge on CNNs, the investigated problem or even genetic algorithms. The proposed algorithm is evaluated on CIFAR10 and CIFAR100 against 18 state-of-the-art peer competitors. Experimental results show that it outperforms state-of-the-art CNNs hand-crafted and CNNs designed by automatic peer competitors in terms of the classification accuracy, and achieves the competitive classification accuracy against semi-automatic peer competitors. In addition, the proposed algorithm consumes much less time than most peer competitors in finding the best CNN architectures.
Variational Inference with Tail-adaptive f-Divergence
Venue: arXiv cs.LG 2019
Year: 2019

Variational inference with α-divergences has been widely used in modern probabilistic machine learning. Compared to Kullback-Leibler (KL) divergence, a major advantage of using α-divergences (with positive α values) is their mass-covering property. However, estimating and optimizing α-divergences require to use importance sampling, which could have extremely large or infinite variances due to heavy tails of importance weights. In this paper, we propose a new class of tail-adaptive f-divergences that adaptively change the convex function f with the tail of the importance weights, in a way that theoretically guarantees finite moments, while simultaneously achieving mass-covering properties. We test our methods on Bayesian neural networks, as well as deep reinforcement learning in which our method is applied to improve a recent soft actor-critic (SAC) algorithm. Our results show that our approach yields significant advantages compared with existing methods based on classical KL and α-divergences.
A Pragmatic Guide to Geoparsing Evaluation
Venue: arXiv cs.CL 2019
Year: 2019

Empirical methods in geoparsing have thus far lacked a standard evaluation framework describing the task, metrics and data used to compare state-of-the-art systems. Evaluation is further made inconsistent, even unrepresentative of real-world usage by the lack of distinction between the different types of toponyms, which necessitates new guidelines, a consolidation of metrics and a detailed toponym taxonomy with implications for Named Entity Recognition (NER) and beyond. To address these deficiencies, our manuscript introduces a new framework in three parts. Part 1) Task Definition: clarified via corpus linguistic analysis proposing a fine-grained Pragmatic Taxonomy of Toponyms. Part 2) Metrics: discussed and reviewed for a rigorous evaluation including recommendations for NER/Geoparsing practitioners. Part 3) Evaluation Data: shared via a new dataset called GeoWebNews to provide test/train examples and enable immediate use of our contributions. In addition to fine-grained Geotagging and Toponym Resolution (Geocoding), this dataset is also suitable for prototyping and evaluating machine learning NLP models.
Conditionals in Homomorphic Encryption and Machine Learning Applications
Venue: arXiv cs.CR 2019
Year: 2019

Homomorphic encryption aims at allowing computations on encrypted data without decryption other than that of the final result. This could provide an elegant solution to the issue of privacy preservation in data-based applications, such as those using machine learning, but several open issues hamper this plan. In this work we assess the possibility for homomorphic encryption to fully implement its program without relying on other techniques, such as multiparty computation (SMPC), which may be impossible in many use cases (for instance due to the high level of communication required). We proceed in two steps: i) on the basis of the structured program theorem (Bohm-Jacopini theorem) we identify the relevant minimal set of operations homomorphic encryption must be able to perform to implement any algorithm; and ii) we analyse the possibility to solve -- and propose an implementation for -- the most fundamentally relevant issue as it emerges from our analysis, that is, the implementation of conditionals (requiring comparison and selection/jump operations). We show how this issue clashes with the fundamental requirements of homomorphic encryption and could represent a drawback for its use as a complete solution for privacy preservation in data-based applications, in particular machine learning ones. Our approach for comparisons is novel and entirely embedded in homomorphic encryption, while previous studies relied on other techniques, such as SMPC, demanding high level of communication among parties, and decryption of intermediate results from data-owners. Our protocol is also provably safe (sharing the same safety as the homomorphic encryption schemes), differently from other techniques such as Order-Preserving/Revealing-Encryption (OPE/ORE).
Re-evaluating Continual Learning Scenarios: A Categorization and Case for Strong Baselines
Venue: arXiv cs.LG 2019
Year: 2019

