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Researcher profile

Wen Zhang

Wen Zhang contributes to research discovery and scholarly infrastructure.

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Artificial IntelligenceMachine LearningComputation and Languagecond-mat.mtrl-sciComputer Science and Game TheoryComputer VisionGenomicsmath.NANumerical AnalysisQuantitative MethodsSocial and Information Networksastro-ph.GABiomoleculesComputationcond-mat.str-elCryptography and SecurityDatabaseseess.SPHuman-Computer InteractionInformation RetrievalLogic in Computer Sciencemath.FAMethodologyNetworking and Internet Architecturephysics.chem-phq-fin.RM

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Published work

37 published item(s)

preprint2026arXiv

Engineering Robustness into Personal Agents with the AI Workflow Store

The dominant paradigm for AI agents is an "on-the-fly" loop in which agents synthesize plans and execute actions within seconds or minutes in response to user prompts. We argue that this paradigm short-circuits disciplined software engineering (SE) processes -- iterative design, rigorous testing, adversarial evaluation, staged deployment, and more -- that have delivered the (relatively) reliable and secure systems we use today. By focusing on rapid, real-time synthesis, are AI agents effectively delivering users improvised prototypes rather than systems fit for high-stakes scenarios in which users may unwittingly apply them? This paper argues for the need to integrate rigorous SE processes into the agentic loop to produce production-grade, hardened, and deterministically-constrained agent *workflows* that substantially outperform the potentially brittle and vulnerable results of on-the-fly synthesis. Doing so may require extra compute and time, and if so, we must amortize the cost of rigor through reuse across a broad user community. We envision an *AI Workflow Store* that consists of hardened and reusable workflows that agents can invoke with far greater reliability and security than improvised tool chains. We outline the research challenges of this vision, which stem from a broader flexibility-robustness tension that we argue requires moving beyond the ``on-the-fly'' paradigm to navigate effectively.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

First Submillimeter Lights from Dome A: Tracing the Carbon Cycle in the Feedback of Massive Stars

The cycling of carbon between its ionized, atomic, and molecular phases shapes the chemical compositions and physical conditions of the interstellar medium (ISM). However, ground-based studies of the full carbon cycle have been limited by atmospheric absorption. Dome~A, the most promising site for submillimeter astronomy, has long resisted successful submillimeter astronomical observations. Using the 60~cm Antarctic Terahertz Explorer, we present the first successful CO ($4-3$) and [CI] ($^3P_1 - ^3P_0$) mapping observations of two archetypal triggered massive star-formation regions at Dome~A. These data, together with archival [CII], provide the first complete characterization of all three carbon phases in these environments. We find elevated C$^{0}$/CO abundance ratios in high-extinction regions, plausibly driven by deep penetration of intense radiation fields from massive stars into a clumpy ISM. These findings mark a major milestone for submillimeter astronomy at Dome~A and offer valuable insights into the impact of massive star feedback on the surrounding ISM.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Mind Your Moras: Orthography-Aware Error Analysis of Neural Japanese Morphological Generation

We present an orthography-aware error analysis of Japanese past-tense morphological inflection, treating hiragana not merely as a transcriptional medium, but as a representational system encoding morphophonological distinctions that may influence model generalization. We evaluate two character-level sequence-to-sequence architectures on past-tense formation using datasets formatted according to the SIGMORPHON 2020 and 2023 shared task conventions. Despite high aggregate accuracy, models exhibit systematic, linguistically interpretable errors that cluster around specific orthographic properties of hiragana. We introduce a concise error taxonomy capturing seven primary failure modes and provide both quantitative and qualitative analyses. Gemination-related errors dominate residual failures, accounting for 75-80% of errors, particularly in verbs whose stems end in the vowel e and require gemination before the past-tense suffix. Error patterns remain highly consistent across architectures and random seeds, suggesting a robust interaction between orthographic representation, morphological structure, and data frequency effects in shaping model generalization. These results underscore the necessity of orthography-aware evaluation for understanding neural generalization in morphologically complex languages.

0 citations0 reviewsNo code linkedOpen access
preprint2024arXiv

A Multi-Modal Contrastive Diffusion Model for Therapeutic Peptide Generation

Therapeutic peptides represent a unique class of pharmaceutical agents crucial for the treatment of human diseases. Recently, deep generative models have exhibited remarkable potential for generating therapeutic peptides, but they only utilize sequence or structure information alone, which hinders the performance in generation. In this study, we propose a Multi-Modal Contrastive Diffusion model (MMCD), fusing both sequence and structure modalities in a diffusion framework to co-generate novel peptide sequences and structures. Specifically, MMCD constructs the sequence-modal and structure-modal diffusion models, respectively, and devises a multi-modal contrastive learning strategy with intercontrastive and intra-contrastive in each diffusion timestep, aiming to capture the consistency between two modalities and boost model performance. The inter-contrastive aligns sequences and structures of peptides by maximizing the agreement of their embeddings, while the intra-contrastive differentiates therapeutic and non-therapeutic peptides by maximizing the disagreement of their sequence/structure embeddings simultaneously. The extensive experiments demonstrate that MMCD performs better than other state-of-theart deep generative methods in generating therapeutic peptides across various metrics, including antimicrobial/anticancer score, diversity, and peptide-docking.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

