OpenRaiser/Intern-Atlas huggingface dataset:
HPSLPred: An Ensemble Multi-label Classifier for Human Protein Subcellular Location Prediction with Imbalanced Source
Venue: arXiv cs.LG 2017
Year: 2017

Predicting the subcellular localization of proteins is an important and challenging problem. Traditional experimental approaches are often expensive and time-consuming. Consequently, a growing number of research efforts employ a series of machine learning approaches to predict the subcellular location of proteins. There are two main challenges among the state-of-the-art prediction methods. First, most of the existing techniques are designed to deal with multi-class rather than multi-label classification, which ignores connections between multiple labels. In reality, multiple locations of particular proteins implies that there are vital and unique biological significances that deserve special focus and cannot be ignored. Second, techniques for handling imbalanced data in multi-label classification problems are necessary, but never employed. For solving these two issues, we have developed an ensemble multi-label classifier called HPSLPred, which can be applied for multi-label classification with an imbalanced protein source. For convenience, a user-friendly webserver has been established at http://server.malab.cn/HPSLPred.
Multisensory Omni-directional Long-term Place Recognition: Benchmark Dataset and Analysis
Venue: arXiv cs.RO 2017
Year: 2017

Recognizing a previously visited place, also known as place recognition (or loop closure detection) is the key towards fully autonomous mobile robots and self-driving vehicle navigation. Augmented with various Simultaneous Localization and Mapping techniques (SLAM), loop closure detection allows for incremental pose correction and can bolster efficient and accurate map creation. However, repeated and similar scenes (perceptual aliasing) and long term appearance changes (e.g. weather variations) are major challenges for current place recognition algorithms. We introduce a new dataset Multisensory Omnidirectional Long-term Place recognition (MOLP) comprising omnidirectional intensity and disparity images. This dataset presents many of the challenges faced by outdoor mobile robots and current place recognition algorithms. Using MOLP dataset, we formulate the place recognition problem as a regularized sparse convex optimization problem. We conclude that information extracted from intensity image is superior to disparity image in isolating discriminative features for successful long term place recognition. Furthermore, when these discriminative features are extracted from an omnidirectional vision sensor, a robust bidirectional loop closure detection approach is established, allowing mobile robots to close the loop, regardless of the difference in the direction when revisiting a place.
Grammar-Based Graph Compression
Venue: arXiv cs.DS 2017
Year: 2017

We present a new graph compressor that works by recursively detecting repeated substructures and representing them through grammar rules. We show that for a large number of graphs the compressor obtains smaller representations than other approaches. Specific queries such as reachability between two nodes or regular path queries can be evaluated in linear time (or quadratic times, respectively), over the grammar, thus allowing speed-ups proportional to the compression ratio.
Specifying Graph Languages with Type Graphs
Venue: arXiv cs.FL 2017
Year: 2017

We investigate three formalisms to specify graph languages, i.e. sets of graphs, based on type graphs. First, we are interested in (pure) type graphs, where the corresponding language consists of all graphs that can be mapped homomorphically to a given type graph. In this context, we also study languages specified by restriction graphs and their relation to type graphs. Second, we extend this basic approach to a type graph logic and, third, to type graphs with annotations. We present decidability results and closure properties for each of the formalisms.
Joint Domain Based Massive Access for Small Packets Traffic of Uplink Wireless Channel
Venue: arXiv cs.IT 2017
Year: 2017

The fifth generation (5G) communication scenarios such as the cellular network and the emerging machine type communications will produce massive small packets. To support massive connectivity and avoid signaling overhead caused by the transmission of those small packets, this paper proposes a novel method to improve the transmission efficiency for massive connections of wireless uplink channel. The proposed method combines compressive sensing (CS) with power domain NOMA jointly, especially neither the scheduling nor the centralized power allocation is necessary in the method. Both the analysis and simulation show that the method can support up to two or three times overloading.
How to exploit prior information in low-complexity models
Venue: arXiv cs.IT 2017
Year: 2017

Compressed Sensing refers to extracting a low-dimensional structured signal of interest from its incomplete random linear observations. A line of recent work has studied that, with the extra prior information about the signal, one can recover the signal with much fewer observations. For this purpose, the general approach is to solve weighted convex function minimization problem. In such settings, the convex function is chosen to promote the low-dimensional structure and the optimal weights are so chosen to reduce the number of measurements required for the optimization problem. In this paper, we consider a generalized non-uniform model in which the structured signal falls into some partitions, with entries of each partition having a definite probability to be an element of the structure support. Given these probabilities and regarding the recent developments in conic integral geometry, we provide a method to choose the unique optimal weights for any general low-dimensional signal model. This class of low-dimensional signal model includes many popular examples such as $\ell_1$ analysis (entry-wise sparsity in an arbitrary redundant dictionary), $\ell_{1,2}$ norm (block sparsity) and total variation semi-norm (for piece-wise constant signals). We show through precise analysis and simulations that the weighted convex optimization problem significantly improves the regular convex optimization problem as we choose the unique optimal weights.
Energy Efficient Beamforming for Massive MIMO Public Channel
Venue: arXiv cs.IT 2017
Year: 2017

