Adverse Drug Reactions (ADRs) are characterized within randomized clinical trials and postmarketing pharmacovigilance, but their molecular mechanism remains unknown in most cases. Aside from clinical trials, many elements of knowledge about drug ingredients are available in open-access knowledge graphs. In addition, drug classifications that label drugs as either causative or not for several ADRs, have been established. We propose to mine knowledge graphs for identifying biomolecular features that may enable reproducing automatically expert classifications that distinguish drug causative or not for a given type of ADR. In an explainable AI perspective, we explore simple classification techniques such as Decision Trees and Classification Rules because they provide human-readable models, which explain the classification itself, but may also provide elements of explanation for molecular mechanisms behind ADRs. In summary, we mine a knowledge graph for features; we train classifiers at distinguishing, drugs associated or not with ADRs; we isolate features that are both efficient in reproducing expert classifications and interpretable by experts (i.e., Gene Ontology terms, drug targets, or pathway names); and we manually evaluate how they may be explanatory. Extracted features reproduce with a good fidelity classifications of drugs causative or not for DILI and SCAR. Experts fully agreed that 73% and 38% of the most discriminative features are possibly explanatory for DILI and SCAR, respectively; and partially agreed (2/3) for 90% and 77% of them. Knowledge graphs provide diverse features to enable simple and explainable models to distinguish between drugs that are causative or not for ADRs. In addition to explaining classifications, most discriminative features appear to be good candidates for investigating ADR mechanisms further.
Although the scientific digital library is growing at a rapid pace, scholars/students often find reading Science, Technology, Engineering, and Mathematics (STEM) literature daunting, especially for the math-content/formula. In this paper, we propose a novel problem, ``mathematics content understanding'', for cyberlearning and cyberreading. To address this problem, we create a Formula Evolution Map (FEM) offline and implement a novel online learning/reading environment, PDF Reader with Math-Assistant (PRMA), which incorporates innovative math-scaffolding methods. The proposed algorithm/system can auto-characterize student emerging math-information need while reading a paper and enable students to readily explore the formula evolution trajectory in FEM. Based on a math-information need, PRMA utilizes innovative joint embedding, formula evolution mining, and heterogeneous graph mining algorithms to recommend high quality Open Educational Resources (OERs), e.g., video, Wikipedia page, or slides, to help students better understand the math-content in the paper. Evaluation and exit surveys show that the PRMA system and the proposed formula understanding algorithm can effectively assist master and PhD students better understand the complex math-content in the class readings.
Named entity discovery (NED) is an important information retrieval problem that can be decomposed into two sub-problems. The first sub-problem, named entity recognition (NER), aims to tag pre-defined sets of words in a vocabulary (called "named entities": names, places, locations, ...) when they appear in natural language. The second subproblem, named entity linking/identification (NEL), considers these entity mentions as queries to be identified in a pre-existing database. In this paper, we consider the NEL problem, and assume a set of queries (or mentions) that have to be identified within a knowledge base. This knowledge base is represented by a text database paired with a semantic graph. We present state-of-the-art methods in NEL, and propose a 2-step method for individual identification of named entities. Our approach is well-motivated by the limitations brought by recent deep learning approaches that lack interpratability, and require lots of parameter tuning along with large volume of annotated data. First of all, we propose a filtering algorithm designed with information retrieval and text mining techniques, aiming to maximize precision at K (typically for 5 <= K <=20). Then, we introduce two graph-based methods for named entity identification to maximize precision at 1 by re-ranking the remaining top entity candidates. The first identification method is using parametrized graph mining, and the second similarity with graph kernels. Our approach capitalizes on a fine-grained classification of entities from annotated web data. We present our algorithms in details, and show experimentally on standard datasets (NIST TAC-KBP, CONLL/AIDA) their performance in terms of precision are better than any graph-based method reported, and competitive with state-of-the-art systems. Finally, we conclude on the advantages of our graph-based approach compared to recent deep learning methods.