A Deep Learning Galerkin Method for the Closed-Loop Geothermal System

There has been an arising trend of adopting deep learning methods to study partial differential equations (PDEs). This article is to propose a Deep Learning Galerkin Method (DGM) for the closed-loop geothermal system, which is a new coupled multi-physics PDEs and mainly consists of a framework of underground heat exchange pipelines to extract the geothermal heat from the geothermal reservoir. This method is a natural combination of Galerkin Method and machine learning with the solution approximated by a neural network instead of a linear combination of basis functions. We train the neural network by randomly sampling the spatiotemporal points and minimize loss function to satisfy the differential operators, initial condition, boundary and interface conditions. Moreover, the approximate ability of the neural network is proved by the convergence of the loss function and the convergence of the neural network to the exact solution in L^2 norm under certain conditions. Finally, some numerical examples are carried out to demonstrate the approximation ability of the neural networks intuitively.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Blockaid: Data Access Policy Enforcement for Web Applications

Modern web applications serve large amounts of sensitive user data, access to which is typically governed by data-access policies. Enforcing such policies is crucial to preventing improper data access, and prior work has proposed many enforcement mechanisms. However, these prior methods either alter application semantics or require adopting a new programming model; the former can result in unexpected application behavior, while the latter cannot be used with existing web frameworks. Blockaid is an access-policy enforcement system that preserves application semantics and is compatible with existing web frameworks. It intercepts database queries from the application, attempts to verify that each query is policy-compliant, and blocks queries that are not. It verifies policy compliance using SMT solvers and generalizes and caches previous compliance decisions for better performance. We show that Blockaid supports existing web applications while requiring minimal code changes and adding only modest overheads.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

CDNNs: The coupled deep neural networks for coupling of the Stokes and Darcy-Forchheimer problems

In this article, we present an efficient deep learning method called coupled deep neural networks (CDNNs) for coupled physical problems. Our method compiles the interface conditions of the coupled PDEs into the networks properly and can be served as an efficient alternative to the complex coupled problems. To impose energy conservation constraints, the CDNNs utilize simple fully connected layers and a custom loss function to perform the model training process as well as the physical property of the exact solution. The approach can be beneficial for the following reasons: Firstly, we sampled randomly and only input spatial coordinates without being restricted by the nature of samples. Secondly, our method is meshfree which makes it more efficient than the traditional methods. Finally, our method is parallel and can solve multiple variables independently at the same time. We give the theory to guarantee the convergence of the loss function and the convergence of the neural networks to the exact solution. Some numerical experiments are performed and discussed to demonstrate the performance of the proposed method.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Disentangled Ontology Embedding for Zero-shot Learning

Knowledge Graph (KG) and its variant of ontology have been widely used for knowledge representation, and have shown to be quite effective in augmenting Zero-shot Learning (ZSL). However, existing ZSL methods that utilize KGs all neglect the intrinsic complexity of inter-class relationships represented in KGs. One typical feature is that a class is often related to other classes in different semantic aspects. In this paper, we focus on ontologies for augmenting ZSL, and propose to learn disentangled ontology embeddings guided by ontology properties to capture and utilize more fine-grained class relationships in different aspects. We also contribute a new ZSL framework named DOZSL, which contains two new ZSL solutions based on generative models and graph propagation models, respectively, for effectively utilizing the disentangled ontology embeddings. Extensive evaluations have been conducted on five benchmarks across zero-shot image classification (ZS-IMGC) and zero-shot KG completion (ZS-KGC). DOZSL often achieves better performance than the state-of-the-art, and its components have been verified by ablation studies and case studies. Our codes and datasets are available at https://github.com/zjukg/DOZSL.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Energy Harvesting Aware Multi-hop Routing Policy in Distributed IoT System Based on Multi-agent Reinforcement Learning

Energy harvesting technologies offer a promising solution to sustainably power an ever-growing number of Internet of Things (IoT) devices. However, due to the weak and transient natures of energy harvesting, IoT devices have to work intermittently rendering conventional routing policies and energy allocation strategies impractical. To this end, this paper, for the very first time, developed a distributed multi-agent reinforcement algorithm known as global actor-critic policy (GAP) to address the problem of routing policy and energy allocation together for the energy harvesting powered IoT system. At the training stage, each IoT device is treated as an agent and one universal model is trained for all agents to save computing resources. At the inference stage, packet delivery rate can be maximized. The experimental results show that the proposed GAP algorithm achieves around 1.28 times and 1.24 times data transmission rate than that of the Q-table and ESDSRAA algorithm, respectively.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Evidence of Spin Frustration in Vanadium Diselenide Monolayer Magnet