For massive MIMO public channel with any sector size in either microwave or millimeter wave (mmwave) band, this paper studies the beamforming design to minimize the transmit power while guaranteeing the quality of service (QoS) for randomly deployed users. First the ideal beampattern is derived via Parseval Identity, based on which a beamforming design problem is formulated to minimize the gap with the idea beampattern. The problem is transformable to a multiconvex one and an iterative optimization algorithm is used to obtain the full-digital beamformer. In addition, with the help of same beampattern theorem, the power amplifier (PA) efficiency of the beamformer is improved with unchanged beampattern. Finally, the practical hybrid implementation is obtained that achieves the full-digital beamformer solution. Simulations verify the advantages of the proposed scheme over existing ones.
Risk-limiting Load Restoration for Resilience Enhancement with Intermittent Energy Resources
Venue: arXiv cs.SY 2017
Year: 2017

Microgrids are resources that can be used to restore critical loads after a natural disaster, enhancing resilience of a distribution network. To deal with the stochastic nature of intermittent energy resources, such as wind turbines (WTs) and photovoltaics (PVs), many methods rely on forecast information. However, some microgrids may not be equipped with power forecasting tools. To fill this gap, a risk-limiting strategy based on measurements is proposed. Gaussian mixture model (GMM) is used to represent a prior joint probability density function (PDF) of power outputs of WTs and PVs over multiple periods. As time rolls forward, the distribution of WT/PV generation is updated based the latest measurement data in a recursive manner. The updated distribution is used as an input for the risk-limiting load restoration problem, enabling an equivalent transformation of the original chance constrained problem into a mixed integer linear programming (MILP). Simulation cases on a distribution system with three microgrids demonstrate the effectiveness of the proposed method. Results also indicate that networked microgrids have better uncertainty management capabilities than stand-alone microgrids.
Computing Reformulated First Zagreb Index of Some Chemical Graphs as an Application of Generalized Hierarchical Product of Graphs
Venue: arXiv cs.DM 2017
Year: 2017

The generalized hierarchical product of graphs was introduced by L. Barriére et al in 2009. In this paper, reformulated first Zagreb index of generalized hierarchical product of two connected graphs and hence as a special case cluster product of graphs are obtained. Finally using the derived results the reformulated first Zagreb index of some chemically important graphs such as square comb lattice, hexagonal chain, molecular graph of truncated cube, dimer fullerene, zig-zag polyhex nanotube and dicentric dendrimers are computed.
Making Sense of Unstructured Text Data
Venue: arXiv cs.SI 2017
Year: 2017

Many network analysis tasks in social sciences rely on pre-existing data sources that were created with explicit relations or interactions between entities under consideration. Examples include email logs, friends and followers networks on social media, communication networks, etc. In these data, it is relatively easy to identify who is connected to whom and how they are connected. However, most of the data that we encounter on a daily basis are unstructured free-text data, e.g., forums, online marketplaces, etc. It is considerably more difficult to extract network data from unstructured text. In this work, we present an end-to-end system for analyzing unstructured text data and transforming the data into structured graphs that are directly applicable to a downstream application. Specifically, we look at social media data and attempt to predict the most indicative words from users' posts. The resulting keywords can be used to construct a context+content network for downstream processing such as graph-based analysis and learning. With that goal in mind, we apply our methods to the application of cross-domain entity resolution. The performance of the resulting system with automatic keywords shows improvement over the system with user-annotated hashtags.
Optimal Posted Prices for Online Cloud Resource Allocation
Venue: arXiv cs.NI 2017
Year: 2017

We study online resource allocation in a cloud computing platform, through a posted pricing mechanism: The cloud provider publishes a unit price for each resource type, which may vary over time; upon arrival at the cloud system, a cloud user either takes the current prices, renting resources to execute its job, or refuses the prices without running its job there. We design pricing functions based on the current resource utilization ratios, in a wide array of demand-supply relationships and resource occupation durations, and prove worst-case competitive ratios of the pricing functions in terms of social welfare. In the basic case of a single-type, non-recycled resource (i.e., allocated resources are not later released for reuse), we prove that our pricing function design is optimal, in that any other pricing function can only lead to a worse competitive ratio. Insights obtained from the basic cases are then used to generalize the pricing functions to more realistic cloud systems with multiple types of resources, where a job occupies allocated resources for a number of time slots till completion, upon which time the resources are returned back to the cloud resource pool.
Predicting Role Relevance with Minimal Domain Expertise in a Financial Domain
Venue: arXiv cs.CL 2017
Year: 2017

