arXiv subjects

Sheng Wang

Publications and source records attributed to Sheng Wang.

At least 289 records · Page 16Linked to original sources

arXiv2018

ForkBase: An Efficient Storage Engine for Blockchain and Forkable Applications

Existing data storage systems offer a wide range of functionalities to accommodate an equally diverse range of applications. However, new classes of applications have emerged, e.g., blockchain and collaborative analytics, featuring data versioning, fork semantics, tamper-evidence or any combination thereof. They present new opportunities for storage systems to efficiently support such applications by embedding the above requirements into the storage. In this paper, we present ForkBase, a storage engine specifically designed to provide efficient support for blockchain and forkable applications. By integrating the core application properties into the storage, ForkBase not only delivers high performance but also reduces development effort. Data in ForkBase is multi-versioned, and each version uniquely identifies the data content and its history. Two variants of fork semantics are supported in ForkBase to facilitate any collaboration workflows. A novel index structure is introduced to efficiently identify and eliminate duplicate content across data objects. Consequently, ForkBase is not only efficient in performance, but also in space requirement. We demonstrate the performance of ForkBase using three applications: a blockchain platform, a wiki engine and a collaborative analytics application. We conduct extensive experimental evaluation of these applications against respective state-of-the-art system. The results show that ForkBase achieves superior performance while significantly lowering the development cost.

cs.DB↗

arXiv2018

Adaptive Graph Convolutional Neural Networks

Graph Convolutional Neural Networks (Graph CNNs) are generalizations of classical CNNs to handle graph data such as molecular data, point could and social networks. Current filters in graph CNNs are built for fixed and shared graph structure. However, for most real data, the graph structures varies in both size and connectivity. The paper proposes a generalized and flexible graph CNN taking data of arbitrary graph structure as input. In that way a task-driven adaptive graph is learned for each graph data while training. To efficiently learn the graph, a distance metric learning is proposed. Extensive experiments on nine graph-structured datasets have demonstrated the superior performance improvement on both convergence speed and predictive accuracy.

cs.LG↗

arXiv2017

Real-value and confidence prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning

Background. Protein dihedral angles provide a detailed description of protein local conformation. Predicted dihedral angles can be used to narrow down the conformational space of the whole polypeptide chain significantly, thus aiding protein tertiary structure prediction. However, direct angle prediction from sequence alone is challenging. Method. In this study, we present a novel method to predict real-valued angles by combining clustering and deep learning. That is, we first generate certain clusters of angles (each assigned a label) and then apply a deep residual neural network to predict the label posterior probability. Finally, we output real-valued prediction by a mixture of the clusters with their predicted probabilities. At the same time, we also estimate the bound of the prediction errors at each residue from the predicted label probabilities. Result. In this article, we present a novel method (named RaptorX-Angle) to predict real-valued angles by combining clustering and deep learning. Tested on a subset of PDB25 and the targets in the latest two Critical Assessment of protein Structure Prediction (CASP), our method outperforms the existing state-of-art method SPIDER2 in terms of Pearson Correlation Coefficient (PCC) and Mean Absolute Error (MAE). Our result also shows approximately linear relationship between the real prediction errors and our estimated bounds. That is, the real prediction error can be well approximated by our estimated bounds. Conclusions. Our study provides an alternative and more accurate prediction of dihedral angles, which may facilitate protein structure prediction and functional study.

q-bio.BM↗

arXiv2017

Folding membrane proteins by deep transfer learning

Computational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling. Here we describe a high-throughput deep transfer learning method that first predicts MP contacts by learning from non-membrane proteins (non-MPs) and then predicting three-dimensional structure models using the predicted contacts as distance restraints. Tested on 510 non-redundant MPs, our method has contact prediction accuracy at least 0.18 better than existing methods, predicts correct folds for 218 MPs (TMscore at least 0.6), and generates three-dimensional models with RMSD less than 4 Angstrom and 5 Angstrom for 57 and 108 MPs, respectively. A rigorous blind test in the continuous automated model evaluation (CAMEO) project shows that our method predicted high-resolution three-dimensional models for two recent test MPs of 210 residues with RMSD close to 2 Angstrom. We estimated that our method could predict correct folds for between 1,345 and 1,871 reviewed human multi-pass MPs including a few hundred new folds, which shall facilitate the discovery of drugs targeting at membrane proteins.