Monolayer VSe2, featuring both charge density wave and magnetism phenomena, represents a unique van der Waals magnet in the family of metallic two-dimensional transition-metal dichalcogenides (2D-TMDs). Herein, by means of in-situ microscopic and spectroscopic techniques, including scanning tunneling microscopy/spectroscopy, synchrotron X-ray and angle-resolved photoemission, and X-ray absorption, direct spectroscopic signatures are established, that identify the metallic 1T-phase and vanadium 3d1 electronic configuration in monolayer VSe2 grown on graphite by molecular-beam epitaxy. Element-specific X-ray magnetic circular dichroism, complemented with magnetic susceptibility measurements, further reveals monolayer VSe2 as a frustrated magnet, with its spins exhibiting subtle correlations, albeit in the absence of a long-range magnetic order down to 2 K and up to a 7 T magnetic field. This observation is attributed to the relative stability of the ferromagnetic and antiferromagnetic ground states, arising from its atomic-scale structural features, such as rotational disorders and edges. The results of this study extend the current understanding of metallic 2D-TMDs in the search for exotic low-dimensional quantum phenomena, and stimulate further theoretical and experimental studies on van der Waals monolayer magnets.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Investigating the efficiency of marginalising over discrete parameters in Bayesian computations

Bayesian analysis methods often use some form of iterative simulation such as Monte Carlo computation. Models that involve discrete variables can sometime pose a challenge, either because the methods used do not support such variables (e.g. Hamiltonian Monte Carlo) or because the presence of such variables can slow down the computation. A common workaround is to marginalise the discrete variables out of the model. While it is reasonable to expect that such marginalisation would also lead to more time-efficient computations, to our knowledge this has not been demonstrated beyond a few specialised models. We explored the impact of marginalisation on the computational efficiency for a few simple statistical models. Specifically, we considered two- and three-component Gaussian mixture models, and also the Dawid-Skene model for categorical ratings. We explored each with two software implementations of Markov chain Monte Carlo techniques: JAGS and Stan. We directly compared marginalised and non-marginalised versions of the same model using the samplers on the same software. Our results show that marginalisation on its own does not necessarily boost performance. Nevertheless, the best performance was usually achieved with Stan, which requires marginalisation. We conclude that there is no simple answer to whether or not marginalisation is helpful. It is not necessarily the case that, when turned 'on', this technique can be assured to provide computational benefit independent of other factors, nor is it likely to be the model component that has the largest impact on computational efficiency.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Joint-optimization of Node placement and UAV's Trajectory for Self-sustaining Air-Ground IoT system

Due to the sustainable power supply and environment-friendly features, self-powered IoT devices have been increasingly employed in various fields such as providing observation data in remote areas, especially in rural areas or post-disaster scenarios. Generally, through multi-hop relay, the sensed data of those self-powered IoT devices are collected by the sink node which connects to the IoT backbones. However, due to the remoteness, the sink needs to be located at the border of the monitoring area where both the backbone of IoT and electrical infrastructures are accessible. Under such deployment, significant data flow and relay overhead will incur considering the large scale of the monitoring area. Motivated by this issue, this paper aims to design a UAV-assisted self-powered heterogeneous system to provide comprehensive monitoring data. In this system, because of the superiority of the unmanned aerial vehicle (UAV) in the easy deployment, We dispatch UAV collects data from self-powered IoT devices, periodically so as to alleviate the data overflow. Moreover, based on that the self-powered IoT devices are expected to have a more considerable capability in the heavy data flow area, we also developed a placement upgrade strategy to upgrade the general homogeneous self-powered IoT system to the heterogeneous self-powered IoT system. Simulation results indicated the developed UAV-assisted self-powered heterogeneous system can achieve around $1.28\times$ the amount of data delivery to sink compared with the homogeneous self-powered IoT system.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Knowledge Graph Reasoning with Logics and Embeddings: Survey and Perspective

Knowledge graph (KG) reasoning is becoming increasingly popular in both academia and industry. Conventional KG reasoning based on symbolic logic is deterministic, with reasoning results being explainable, while modern embedding-based reasoning can deal with uncertainty and predict plausible knowledge, often with high efficiency via vector computation. A promising direction is to integrate both logic-based and embedding-based methods, with the vision to have advantages of both. It has attracted wide research attention with more and more works published in recent years. In this paper, we comprehensively survey these works, focusing on how logics and embeddings are integrated. We first briefly introduce preliminaries, then systematically categorize and discuss works of logic and embedding-aware KG reasoning from different perspectives, and finally conclude and discuss the challenges and further directions.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Magnetic Transition in Monolayer VSe2 via Interface Hybridization