Continual learning has received a great deal of attention recently with several approaches being proposed. However, evaluations involve a diverse set of scenarios making meaningful comparison difficult. This work provides a systematic categorization of the scenarios and evaluates them within a consistent framework including strong baselines and state-of-the-art methods. The results provide an understanding of the relative difficulty of the scenarios and that simple baselines (Adagrad, L2 regularization, and naive rehearsal strategies) can surprisingly achieve similar performance to current mainstream methods. We conclude with several suggestions for creating harder evaluation scenarios and future research directions. The code is available at https://github.com/GT-RIPL/Continual-Learning-Benchmark
DeepGRU: Deep Gesture Recognition Utility
Venue: arXiv cs.CV 2019
Year: 2019

We propose DeepGRU, a novel end-to-end deep network model informed by recent developments in deep learning for gesture and action recognition, that is streamlined and device-agnostic. DeepGRU, which uses only raw skeleton, pose or vector data is quickly understood, implemented, and trained, and yet achieves state-of-the-art results on challenging datasets. At the heart of our method lies a set of stacked gated recurrent units (GRU), two fully-connected layers and a novel global attention model. We evaluate our method on seven publicly available datasets, containing various number of samples and spanning over a broad range of interactions (full-body, multi-actor, hand gestures, etc.). In all but one case we outperform the state-of-the-art pose-based methods. For instance, we achieve a recognition accuracy of 84.9% and 92.3% on cross-subject and cross-view tests of the NTU RGB+D dataset respectively, and also 100% recognition accuracy on the UT-Kinect dataset. While DeepGRU works well on large datasets with many training samples, we show that even in the absence of a large number of training data, and with as little as four samples per class, DeepGRU can beat traditional methods specifically designed for small training sets. Lastly, we demonstrate that even without powerful hardware, and using only the CPU, our method can still be trained in under 10 minutes on small-scale datasets, making it an enticing choice for rapid application prototyping and development.
Advancing PICO Element Detection in Biomedical Text via Deep Neural Networks
Venue: arXiv cs.CL 2019
Year: 2019

In evidence-based medicine (EBM), defining a clinical question in terms of the specific patient problem aids the physicians to efficiently identify appropriate resources and search for the best available evidence for medical treatment. In order to formulate a well-defined, focused clinical question, a framework called PICO is widely used, which identifies the sentences in a given medical text that belong to the four components typically reported in clinical trials: Participants/Problem (P), Intervention (I), Comparison (C) and Outcome (O). In this work, we propose a novel deep learning model for recognizing PICO elements in biomedical abstracts. Based on the previous state-of-the-art bidirectional long-short term memory (biLSTM) plus conditional random field (CRF) architecture, we add another layer of biLSTM upon the sentence representation vectors so that the contextual information from surrounding sentences can be gathered to help infer the interpretation of the current one. In addition, we propose two methods to further generalize and improve the model: adversarial training and unsupervised pre-training over large corpora. We tested our proposed approach over two benchmark datasets. One is the PubMed-PICO dataset, where our best results outperform the previous best by 5.5%, 7.9%, and 5.8% for P, I, and O elements in terms of F1 score, respectively. And for the other dataset named NICTA-PIBOSO, the improvements for P/I/O elements are 2.4%, 13.6%, and 1.0% in F1 score, respectively. Overall, our proposed deep learning model can obtain unprecedented PICO element detection accuracy while avoiding the need for any manual feature selection.
Introducing SPAIN (SParse Audio INpainter)
Venue: arXiv cs.SD 2019
Year: 2019

A novel sparsity-based algorithm for audio inpainting is proposed. It is an adaptation of the SPADE algorithm by Kitić et al., originally developed for audio declipping, to the task of audio inpainting. The new SPAIN (SParse Audio INpainter) comes in synthesis and analysis variants. Experiments show that both A-SPAIN and S-SPAIN outperform other sparsity-based inpainting algorithms. Moreover, A-SPAIN performs on a par with the state-of-the-art method based on linear prediction in terms of the SNR, and, for larger gaps, SPAIN is even slightly better in terms of the PEMO-Q psychoacoustic criterion.
Making root cause analysis feasible for large code bases: a solution approach for a climate model
Venue: arXiv cs.DC 2019
Year: 2019