q-bio.BM↗

arXiv2017

Robust Contextual Bandit via the Capped-$\ell_{2}$ norm

This paper considers the actor-critic contextual bandit for the mobile health (mHealth) intervention. The state-of-the-art decision-making methods in mHealth generally assume that the noise in the dynamic system follows the Gaussian distribution. Those methods use the least-square-based algorithm to estimate the expected reward, which is prone to the existence of outliers. To deal with the issue of outliers, we propose a novel robust actor-critic contextual bandit method for the mHealth intervention. In the critic updating, the capped-$\ell_{2}$ norm is used to measure the approximation error, which prevents outliers from dominating our objective. A set of weights could be achieved from the critic updating. Considering them gives a weighted objective for the actor updating. It provides the badly noised sample in the critic updating with zero weights for the actor updating. As a result, the robustness of both actor-critic updating is enhanced. There is a key parameter in the capped-$\ell_{2}$ norm. We provide a reliable method to properly set it by making use of one of the most fundamental definitions of outliers in statistics. Extensive experiment results demonstrate that our method can achieve almost identical results compared with the state-of-the-art methods on the dataset without outliers and dramatically outperform them on the datasets noised by outliers.

cs.LG↗

arXiv2017

Study of the Magnetizing Relationship of the Kickers for CSNS

The extraction system of CSNS mainly consists of two kinds of magnets: eight kickers and one lambertson magnet. In this paper, firstly, the magnetic test results of the eight kickers were introduced and then the filed uniformity and magnetizing relationship of the kickers were given. Secondly, during the beam commissioning in the future, in order to obtain more accurate magnetizing relationship, a new method to measure the magnetizing coefficients of the kickers by the real extraction beam was given and the data analysis would also be processed.

physics.acc-ph↗

arXiv2017

Predicting membrane protein contacts from non-membrane proteins by deep transfer learning

Computational prediction of membrane protein (MP) structures is very challenging partially due to lack of sufficient solved structures for homology modeling. Recently direct evolutionary coupling analysis (DCA) sheds some light on protein contact prediction and accordingly, contact-assisted folding, but DCA is effective only on some very large-sized families since it uses information only in a single protein family. This paper presents a deep transfer learning method that can significantly improve MP contact prediction by learning contact patterns and complex sequence-contact relationship from thousands of non-membrane proteins (non-MPs). Tested on 510 non-redundant MPs, our deep model (learned from only non-MPs) has top L/10 long-range contact prediction accuracy 0.69, better than our deep model trained by only MPs (0.63) and much better than a representative DCA method CCMpred (0.47) and the CASP11 winner MetaPSICOV (0.55). The accuracy of our deep model can be further improved to 0.72 when trained by a mix of non-MPs and MPs. When only contacts in transmembrane regions are evaluated, our method has top L/10 long-range accuracy 0.62, 0.57, and 0.53 when trained by a mix of non-MPs and MPs, by non-MPs only, and by MPs only, respectively, still much better than MetaPSICOV (0.45) and CCMpred (0.40). All these results suggest that sequence-structure relationship learned by our deep model from non-MPs generalizes well to MP contact prediction. Improved contact prediction also leads to better contact-assisted folding. Using only top predicted contacts as restraints, our deep learning method can fold 160 and 200 of 510 MPs with TMscore>0.6 when trained by non-MPs only and by a mix of non-MPs and MPs, respectively, while CCMpred and MetaPSICOV can do so for only 56 and 77 MPs, respectively. Our contact-assisted folding also greatly outperforms homology modeling.

q-bio.BM↗

arXiv2017

Reverse k Nearest Neighbor Search over Trajectories

GPS enables mobile devices to continuously provide new opportunities to improve our daily lives. For example, the data collected in applications created by Uber or Public Transport Authorities can be used to plan transportation routes, estimate capacities, and proactively identify low coverage areas. In this paper, we study a new kind of query-Reverse k Nearest Neighbor Search over Trajectories (RkNNT), which can be used for route planning and capacity estimation. Given a set of existing routes DR, a set of passenger transitions DT, and a query route Q, a RkNNT query returns all transitions that take Q as one of its k nearest travel routes. To solve the problem, we first develop an index to handle dynamic trajectory updates, so that the most up-to-date transition data are available for answering a RkNNT query. Then we introduce a filter refinement framework for processing RkNNT queries using the proposed indexes. Next, we show how to use RkNNT to solve the optimal route planning problem MaxRkNNT (MinRkNNT), which is to search for the optimal route from a start location to an end location that could attract the maximum (or minimum) number of passengers based on a pre-defined travel distance threshold. Experiments on real datasets demonstrate the efficiency and scalability of our approaches. To the best of our best knowledge, this is the first work to study the RkNNT problem for route planning.