Magnetism in monolayer (ML) VSe2 has attracted broad interest in spintronics while existing reports have not reached consensus. Using element-specific X-ray magnetic circular dichroism, a magnetic transition in ML VSe2 has been demonstrated at the contamination-free interface between Co and VSe2. Via interfacial hybridization with Co atomic overlayer, a magnetic moment of about 0.4 uB per V atom in ML VSe2 is revealed, approaching values predicted by previous theoretical calculations. Promotion of the ferromagnetism in ML VSe2 is accompanied by its antiferromagnetic coupling to Co and a reduction in the spin moment of Co. In comparison to the absence of this interface-induced ferromagnetism at the Fe/MLMoSe2 interface, these findings at the Co/ML-VSe2 interface provide clear proof that the ML VSe2, initially with magnetic disorder, is on the verge of magnetic transition.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Meta-Knowledge Transfer for Inductive Knowledge Graph Embedding

Knowledge graphs (KGs) consisting of a large number of triples have become widespread recently, and many knowledge graph embedding (KGE) methods are proposed to embed entities and relations of a KG into continuous vector spaces. Such embedding methods simplify the operations of conducting various in-KG tasks (e.g., link prediction) and out-of-KG tasks (e.g., question answering). They can be viewed as general solutions for representing KGs. However, existing KGE methods are not applicable to inductive settings, where a model trained on source KGs will be tested on target KGs with entities unseen during model training. Existing works focusing on KGs in inductive settings can only solve the inductive relation prediction task. They can not handle other out-of-KG tasks as general as KGE methods since they don't produce embeddings for entities. In this paper, to achieve inductive knowledge graph embedding, we propose a model MorsE, which does not learn embeddings for entities but learns transferable meta-knowledge that can be used to produce entity embeddings. Such meta-knowledge is modeled by entity-independent modules and learned by meta-learning. Experimental results show that our model significantly outperforms corresponding baselines for in-KG and out-of-KG tasks in inductive settings.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Meta-Learning Based Knowledge Extrapolation for Knowledge Graphs in the Federated Setting

We study the knowledge extrapolation problem to embed new components (i.e., entities and relations) that come with emerging knowledge graphs (KGs) in the federated setting. In this problem, a model trained on an existing KG needs to embed an emerging KG with unseen entities and relations. To solve this problem, we introduce the meta-learning setting, where a set of tasks are sampled on the existing KG to mimic the link prediction task on the emerging KG. Based on sampled tasks, we meta-train a graph neural network framework that can construct features for unseen components based on structural information and output embeddings for them. Experimental results show that our proposed method can effectively embed unseen components and outperforms models that consider inductive settings for KGs and baselines that directly use conventional KG embedding methods.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Molecular Contrastive Learning with Chemical Element Knowledge Graph

Molecular representation learning contributes to multiple downstream tasks such as molecular property prediction and drug design. To properly represent molecules, graph contrastive learning is a promising paradigm as it utilizes self-supervision signals and has no requirements for human annotations. However, prior works fail to incorporate fundamental domain knowledge into graph semantics and thus ignore the correlations between atoms that have common attributes but are not directly connected by bonds. To address these issues, we construct a Chemical Element Knowledge Graph (KG) to summarize microscopic associations between elements and propose a novel Knowledge-enhanced Contrastive Learning (KCL) framework for molecular representation learning. KCL framework consists of three modules. The first module, knowledge-guided graph augmentation, augments the original molecular graph based on the Chemical Element KG. The second module, knowledge-aware graph representation, extracts molecular representations with a common graph encoder for the original molecular graph and a Knowledge-aware Message Passing Neural Network (KMPNN) to encode complex information in the augmented molecular graph. The final module is a contrastive objective, where we maximize agreement between these two views of molecular graphs. Extensive experiments demonstrated that KCL obtained superior performances against state-of-the-art baselines on eight molecular datasets. Visualization experiments properly interpret what KCL has learned from atoms and attributes in the augmented molecular graphs. Our codes and data are available at https://github.com/ZJU-Fangyin/KCL.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

NeuralKG: An Open Source Library for Diverse Representation Learning of Knowledge Graphs

NeuralKG is an open-source Python-based library for diverse representation learning of knowledge graphs. It implements three different series of Knowledge Graph Embedding (KGE) methods, including conventional KGEs, GNN-based KGEs, and Rule-based KGEs. With a unified framework, NeuralKG successfully reproduces link prediction results of these methods on benchmarks, freeing users from the laborious task of reimplementing them, especially for some methods originally written in non-python programming languages. Besides, NeuralKG is highly configurable and extensible. It provides various decoupled modules that can be mixed and adapted to each other. Thus with NeuralKG, developers and researchers can quickly implement their own designed models and obtain the optimal training methods to achieve the best performance efficiently. We built an website in http://neuralkg.zjukg.cn to organize an open and shared KG representation learning community. The source code is all publicly released at https://github.com/zjukg/NeuralKG.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Overpotential decomposition enabled decoupling of complex kinetic processes in battery electrodes