Word embeddings have made enormous inroads in recent years in a wide variety of text mining applications. In this paper, we explore a word embedding-based architecture for predicting the relevance of a role between two financial entities within the context of natural language sentences. In this extended abstract, we propose a pooled approach that uses a collection of sentences to train word embeddings using the skip-gram word2vec architecture. We use the word embeddings to obtain context vectors that are assigned one or more labels based on manual annotations. We train a machine learning classifier using the labeled context vectors, and use the trained classifier to predict contextual role relevance on test data. Our approach serves as a good minimal-expertise baseline for the task as it is simple and intuitive, uses open-source modules, requires little feature crafting effort and performs well across roles.
Loop Quasi-Invariant Chunk Motion by peeling with statement composition
Venue: arXiv cs.PL 2017
Year: 2017

Several techniques for analysis and transformations are used in compilers. Among them, the peeling of loops for hoisting quasi-invariants can be used to optimize generated code, or simply ease developers' lives. In this paper, we introduce a new concept of dependency analysis borrowed from the field of Implicit Computational Complexity (ICC), allowing to work with composed statements called Chunks to detect more quasi-invariants. Based on an optimization idea given on a WHILE language, we provide a transformation method - reusing ICC concepts and techniques - to compilers. This new analysis computes an invariance degree for each statement or chunks of statements by building a new kind of dependency graph, finds the maximum or worst dependency graph for loops, and recognizes if an entire block is Quasi-Invariant or not. This block could be an inner loop, and in that case the computational complexity of the overall program can be decreased. We already implemented a proof of concept on a toy C parser 1 analysing and transforming the AST representation. In this paper, we introduce the theory around this concept and present a prototype analysis pass implemented on LLVM. In a very near future, we will implement the corresponding transformation and provide benchmarks comparisons.
Insensitive Stochastic Gradient Twin Support Vector Machine for Large Scale Problems
Venue: arXiv cs.LG 2017
Year: 2017

Stochastic gradient descent algorithm has been successfully applied on support vector machines (called PEGASOS) for many classification problems. In this paper, stochastic gradient descent algorithm is investigated to twin support vector machines for classification. Compared with PEGASOS, the proposed stochastic gradient twin support vector machines (SGTSVM) is insensitive on stochastic sampling for stochastic gradient descent algorithm. In theory, we prove the convergence of SGTSVM instead of almost sure convergence of PEGASOS. For uniformly sampling, the approximation between SGTSVM and twin support vector machines is also given, while PEGASOS only has an opportunity to obtain an approximation of support vector machines. In addition, the nonlinear SGTSVM is derived directly from its linear case. Experimental results on both artificial datasets and large scale problems show the stable performance of SGTSVM with a fast learning speed.
Dependency resolution and semantic mining using Tree Adjoining Grammars for Tamil Language
Venue: arXiv cs.CL 2017
Year: 2017

Tree adjoining grammars (TAGs) provide an ample tool to capture syntax of many Indian languages. Tamil represents a special challenge to computational formalisms as it has extensive agglutinative morphology and a comparatively difficult argument structure. Modelling Tamil syntax and morphology using TAG is an interesting problem which has not been in focus even though TAGs are over 4 decades old, since its inception. Our research with Tamil TAGs have shown us that we can not only represent syntax of the language, but to an extent mine out semantics through dependency resolution of the sentence. But in order to demonstrate this phenomenal property, we need to parse Tamil language sentences using TAGs we have built and through parsing obtain a derivation we could use to resolve dependencies, thus proving the semantic property. We use an in-house developed pseudo lexical TAG chart parser; algorithm given by Schabes and Joshi (1988), for generating derivations of sentences. We do not use any statistics to rank out ambiguous derivations but rather use all of them to understand the mentioned semantic relation with in TAGs for Tamil. We shall also present a brief parser analysis for the completeness of our discussions.
Deduplication in a massive clinical note dataset
Venue: arXiv cs.DB 2017
Year: 2017

Duplication, whether exact or partial, is a common issue in many datasets. In clinical notes data, duplication (and near duplication) can arise for many reasons, such as the pervasive use of templates, copy-pasting, or notes being generated by automated procedures. A key challenge in removing such near duplicates is the size of such datasets; our own dataset consists of more than 10 million notes. To detect and correct such duplicates requires algorithms that both accurate and highly scalable. We describe a solution based on Minhashing with Locality Sensitive Hashing. In this paper, we present the theory behind this method and present a database-inspired approach to make the method scalable. We also present a clustering technique using disjoint sets to produce dense clusters, which speeds up our algorithm.
Skeleton based action recognition using translation-scale invariant image mapping and multi-scale deep cnn
Venue: arXiv cs.CV 2017
Year: 2017