cs.DB↗

arXiv2017

Intra-protein binding peptide fragments have specific and intrinsic sequence patterns

The key finding in the DNA double helix model is the specific pairing or binding between nucleotides A-T and C-G, and the pairing rules are the molecule basis of genetic code. Unfortunately, no such rules have been discovered for proteins. Here we show that similar rules and intrinsic sequence patterns between intra-protein binding peptide fragments do exist, and they can be extracted using a deep learning algorithm. Multi-millions of binding and non-binding peptide fragments from currently available protein X-ray structures are classified with an accuracy of up to 93%. This discovery has the potential in helping solve protein folding and protein-protein interaction problems, two open and fundamental problems in molecular biology.

q-bio.BM↗

arXiv2017

UStore: A Distributed Storage With Rich Semantics

Today's storage systems expose abstractions which are either too low-level (e.g., key-value store, raw-block store) that they require developers to re-invent the wheels, or too high-level (e.g., relational databases, Git) that they lack generality to support many classes of applications. In this work, we propose and implement a general distributed data storage system, called UStore, which has rich semantics. UStore delivers three key properties, namely immutability, sharing and security, which unify and add values to many classes of today's applications, and which also open the door for new applications. By keeping the core properties within the storage, UStore helps reduce application development efforts while offering high performance at hand. The storage embraces current hardware trends as key enablers. It is built around a data-structure similar to that of Git, a popular source code versioning system, but it also synthesizes many designs from distributed systems and databases. Our current implementation of UStore has better performance than general in-memory key-value storage systems, especially for version scan operations. We port and evaluate four applications on top of UStore: a Git-like application, a collaborative data science application, a transaction management application, and a blockchain application. We demonstrate that UStore enables faster development and the UStore-backed applications can have better performance than the existing implementations.

cs.DB↗

arXiv2017

High-order schemes for the Euler equations in cylindrical/spherical coordinates

We consider implementations of high-order finite difference Weighted Essentially Non-Oscillatory (WENO) schemes for the Euler equations in cylindrical and spherical coordinate systems with radial dependence only. The main concern of this work lies in ensuring both high-order accuracy and conservation. Three different spatial discretizations are assessed: one that is shown to be high-order accurate but not conservative, one conservative but not high-order accurate, and a new approach that is both high-order accurate and conservative. For cylindrical and spherical coordinates, we present convergence results for the advection equation and the Euler equations with an acoustics problem; we then use the Sod shock tube and the Sedov point-blast problems in cylindrical coordinates to verify our analysis and implementations.

math.NA↗

arXiv2016

Collective electronic excitation in a trapped ensemble of photogenerated dipolar excitons and free holes revealed by inelastic light scattering

Photogenerated excitonic ensembles confined in coupled GaAs quantum wells are probed by a complementary approach of emission spectroscopy and resonant inelastic light scattering. Lateral electrostatic trap geometries are used to create dense systems of spatially indirect excitons and excess holes with similar densities in the order of 10$^{11}$ cm$^{-2}$. Inelastic light scattering spectra reveal a very sharp low-lying collective mode that is identified at an energy of 0.44 meV and a FWHM of only ~50 $μ$eV. This mode is interpreted as a plasmon excitation of the excess hole system coupled to the photogenerated indirect excitons. The emission energy of the indirect excitons shifts under the application of a perpendicular applied electric field with the quantum-confined Stark effect unperturbed from the presence of free charge carriers. Our results illustrate the potential of studying low-lying collective excitations in photogenerated exciton systems to explore the many-body phase diagram, related phase transitions, and interaction physics.