Identifying overpotential components of electrochemical systems enables quantitative analysis of polarization contributions of kinetic processes under practical operating conditions. However, the inherently coupled kinetic processes lead to an enormous challenge in measuring individual overpotentials, particularly in composite electrodes of lithium-ion batteries. Herein, the full decomposition of electrode overpotential is realized by the collaboration of single-layer structured particle electrode (SLPE) constructions and time-resolved potential measurements, explicitly revealing the evolution of kinetic processes. Perfect prediction of the discharging profiles is achieved via potential measurements on SLPEs, even in extreme polarization conditions. By decoupling overpotentials in different electrode/cell structures and material systems, the dominant limiting processes of battery rate performance are uncovered, based on which the optimization of electrochemical kinetics can be conducted. Our study not only shades light on decoupling complex kinetics in electrochemical systems, but also provides vitally significant guidance for the rational design of high-performance batteries.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

PKGM: A Pre-trained Knowledge Graph Model for E-commerce Application

In recent years, knowledge graphs have been widely applied as a uniform way to organize data and have enhanced many tasks requiring knowledge. In online shopping platform Taobao, we built a billion-scale e-commerce product knowledge graph. It organizes data uniformly and provides item knowledge services for various tasks such as item recommendation. Usually, such knowledge services are provided through triple data, while this implementation includes (1) tedious data selection works on product knowledge graph and (2) task model designing works to infuse those triples knowledge. More importantly, product knowledge graph is far from complete, resulting error propagation to knowledge enhanced tasks. To avoid these problems, we propose a Pre-trained Knowledge Graph Model (PKGM) for the billion-scale product knowledge graph. On the one hand, it could provide item knowledge services in a uniform way with service vectors for embedding-based and item-knowledge-related task models without accessing triple data. On the other hand, it's service is provided based on implicitly completed product knowledge graph, overcoming the common the incomplete issue. We also propose two general ways to integrate the service vectors from PKGM into downstream task models. We test PKGM in five knowledge-related tasks, item classification, item resolution, item recommendation, scene detection and sequential recommendation. Experimental results show that PKGM introduces significant performance gains on these tasks, illustrating the useful of service vectors from PKGM.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Relational Message Passing for Fully Inductive Knowledge Graph Completion

In knowledge graph completion (KGC), predicting triples involving emerging entities and/or relations, which are unseen when the KG embeddings are learned, has become a critical challenge. Subgraph reasoning with message passing is a promising and popular solution. Some recent methods have achieved good performance, but they (i) usually can only predict triples involving unseen entities alone, failing to address more realistic fully inductive situations with both unseen entities and unseen relations, and (ii) often conduct message passing over the entities with the relation patterns not fully utilized. In this study, we propose a new method named RMPI which uses a novel Relational Message Passing network for fully Inductive KGC. It passes messages directly between relations to make full use of the relation patterns for subgraph reasoning with new techniques on graph transformation, graph pruning, relation-aware neighborhood attention, addressing empty subgraphs, etc., and can utilize the relation semantics defined in the ontological schema of KG. Extensive evaluation on multiple benchmarks has shown the effectiveness of techniques involved in RMPI and its better performance compared with the existing methods that support fully inductive KGC. RMPI is also comparable to the state-of-the-art partially inductive KGC methods with very promising results achieved. Our codes and data are available at https://github.com/zjukg/RMPI.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Ruleformer: Context-aware Differentiable Rule Mining over Knowledge Graph

Rule mining is an effective approach for reasoning over knowledge graph (KG). Existing works mainly concentrate on mining rules. However, there might be several rules that could be applied for reasoning for one relation, and how to select appropriate rules for completion of different triples has not been discussed. In this paper, we propose to take the context information into consideration, which helps select suitable rules for the inference tasks. Based on this idea, we propose a transformer-based rule mining approach, Ruleformer. It consists of two blocks: 1) an encoder extracting the context information from subgraph of head entities with modified attention mechanism, and 2) a decoder which aggregates the subgraph information from the encoder output and generates the probability of relations for each step of reasoning. The basic idea behind Ruleformer is regarding rule mining process as a sequence to sequence task. To make the subgraph a sequence input to the encoder and retain the graph structure, we devise a relational attention mechanism in Transformer. The experiment results show the necessity of considering these information in rule mining task and the effectiveness of our model.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Collaborative Data Acquisition

We consider a requester who acquires a set of data (e.g. images) that is not owned by one party. In order to collect as many data as possible, crowdsourcing mechanisms have been widely used to seek help from the crowd. However, existing mechanisms rely on third-party platforms, and the workers from these platforms are not necessarily helpful and redundant data are also not properly handled. To combat this problem, we propose a novel crowdsourcing mechanism based on social networks, where the rewards of the workers are calculated by information entropy and a modified Shapley value. This mechanism incentivizes the workers from the network to not only provide all data they have but also further invite their neighbours to offer more data. Eventually, the mechanism is able to acquire all data from all workers on the network and the requester's cost is no more than the value of the data acquired. The experiments show that our mechanism outperforms traditional crowdsourcing mechanisms.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Deep Representation Learning For Multimodal Brain Networks