Large-scale graph-structured data arising from social networks, databases, knowledge bases, web graphs, etc. is now available for analysis and mining. Graph-mining often involves 'relationship queries', which seek a ranked list of interesting interconnections among a given set of entities, corresponding to nodes in the graph. While relationship queries have been studied for many years, using various terminologies, e.g., keyword-search, Steiner-tree in a graph etc., the solutions proposed in the literature so far have not focused on scaling relationship queries to large graphs having billions of nodes and edges, such are now publicly available in the form of 'linked-open-data'. In this paper, we present an algorithm for distributed keyword search (DKS) on large graphs, based on the graph-parallel computing paradigm Pregel. We also present an analytical proof that our algorithm produces an optimally ranked list of answers if run to completion. Even if terminated early, our algorithm produces approximate answers along with bounds. We describe an optimized implementation of our DKS algorithm along with time-complexity analysis. Finally, we report and analyze experiments using an implementation of DKS on Giraph the graph-parallel computing framework based on Pregel, and demonstrate that we can efficiently process relationship queries on large-scale subsets of linked-open-data.
Graph theory and graph mining constitute rich fields of computational techniques to study the structures, topologies and properties of graphs. These techniques constitute a good asset in bioinformatics if there exist efficient methods for transforming biological data into graphs. In this paper, we present Protein Graph Repository (PGR), a novel database of protein 3D-structures transformed into graphs allowing the use of the large repertoire of graph theory techniques in protein mining. This repository contains graph representations of all currently known protein 3D-structures described in the Protein Data Bank (PDB). PGR also provides an efficient online converter of protein 3D-structures into graphs, biological and graph-based description, pre-computed protein graph attributes and statistics, visualization of each protein graph, as well as graph-based protein similarity search tool. Such repository presents an enrichment of existing online databases that will help bridging the gap between graph mining and protein structure analysis. PGR data and features are unique and not included in any other protein database. The repository is available at http://wjdi.bioinfo.uqam.ca/.
Graph data is ubiquitous in academia and industry, from social networks to bioinformatics. The pervasiveness of graphs today has raised the demand for algorithms that can answer various questions: Which products would a user like to purchase given her order list? Which users are buying fake followers to increase their public reputation? Myriads of new graph mining algorithms are proposed every year to answer such questions - each with a distinct problem formulation, computational time, and memory footprint. This lack of unity makes it difficult for a practitioner to compare different algorithms and pick the most suitable one for a specific application. These challenges - even more severe for non-experts - create a gap in which state-of-the-art techniques developed in academic settings fail to be optimally deployed in real-world applications. To bridge this gap, we propose AUTOGM, an automated system for graph mining algorithm development. We first define a unified framework UNIFIEDGM that integrates various message-passing based graph algorithms, ranging from conventional algorithms like PageRank to graph neural networks. Then UNIFIEDGM defines a search space in which five parameters are required to determine a graph algorithm. Under this search space, AUTOGM explicitly optimizes for the optimal parameter set of UNIFIEDGM using Bayesian Optimization. AUTOGM defines a novel budget-aware objective function for the optimization to incorporate a practical issue - finding the best speed-accuracy trade-off under a computation budget - into the graph algorithm generation problem. Experiments on real-world benchmark datasets demonstrate that AUTOGM generates novel graph mining algorithms with the best speed/accuracy trade-off compared to existing models with heuristic parameters.
Many optimizers have been proposed for training deep neural networks, and they often have multiple hyperparameters, which make it tricky to benchmark their performance. In this work, we propose a new benchmarking protocol to evaluate both end-to-end efficiency (training a model from scratch without knowing the best hyperparameter) and data-addition training efficiency (the previously selected hyperparameters are used for periodically re-training the model with newly collected data). For end-to-end efficiency, unlike previous work that assumes random hyperparameter tuning, which over-emphasizes the tuning time, we propose to evaluate with a bandit hyperparameter tuning strategy. A human study is conducted to show that our evaluation protocol matches human tuning behavior better than the random search. For data-addition training, we propose a new protocol for assessing the hyperparameter sensitivity to data shift. We then apply the proposed benchmarking framework to 7 optimizers and various tasks, including computer vision, natural language processing, reinforcement learning, and graph mining. Our results show that there is no clear winner across all the tasks.