This paper presents an image classification based approach for skeleton-based video action recognition problem. Firstly, A dataset independent translation-scale invariant image mapping method is proposed, which transformes the skeleton videos to colour images, named skeleton-images. Secondly, A multi-scale deep convolutional neural network (CNN) architecture is proposed which could be built and fine-tuned on the powerful pre-trained CNNs, e.g., AlexNet, VGGNet, ResNet etal.. Even though the skeleton-images are very different from natural images, the fine-tune strategy still works well. At last, we prove that our method could also work well on 2D skeleton video data. We achieve the state-of-the-art results on the popular benchmard datasets e.g. NTU RGB+D, UTD-MHAD, MSRC-12, and G3D. Especially on the largest and challenge NTU RGB+D, UTD-MHAD, and MSRC-12 dataset, our method outperforms other methods by a large margion, which proves the efficacy of the proposed method.
Effects of the optimisation of the margin distribution on generalisation in deep architectures
Venue: arXiv cs.LG 2017
Year: 2017

Despite being so vital to success of Support Vector Machines, the principle of separating margin maximisation is not used in deep learning. We show that minimisation of margin variance and not maximisation of the margin is more suitable for improving generalisation in deep architectures. We propose the Halfway loss function that minimises the Normalised Margin Variance (NMV) at the output of a deep learning models and evaluate its performance against the Softmax Cross-Entropy loss on the MNIST, smallNORB and CIFAR-10 datasets.
Vehicular Communications: A Physical Layer Perspective
Venue: arXiv cs.IT 2017
Year: 2017

Vehicular communications have attracted more and more attention recently from both industry and academia due to its strong potential to enhance road safety, improve traffic efficiency, and provide rich on-board information and entertainment services. In this paper, we discuss fundamental physical layer issues that enable efficient vehicular communications and present a comprehensive overview of the state-of-the-art research. We first introduce vehicular channel characteristics and modeling, which are the key underlying features differentiating vehicular communications from other types of wireless systems. We then present schemes to estimate the time-varying vehicular channels and various modulation techniques to deal with high-mobility channels. After reviewing resource allocation for vehicular communications, we discuss the potential to enable vehicular communications over the millimeter wave bands. Finally, we identify the challenges and opportunities associated with vehicular communications.
A location-aware embedding technique for accurate landmark recognition
Venue: arXiv cs.CV 2017
Year: 2017

The current state of the research in landmark recognition highlights the good accuracy which can be achieved by embedding techniques, such as Fisher vector and VLAD. All these techniques do not exploit spatial information, i.e. consider all the features and the corresponding descriptors without embedding their location in the image. This paper presents a new variant of the well-known VLAD (Vector of Locally Aggregated Descriptors) embedding technique which accounts, at a certain degree, for the location of features. The driving motivation comes from the observation that, usually, the most interesting part of an image (e.g., the landmark to be recognized) is almost at the center of the image, while the features at the borders are irrelevant features which do no depend on the landmark. The proposed variant, called locVLAD (location-aware VLAD), computes the mean of the two global descriptors: the VLAD executed on the entire original image, and the one computed on a cropped image which removes a certain percentage of the image borders. This simple variant shows an accuracy greater than the existing state-of-the-art approach. Experiments are conducted on two public datasets (ZuBuD and Holidays) which are used both for training and testing. Morever a more balanced version of ZuBuD is proposed.
Redefining Context Windows for Word Embedding Models: An Experimental Study
Venue: arXiv cs.CL 2017
Year: 2017

Distributional semantic models learn vector representations of words through the contexts they occur in. Although the choice of context (which often takes the form of a sliding window) has a direct influence on the resulting embeddings, the exact role of this model component is still not fully understood. This paper presents a systematic analysis of context windows based on a set of four distinct hyper-parameters. We train continuous Skip-Gram models on two English-language corpora for various combinations of these hyper-parameters, and evaluate them on both lexical similarity and analogy tasks. Notable experimental results are the positive impact of cross-sentential contexts and the surprisingly good performance of right-context windows.
Aggregation and visualization of spatial data with application to classification of land use and land cover
Venue: arXiv cs.DB 2017
Year: 2017

Aggregation and visualization of geographical data are an important part of environmental data mining, environmental modelling, and agricultural management. However, it is difficult to aggregate geospatial data of the various formats, such as maps, census and survey data. This paper presents a framework named PlaniSphere, which can aggregate the various geospatial datasets, and synthesizes raw data. We developed an algorithm in PlaniSphere to aggregate remote sensing images with census data for classification and visualization of land use and land cover (LULC). The results show that the framework is able to classify geospatial data sets of LULC from multiple formats. National census data sets can be used for calibration of remote sensing LULC classifications. This provides a new approach for the classification of remote sensing data. This approach proposed in this paper should be useful for LULC classification in environmental spatial analysis.