Applying network science approaches to investigate the functions and anatomy of the human brain is prevalent in modern medical imaging analysis. Due to the complex network topology, for an individual brain, mining a discriminative network representation from the multimodal brain networks is non-trivial. The recent success of deep learning techniques on graph-structured data suggests a new way to model the non-linear cross-modality relationship. However, current deep brain network methods either ignore the intrinsic graph topology or require a network basis shared within a group. To address these challenges, we propose a novel end-to-end deep graph representation learning (Deep Multimodal Brain Networks - DMBN) to fuse multimodal brain networks. Specifically, we decipher the cross-modality relationship through a graph encoding and decoding process. The higher-order network mappings from brain structural networks to functional networks are learned in the node domain. The learned network representation is a set of node features that are informative to induce brain saliency maps in a supervised manner. We test our framework in both synthetic and real image data. The experimental results show the superiority of the proposed method over some other state-of-the-art deep brain network models.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Discriminative Joint Probability Maximum Mean Discrepancy (DJP-MMD) for Domain Adaptation

Maximum mean discrepancy (MMD) has been widely adopted in domain adaptation to measure the discrepancy between the source and target domain distributions. Many existing domain adaptation approaches are based on the joint MMD, which is computed as the (weighted) sum of the marginal distribution discrepancy and the conditional distribution discrepancy; however, a more natural metric may be their joint probability distribution discrepancy. Additionally, most metrics only aim to increase the transferability between domains, but ignores the discriminability between different classes, which may result in insufficient classification performance. To address these issues, discriminative joint probability MMD (DJP-MMD) is proposed in this paper to replace the frequently-used joint MMD in domain adaptation. It has two desirable properties: 1) it provides a new theoretical basis for computing the distribution discrepancy, which is simpler and more accurate; 2) it increases the transferability and discriminability simultaneously. We validate its performance by embedding it into a joint probability domain adaptation framework. Experiments on six image classification datasets demonstrated that the proposed DJP-MMD can outperform traditional MMDs.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

EPIHC: Improving Enhancer-Promoter Interaction Prediction by using Hybrid features and Communicative learning

Enhancer-promoter interactions (EPIs) regulate the expression of specific genes in cells, and EPIs are important for understanding gene regulation, cell differentiation and disease mechanisms. EPI identification through the wet experiments is costly and time-consuming, and computational methods are in demand. In this paper, we propose a deep neural network-based method EPIHC based on sequence-derived features and genomic features for the EPI prediction. EPIHC extracts features from enhancer and promoter sequences respectively using convolutional neural networks (CNN), and then design a communicative learning module to captures the communicative information between enhancer and promoter sequences. EPIHC also take the genomic features of enhancers and promoters into account. At last, EPIHC combines sequence-derived features and genomic features to predict EPIs. The computational experiments show that EPIHC outperforms the existing state-of-the-art EPI prediction methods on the benchmark datasets and chromosome-split datasets, and the study reveal that the communicative learning module can bring explicit information about EPIs, which is ignore by CNN. Moreover, we consider two strategies to improve performances of EPIHC in the cross-cell line prediction, and experimental results show that EPIHC constructed on training cell lines exhibit improved performances for the other cell lines.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Graph Embedding on Biomedical Networks: Methods, Applications, and Evaluations

Graph embedding learning that aims to automatically learn low-dimensional node representations, has drawn increasing attention in recent years. To date, most recent graph embedding methods are evaluated on social and information networks and are not comprehensively studied on biomedical networks under systematic experiments and analyses. On the other hand, for a variety of biomedical network analysis tasks, traditional techniques such as matrix factorization (which can be seen as a type of graph embedding methods) have shown promising results, and hence there is a need to systematically evaluate the more recent graph embedding methods (e.g. random walk-based and neural network-based) in terms of their usability and potential to further the state-of-the-art. We select 11 representative graph embedding methods and conduct a systematic comparison on 3 important biomedical link prediction tasks: drug-disease association (DDA) prediction, drug-drug interaction (DDI) prediction, protein-protein interaction (PPI) prediction; and 2 node classification tasks: medical term semantic type classification, protein function prediction. Our experimental results demonstrate that the recent graph embedding methods achieve promising results and deserve more attention in the future biomedical graph analysis. Compared with three state-of-the-art methods for DDAs, DDIs and protein function predictions, the recent graph embedding methods achieve competitive performance without using any biological features and the learned embeddings can be treated as complementary representations for the biological features. By summarizing the experimental results, we provide general guidelines for properly selecting graph embedding methods and setting their hyper-parameters for different biomedical tasks.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Incentivize Diffusion with Fair Rewards