Wikipedia is the biggest encyclopedia ever created and the fifth most visited website in the world. Tens of millions of people surf it every day, seeking answers to various questions. Collective user activity on its pages leaves publicly available footprints of human behavior, making Wikipedia an excellent source for analysis of collective behavior. In this work, we propose a distributed graph-based event extraction model, inspired by the Hebbian learning theory. The model exploits collective effect of the dynamics to discover events. We focus on data-streams with underlying graph structure and perform several large-scale experiments on the Wikipedia visitor activity data. We show that the presented model is scalable regarding time-series length and graph density, providing a distributed implementation of the proposed algorithm. We extract dynamical patterns of collective activity and demonstrate that they correspond to meaningful clusters of associated events, reflected in the Wikipedia articles. We also illustrate evolutionary dynamics of the graphs over time to highlight changing nature of visitors' interests. Finally, we discuss clusters of events that model collective recall process and represent collective memories - common memories shared by a group of people.
Graph neural networks (GNNs) are emerging machine learning models on graphs. Permutation-equivariance and proximity-awareness are two important properties highly desirable for GNNs. Both properties are needed to tackle some challenging graph problems, such as finding communities and leaders. In this paper, we first analytically show that the existing GNNs, mostly based on the message-passing mechanism, cannot simultaneously preserve the two properties. Then, we propose Stochastic Message Passing (SMP) model, a general and simple GNN to maintain both proximity-awareness and permutation-equivariance. In order to preserve node proximities, we augment the existing GNNs with stochastic node representations. We theoretically prove that the mechanism can enable GNNs to preserve node proximities, and at the same time, maintain permutation-equivariance with certain parametrization. We report extensive experimental results on ten datasets and demonstrate the effectiveness and efficiency of SMP for various typical graph mining tasks, including graph reconstruction, node classification, and link prediction.
Graph Neural Networks (GNNs) have been widely applied to fraud detection problems in recent years, revealing the suspiciousness of nodes by aggregating their neighborhood information via different relations. However, few prior works have noticed the camouflage behavior of fraudsters, which could hamper the performance of GNN-based fraud detectors during the aggregation process. In this paper, we introduce two types of camouflages based on recent empirical studies, i.e., the feature camouflage and the relation camouflage. Existing GNNs have not addressed these two camouflages, which results in their poor performance in fraud detection problems. Alternatively, we propose a new model named CAmouflage-REsistant GNN (CARE-GNN), to enhance the GNN aggregation process with three unique modules against camouflages. Concretely, we first devise a label-aware similarity measure to find informative neighboring nodes. Then, we leverage reinforcement learning (RL) to find the optimal amounts of neighbors to be selected. Finally, the selected neighbors across different relations are aggregated together. Comprehensive experiments on two real-world fraud datasets demonstrate the effectiveness of the RL algorithm. The proposed CARE-GNN also outperforms state-of-the-art GNNs and GNN-based fraud detectors. We integrate all GNN-based fraud detectors as an opensource toolbox: https://github.com/safe-graph/DGFraud. The CARE-GNN code and datasets are available at https://github.com/YingtongDou/CARE-GNN.
Mining dense subgraphs is an important primitive across a spectrum of graph-mining tasks. In this work, we formally establish that two recurring characteristics of real-world graphs, namely heavy-tailed degree distributions and large clustering coefficients, imply the existence of substantially large vertex neighborhoods with high edge-density. This observation suggests a very simple approach for extracting large quasi-cliques: simply scan the vertex neighborhoods, compute the clustering coefficient of each vertex, and output the best such subgraph. The implementation of such a method requires counting the triangles in a graph, which is a well-studied problem in graph mining. When empirically tested across a number of real-world graphs, this approach reveals a surprise: vertex neighborhoods include maximal cliques of non-trivial sizes, and the density of the best neighborhood often compares favorably to subgraphs produced by dedicated algorithms for maximizing subgraph density. For graphs with small clustering coefficients, we demonstrate that small vertex neighborhoods can be refined using a local-search method to ``grow'' larger cliques and near-cliques. Our results indicate that contrary to worst-case theoretical results, mining cliques and quasi-cliques of non-trivial sizes from real-world graphs is often not a difficult problem, and provides motivation for further work geared towards a better explanation of these empirical successes.