For large-scale simulation codes with huge and complex code bases, where bit-for-bit comparisons are too restrictive, finding the source of statistically significant discrepancies (e.g., from a previous version, alternative hardware or supporting software stack) in output is non-trivial at best. Although there are many tools for program comprehension through debugging or slicing, few (if any) scale to a model as large as the Community Earth System Model (CESM; trademarked), which consists of more than 1.5 million lines of Fortran code. Currently for the CESM, we can easily determine whether a discrepancy exists in the output using a by now well-established statistical consistency testing tool. However, this tool provides no information as to the possible cause of the detected discrepancy, leaving developers in a seemingly impossible (and frustrating) situation. Therefore, our aim in this work is to provide the tools to enable developers to trace a problem detected through the CESM output to its source. To this end, our strategy is to reduce the search space for the root cause(s) to a tractable size via a series of techniques that include creating a directed graph of internal CESM variables, extracting a subgraph (using a form of hybrid program slicing), partitioning into communities, and ranking nodes by centrality. Runtime variable sampling then becomes feasible in this reduced search space. We demonstrate the utility of this process on multiple examples of CESM simulation output by illustrating how sampling can be performed as part of an efficient parallel iterative refinement procedure to locate error sources, including sensitivity to CPU instructions. By providing CESM developers with tools to identify and understand the reason for statistically distinct output, we have positively impacted the CESM software development cycle and, in particular, its focus on quality assurance.
Online learning using multiple times weight updating
Venue: arXiv cs.LG 2019
Year: 2019

Online learning makes sequence of decisions with partial data arrival where next movement of data is unknown. In this paper, we have presented a new technique as multiple times weight updating that update the weight iteratively forsame instance. The proposed technique analyzed with popular state-of-art algorithms from literature and experimented using established tool. The results indicates that mistake rate reduces to zero or close to zero for various datasets and algorithms. The overhead running cost is not too expensive and achieving mistake rate close to zero further strengthen the proposed technique. The present work include bound nature of weight updating for single instance and achieve optimal weight value. This proposed work could be extended to big datasets problems to reduce mistake rate in online learning environment. Also, the proposed technique could be helpful to meet real life challenges.
GA Based Q-Attack on Community Detection
Venue: arXiv cs.SI 2019
Year: 2019

Community detection plays an important role in social networks, since it can help to naturally divide the network into smaller parts so as to simplify network analysis. However, on the other hand, it arises the concern that individual information may be over-mined, and the concept community deception thus is proposed to protect individual privacy on social networks. Here, we introduce and formalize the problem of community detection attack and develop efficient strategies to attack community detection algorithms by rewiring a small number of connections, leading to individual privacy protection. In particular, we first give two heuristic attack strategies, i.e., Community Detection Attack (CDA) and Degree Based Attack (DBA), as baselines, utilizing the information of detected community structure and node degree, respectively. And then we propose a Genetic Algorithm (GA) based Q-Attack, where the modularity Q is used to design the fitness function. We launch community detection attack based on the above three strategies against three modularity based community detection algorithms on two social networks. By comparison, our Q-Attack method achieves much better attack effects than CDA and DBA, in terms of the larger reduction of both modularity Q and Normalized Mutual Information (NMI). Besides, we find that the adversarial networks obtained by Q-Attack on a specific community detection algorithm can be still effective on others, no matter whether they are modularity based or not, indicating its strong transferability.
Data-driven Perception of Neuron Point Process with Unknown Unknowns
Venue: arXiv cs.LG 2019
Year: 2019