cond-mat.quant-gas↗

arXiv2016

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

Recently exciting progress has been made on protein contact prediction, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual networks. This deep neural network allows us to model very complex sequence-contact relationship as well as long-range inter-contact correlation. Our method greatly outperforms existing contact prediction methods and leads to much more accurate contact-assisted protein folding. Tested on three datasets of 579 proteins, the average top L long-range prediction accuracy obtained our method, the representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21 and 0.30, respectively; the average top L/10 long-range accuracy of our method, CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding using our predicted contacts as restraints can yield correct folds (i.e., TMscore>0.6) for 203 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 proteins, respectively. Further, our contact-assisted models have much better quality than template-based models. Using our predicted contacts as restraints, we can (ab initio) fold 208 of the 398 membrane proteins with TMscore>0.5. By contrast, when the training proteins of our method are used as templates, homology modeling can only do so for 10 of them. One interesting finding is that even if we do not train our prediction models with any membrane proteins, our method works very well on membrane protein prediction. Finally, in recent blind CAMEO benchmark our method successfully folded 5 test proteins with a novel fold.

q-bio.BM↗

arXiv2016

Service Function Chaining Resource Allocation: A Survey

Service Function Chaining (SFC) is a crucial technology for future Internet. It aims to overcome the limitation of current deployment models which is rigid and static. Application of this technology relies on algorithms that can optimally mapping SFC to substrate network. This category of algorithms is referred as "Service Function Chaining Resource Allocation (SFC-RA)" algorithms or "VNF placement (VNFP)" algorithms. This paper presents a survey of current researches in SFC-RA algorithms. After presenting the formulation and related problems, several variants of SFC-RA problem are summarized. At last, we discussed several future research directions.

cs.NI↗

arXiv2016

Study on the magnetic measurement results of the injection system for CSNS/RCS

A combination of the H- stripping and phase space painting method is used to accumulate a high intensity beam in the Rapid Cycling Synchrotron (RCS) of the China Spallation Neutron Source (CSNS). The injection system for CSNS/RCS consists of three kinds of magnets: four direct current magnets (BC1-BC4), eight alternating current magnets (BH1-BH4 and BV1-BV4), two septum magnets (ISEP1 and ISEP2). In this paper, the magnetic measurements of the injection system were introduced and the data analysis was processed. The field uniformity and magnetizing curves of these magnets were given, and then the magnetizing fitting equations were obtained.

physics.acc-ph↗

arXiv2016

The optimization for the conceptual design of a 300 MeV proton synchrotron

A research complex for aerospace radiation effects research has been proposed in Harbin Institute of Technology. Its core part is a proton accelerator complex, which consists of a 10 MeV injector, a 300 MeV synchrotron and beam transport lines. The proton beam extracted from the synchrotron is utilized for the radiation effects research. Based on the conceptual design [1], the design study for optimizing the synchrotron has been done. A new lattice design was worked out, and the multi-turn injection and slow extraction system were optimized with the new lattice design. In order to improve the time structure of the extracted beam, a RF knock-out method is employed. To meet the requirement of accurate control of dose, the frequency of the RF kicker is well investigated.

physics.acc-ph↗

arXiv2016

Feature Learning based Deep Supervised Hashing with Pairwise Labels

Recent years have witnessed wide application of hashing for large-scale image retrieval. However, most existing hashing methods are based on hand-crafted features which might not be optimally compatible with the hashing procedure. Recently, deep hashing methods have been proposed to perform simultaneous feature learning and hash-code learning with deep neural networks, which have shown better performance than traditional hashing methods with hand-crafted features. Most of these deep hashing methods are supervised whose supervised information is given with triplet labels. For another common application scenario with pairwise labels, there have not existed methods for simultaneous feature learning and hash-code learning. In this paper, we propose a novel deep hashing method, called deep pairwise-supervised hashing(DPSH), to perform simultaneous feature learning and hash-code learning for applications with pairwise labels. Experiments on real datasets show that our DPSH method can outperform other methods to achieve the state-of-the-art performance in image retrieval applications.

cs.LG↗

arXiv2016

Feasibility study of online tuning of the luminosity in a circular collider with the robust conjugate direction search method

The robust conjugate direction search (RCDS) method has high tolerance to noise in beam experiments. It has been demonstrated that this method can be used to optimize the machine performance of a light source online. In our study, taking BEPCII as an example, the feasibility of online tuning of the luminosity in a circular collider is explored, through numerical simulation and preliminary online experiments. It is shown that the luminosity that is artificially decreased by a deviation of beam orbital offset from optimal trajectory can be recovered with this method.

physics.acc-ph↗