This paper studies a sale promotion mechanism design problem on a social network, where a node (a seller) sells one item to the other nodes on the network to maximize her revenue. However, the seller does not know other nodes except for her neighbours and her neighbours have no incentive to promote the sale. Hence, the goal is to design an auction mechanism such that the seller's neighbours are incentivized to invite their neighbours to join the auction, while the seller's revenue is guaranteed to increase. This is not achievable with traditional mechanisms. One solution has been proposed recently by carefully designing a reward scheme for the nodes who have invited others. However, the solution only gives rewards to some cut-points of the network, but cut-points rarely exist in a well-connected network, which actually disincentivizes nodes' participation. Therefore, we propose another novel mechanism to reward more related participants with fairer rewards, and the seller's revenue is not reduced.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

ItLnc-BXE: a Bagging-XGBoost-ensemble method with multiple features for identification of plant lncRNAs

Motivation: Since long non-coding RNAs (lncRNAs) have involved in a wide range of functions in cellular and developmental processes, an increasing number of methods have been proposed for distinguishing lncRNAs from coding RNAs. However, most of the existing methods are designed for lncRNAs in animal systems, and only a few methods focus on the plant lncRNA identification. Different from lncRNAs in animal systems, plant lncRNAs have distinct characteristics. It is desirable to develop a computational method for accurate and robust identification of plant lncRNAs. Results: Herein, we present a plant lncRNA identification method ItLnc-BXE, which utilizes multiple features and the ensemble learning strategy. First, a diversity of lncRNA features is collected and filtered by feature selection to represent RNA transcripts. Then, several base learners are trained and further combined into a single meta-learner by ensemble learning, and thus an ItLnc-BXE model is constructed. ItLnc-BXE models are evaluated on datasets of six plant species, the results show that ItLnc-BXE outperforms other state-of-the-art plant lncRNA identification methods, achieving better and robust performances (AUC>95.91%). We also perform some experiments about cross-species lncRNA identification, and the results indicate that dicots-based and monocots-based models can be used to accurately identify lncRNAs in lower plant species, such as mosses and algae. Availability: source codes are available at https://github.com/BioMedicalBigDataMiningLab/ItLnc-BXE. Contact: zhangwen@mail.hzau.edu.cn (or) zhangwen@whu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.

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preprint2020arXiv

Kondo scenario of the γ-α phase transition in single crystalline Cerium thin films

The physical mechanism driving the $γ$-$α$ phase transition of face-centre-cubic (fcc) cerium (Ce) remains controversial until now. In this work, high quality single crystalline fcc-Ce thin films were grown on Graphene/6$H$-SiC(0001) substrate, and explored by XRD and ARPES measurement. XRD spectra showed a clear $γ$-$α$ phase transition at $T_{γ-α}\approx$ 50 K, which is retarded by strain effect from substrate comparing with $T_{γ-α}$ (about 140 K) of the bulk Ce metal. However, APRES spectra did not show any signature of $α$-phase emerging in the surface-layer from 300 K to 17 K, which implied that $α$-phase might form at the bulk-layer of our Ce thin films. Besides, an evident Kondo dip near Fermi energy was observed in the APRES spectrum at 80 K, indicting the formation of Kondo singlet states in $γ$-Ce. Furthermore, the DFT+DMFT calculations were performed to simulate the electronic structures and the theoretical spectral functions agreed well with the experimental ARPES spectra. In $γ$-Ce, the behavior of the self-energy's imaginary part at low frequency not only confirmed that the Kondo singlet states emerged at $T_{\rm KS} \geq 80$ K, but also implied that they became coherent states at a lower characteristic temperature ($T_{\rm coh}\sim 40$ K) due to the indirect RKKY interaction among $f$-$f$ electrons. Besides, $T_{\rm coh}$ from the theoretical simulation was close to $T_{γ-α}$ from the XRD spectra. These issues suggested that the Kondo scenario might play an important role in the $γ$-$α$ phase transition of cerium thin films.

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preprint2020arXiv

Manifold Embedded Knowledge Transfer for Brain-Computer Interfaces

Transfer learning makes use of data or knowledge in one problem to help solve a different, yet related, problem. It is particularly useful in brain-computer interfaces (BCIs), for coping with variations among different subjects and/or tasks. This paper considers offline unsupervised cross-subject electroencephalogram (EEG) classification, i.e., we have labeled EEG trials from one or more source subjects, but only unlabeled EEG trials from the target subject. We propose a novel manifold embedded knowledge transfer (MEKT) approach, which first aligns the covariance matrices of the EEG trials in the Riemannian manifold, extracts features in the tangent space, and then performs domain adaptation by minimizing the joint probability distribution shift between the source and the target domains, while preserving their geometric structures. MEKT can cope with one or multiple source domains, and can be computed efficiently. We also propose a domain transferability estimation (DTE) approach to identify the most beneficial source domains, in case there are a large number of source domains. Experiments on four EEG datasets from two different BCI paradigms demonstrated that MEKT outperformed several state-of-the-art transfer learning approaches, and DTE can reduce more than half of the computational cost when the number of source subjects is large, with little sacrifice of classification accuracy.