Identification of patterns from discrete data time-series for statistical inference, threat detection, social opinion dynamics, brain activity prediction has received recent momentum. In addition to the huge data size, the associated challenges are, for example, (i) missing data to construct a closed time-varying complex network, and (ii) contribution of unknown sources which are not probed. Towards this end, the current work focuses on statistical neuron system model with multi-covariates and unknown inputs. Previous research of neuron activity analysis is mainly limited with effects from the spiking history of target neuron and the interaction with other neurons in the system while ignoring the influence of unknown stimuli. We propose to use unknown unknowns, which describes the effect of unknown stimuli, undetected neuron activities and all other hidden sources of error. The maximum likelihood estimation with the fixed-point iteration method is implemented. The fixed-point iterations converge fast, and the proposed methods can be efficiently parallelized and offer computational advantage especially when the input spiking trains are over long time-horizon. The developed framework provides an intuition into the meaning of having extra degrees-of-freedom in the data to support the need for unknowns. The proposed algorithm is applied to simulated spike trains and on real-world experimental data of mouse somatosensory, mouse retina and cat retina. The model shows a successful increasing of system likelihood with respect to the conditional intensity function, and it also reveals the convergence with iterations. Results suggest that the neural connection model with unknown unknowns can efficiently estimate the statistical properties of the process by increasing the network likelihood.
Learning from Large-scale Noisy Web Data with Ubiquitous Reweighting for Image Classification
Venue: arXiv cs.CV 2019
Year: 2019

Many advances of deep learning techniques originate from the efforts of addressing the image classification task on large-scale datasets. However, the construction of such clean datasets is costly and time-consuming since the Internet is overwhelmed by noisy images with inadequate and inaccurate tags. In this paper, we propose a Ubiquitous Reweighting Network (URNet) that learns an image classification model from large-scale noisy data. By observing the web data, we find that there are five key challenges, i.e., imbalanced class sizes, high intra-classes diversity and inter-class similarity, imprecise instances, insufficient representative instances, and ambiguous class labels. To alleviate these challenges, we assume that every training instance has the potential to contribute positively by alleviating the data bias and noise via reweighting the influence of each instance according to different class sizes, large instance clusters, its confidence, small instance bags and the labels. In this manner, the influence of bias and noise in the web data can be gradually alleviated, leading to the steadily improving performance of URNet. Experimental results in the WebVision 2018 challenge with 16 million noisy training images from 5000 classes show that our approach outperforms state-of-the-art models and ranks the first place in the image classification task.
Invertible Residual Networks
Venue: arXiv cs.LG 2019
Year: 2019

We show that standard ResNet architectures can be made invertible, allowing the same model to be used for classification, density estimation, and generation. Typically, enforcing invertibility requires partitioning dimensions or restricting network architectures. In contrast, our approach only requires adding a simple normalization step during training, already available in standard frameworks. Invertible ResNets define a generative model which can be trained by maximum likelihood on unlabeled data. To compute likelihoods, we introduce a tractable approximation to the Jacobian log-determinant of a residual block. Our empirical evaluation shows that invertible ResNets perform competitively with both state-of-the-art image classifiers and flow-based generative models, something that has not been previously achieved with a single architecture.
Optimal Sequence Length Requirements for Phylogenetic Tree Reconstruction with Indels
Venue: arXiv cs.DS 2019
Year: 2019

We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to reconstruct the model tree with high probability. Traditionally, sequences mutate by substitution-only processes, although some recent work considers evolutionary processes with insertions and deletions. In this paper, we improve on previous work by giving a reconstruction algorithm that simultaneously has $O(\text{poly} \log n)$ sequence length and tolerates constant indel probabilities on each edge. Our recursively-reconstructed distance-based technique provably outputs the model tree when the model tree has $O(\text{poly} \log n)$ diameter and discretized branch lengths, allowing for the probability of insertion and deletion to be non-uniform and asymmetric on each edge. Our polylogarithmic sequence length bounds improve significantly over previous polynomial sequence length bounds and match sequence length bounds in the substitution-only models of phylogenetic evolution, thereby challenging the idea that many global misalignments caused by insertions and deletions when $p_{indel}$ is large are a fundamental obstruction to reconstruction with short sequences.