Real time nature of social networks with bursty short messages and their respective large data scale spread among vast variety of topics are research interest of many researchers. These properties of social networks which are known as 5'Vs of big data has led to many unique and enlightenment algorithms and techniques applied to large social networking datasets and data streams. Many of these researches are based on detection and tracking of hot topics and trending social media events that help revealing many unanswered questions. These algorithms and in some cases software products mostly rely on the nature of the language itself. Although, other techniques such as unsupervised data mining methods are language independent but many requirements for a comprehensive solution are not met. Many research issues such as noisy sentences that adverse grammar and new online user invented words are challenging maintenance of a good social network topic detection and tracking methodology; The semantic relationship between words and in most cases, synonyms are also ignored by many of these researches. In this research, we use Transformers combined with an incremental community detection algorithm. Transformer in one hand, provides the semantic relation between words in different contexts. On the other hand, the proposed graph mining technique enhances the resulting topics with aid of simple structural rules. Named entity recognition from multimodal data, image and text, labels the named entities with entity type and the extracted topics are tuned using them. All operations of proposed system has been applied with big social data perspective under NoSQL technologies. In order to present a working and systematic solution, we combined MongoDB with Neo4j as two major database systems of our work. The proposed system shows higher precision and recall compared to other methods in three different datasets.
Node representation learning for directed graphs is critically important to facilitate many graph mining tasks. To capture the directed edges between nodes, existing methods mostly learn two embedding vectors for each node, source vector and target vector. However, these methods learn the source and target vectors separately. For the node with very low indegree or outdegree, the corresponding target vector or source vector cannot be effectively learned. In this paper, we propose a novel Directed Graph embedding framework based on Generative Adversarial Network, called DGGAN. The main idea is to use adversarial mechanisms to deploy a discriminator and two generators that jointly learn each node's source and target vectors. For a given node, the two generators are trained to generate its fake target and source neighbor nodes from the same underlying distribution, and the discriminator aims to distinguish whether a neighbor node is real or fake. The two generators are formulated into a unified framework and could mutually reinforce each other to learn more robust source and target vectors. Extensive experiments show that DGGAN consistently and significantly outperforms existing state-of-the-art methods across multiple graph mining tasks on directed graphs.
On top of a neural network-based dependency parser and a graph-based natural language processing module we design a Prolog-based dialog engine that explores interactively a ranked fact database extracted from a text document. We reorganize dependency graphs to focus on the most relevant content elements of a sentence and integrate sentence identifiers as graph nodes. Additionally, after ranking the graph we take advantage of the implicit semantic information that dependency links and WordNet bring in the form of subject-verb-object, is-a and part-of relations. Working on the Prolog facts and their inferred consequences, the dialog engine specializes the text graph with respect to a query and reveals interactively the document's most relevant content elements. The open-source code of the integrated system is available at https://github.com/ptarau/DeepRank . Under consideration in Theory and Practice of Logic Programming (TPLP).
Dense subgraph discovery aims to find a dense component in edge-weighted graphs. This is a fundamental graph-mining task with a variety of applications and thus has received much attention recently. Although most existing methods assume that each individual edge weight is easily obtained, such an assumption is not necessarily valid in practice. In this paper, we introduce a novel learning problem for dense subgraph discovery in which a learner queries edge subsets rather than only single edges and observes a noisy sum of edge weights in a queried subset. For this problem, we first propose a polynomial-time algorithm that obtains a nearly-optimal solution with high probability. Moreover, to deal with large-sized graphs, we design a more scalable algorithm with a theoretical guarantee. Computational experiments using real-world graphs demonstrate the effectiveness of our algorithms.
Graph embedding techniques, which learn low-dimensional representations of a graph, are achieving state-of-the-art performance in many graph mining tasks. Most existing embedding algorithms assign a single vector to each node, implicitly assuming that a single representation is enough to capture all characteristics of the node. However, across many domains, it is common to observe pervasively overlapping community structure, where most nodes belong to multiple communities, playing different roles depending on the contexts. Here, we propose persona2vec, a graph embedding framework that efficiently learns multiple representations of nodes based on their structural contexts. Using link prediction-based evaluation, we show that our framework is significantly faster than the existing state-of-the-art model while achieving better performance.