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preprint2020arXiv

Neural Entity Summarization with Joint Encoding and Weak Supervision

In a large-scale knowledge graph (KG), an entity is often described by a large number of triple-structured facts. Many applications require abridged versions of entity descriptions, called entity summaries. Existing solutions to entity summarization are mainly unsupervised. In this paper, we present a supervised approach NEST that is based on our novel neural model to jointly encode graph structure and text in KGs and generate high-quality diversified summaries. Since it is costly to obtain manually labeled summaries for training, our supervision is weak as we train with programmatically labeled data which may contain noise but is free of manual work. Evaluation results show that our approach significantly outperforms the state of the art on two public benchmarks.

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preprint2020arXiv

On the sum of simultaneously proximinal sets

In this paper, we show that the sum of a compact convex subset and a simultaneously $τ$-strongly proximinal convex subset (resp. simultaneously approximatively $τ$-compact convex subset) of a Banach space X is simultaneously tau-strongly proximinal (resp. simultaneously approximatively $τ$-compact ), and the sum of weakly compact convex subset and a simultaneously approximatively weakly compact convex subset of X is still simultaneously approximatively weakly compact, where $τ$ is the norm or the weak topology. Moreover, some related results on the sum of simultaneously proximinal subspaces are presented.

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preprint2020arXiv

Redistribution Mechanism on Networks

Redistribution mechanisms have been proposed for more efficient resource allocation but not for profit. We consider redistribution mechanism design in a setting where participants are connected and the resource owner is only connected to some of them. In this setting, to make the resource allocation more efficient, the resource owner has to inform the others who are not her neighbours, but her neighbours do not want more participants to compete with them. Hence, the goal is to design a redistribution mechanism such that participants are incentivized to invite more participants and the resource owner does not earn or lose much money from the allocation. We first show that existing redistribution mechanisms cannot be directly applied in the network setting and prove the impossibility to achieve efficiency without a deficit. Then we propose a novel network-based redistribution mechanism such that all participants on the network are invited, the allocation is more efficient and the resource owner has no deficit.

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preprint2020arXiv

Regularized Wasserstein Means for Aligning Distributional Data

We propose to align distributional data from the perspective of Wasserstein means. We raise the problem of regularizing Wasserstein means and propose several terms tailored to tackle different problems. Our formulation is based on the variational transportation to distribute a sparse discrete measure into the target domain. The resulting sparse representation well captures the desired property of the domain while reducing the mapping cost. We demonstrate the scalability and robustness of our method with examples in domain adaptation, point set registration, and skeleton layout.

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preprint2020arXiv

Towards Playing Full MOBA Games with Deep Reinforcement Learning

MOBA games, e.g., Honor of Kings, League of Legends, and Dota 2, pose grand challenges to AI systems such as multi-agent, enormous state-action space, complex action control, etc. Developing AI for playing MOBA games has raised much attention accordingly. However, existing work falls short in handling the raw game complexity caused by the explosion of agent combinations, i.e., lineups, when expanding the hero pool in case that OpenAI's Dota AI limits the play to a pool of only 17 heroes. As a result, full MOBA games without restrictions are far from being mastered by any existing AI system. In this paper, we propose a MOBA AI learning paradigm that methodologically enables playing full MOBA games with deep reinforcement learning. Specifically, we develop a combination of novel and existing learning techniques, including curriculum self-play learning, policy distillation, off-policy adaption, multi-head value estimation, and Monte-Carlo tree-search, in training and playing a large pool of heroes, meanwhile addressing the scalability issue skillfully. Tested on Honor of Kings, a popular MOBA game, we show how to build superhuman AI agents that can defeat top esports players. The superiority of our AI is demonstrated by the first large-scale performance test of MOBA AI agent in the literature.

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preprint2019arXiv

Cross-sectional Learning of Extremal Dependence among Financial Assets

We propose a novel probabilistic model to facilitate the learning of multivariate tail dependence of multiple financial assets. Our method allows one to construct from known random vectors, e.g., standard normal, sophisticated joint heavy-tailed random vectors featuring not only distinct marginal tail heaviness, but also flexible tail dependence structure. The novelty lies in that pairwise tail dependence between any two dimensions is modeled separately from their correlation, and can vary respectively according to its own parameter rather than the correlation parameter, which is an essential advantage over many commonly used methods such as multivariate $t$ or elliptical distribution. It is also intuitive to interpret, easy to track, and simple to sample comparing to the copula approach. We show its flexible tail dependence structure through simulation. Coupled with a GARCH model to eliminate serial dependence of each individual asset return series, we use this novel method to model and forecast multivariate conditional distribution of stock returns, and obtain notable performance improvements in multi-dimensional coverage tests. Besides, our empirical finding about the asymmetry of tails of the idiosyncratic component as well as the market component is interesting and worth to be well studied in the future.

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