Network embedding is an influential graph mining technique for representing nodes in a graph as distributed vectors. However, the majority of network embedding methods focus on learning a single vector representation for each node, which has been recently criticized for not being capable of modeling multiple aspects of a node. To capture the multiple aspects of each node, existing studies mainly rely on offline graph clustering performed prior to the actual embedding, which results in the cluster membership of each node (i.e., node aspect distribution) fixed throughout training of the embedding model. We argue that this not only makes each node always have the same aspect distribution regardless of its dynamic context, but also hinders the end-to-end training of the model that eventually leads to the final embedding quality largely dependent on the clustering. In this paper, we propose a novel end-to-end framework for multi-aspect network embedding, called asp2vec, in which the aspects of each node are dynamically assigned based on its local context. More precisely, among multiple aspects, we dynamically assign a single aspect to each node based on its current context, and our aspect selection module is end-to-end differentiable via the Gumbel-Softmax trick. We also introduce the aspect regularization framework to capture the interactions among the multiple aspects in terms of relatedness and diversity. We further demonstrate that our proposed framework can be readily extended to heterogeneous networks. Extensive experiments towards various downstream tasks on various types of homogeneous networks and a heterogeneous network demonstrate the superiority of asp2vec.
Opinion dynamics - the research field dealing with how people's opinions form and evolve in a social context - traditionally uses agent-based models to validate the implications of sociological theories. These models encode the causal mechanism that drives the opinion formation process, and have the advantage of being easy to interpret. However, as they do not exploit the availability of data, their predictive power is limited. Moreover, parameter calibration and model selection are manual and difficult tasks. In this work we propose an inference mechanism for fitting a generative, agent-like model of opinion dynamics to real-world social traces. Given a set of observables (e.g., actions and interactions between agents), our model can recover the most-likely latent opinion trajectories that are compatible with the assumptions about the process dynamics. This type of model retains the benefits of agent-based ones (i.e., causal interpretation), while adding the ability to perform model selection and hypothesis testing on real data. We showcase our proposal by translating a classical agent-based model of opinion dynamics into its generative counterpart. We then design an inference algorithm based on online expectation maximization to learn the latent parameters of the model. Such algorithm can recover the latent opinion trajectories from traces generated by the classical agent-based model. In addition, it can identify the most likely set of macro parameters used to generate a data trace, thus allowing testing of sociological hypotheses. Finally, we apply our model to real-world data from Reddit to explore the long-standing question about the impact of backfire effect. Our results suggest a low prominence of the effect in Reddit's political conversation.
Neural networks are the pinnacle of Artificial Intelligence, as in recent years we witnessed many novel architectures, learning and optimization techniques for deep learning. Capitalizing on the fact that neural networks inherently constitute multipartite graphs among neuron layers, we aim to analyze directly their structure to extract meaningful information that can improve the learning process. To our knowledge graph mining techniques for enhancing learning in neural networks have not been thoroughly investigated. In this paper we propose an adapted version of the k-core structure for the complete weighted multipartite graph extracted from a deep learning architecture. As a multipartite graph is a combination of bipartite graphs, that are in turn the incidence graphs of hypergraphs, we design k-hypercore decomposition, the hypergraph analogue of k-core degeneracy. We applied k-hypercore to several neural network architectures, more specifically to convolutional neural networks and multilayer perceptrons for image recognition tasks after a very short pretraining. Then we used the information provided by the hypercore numbers of the neurons to re-initialize the weights of the neural network, thus biasing the gradient optimization scheme. Extensive experiments proved that k-hypercore outperforms the state-of-the-art initialization methods.
We present Karate Club a Python framework combining more than 30 state-of-the-art graph mining algorithms which can solve unsupervised machine learning tasks. The primary goal of the package is to make community detection, node and whole graph embedding available to a wide audience of machine learning researchers and practitioners. We designed Karate Club with an emphasis on a consistent application interface, scalability, ease of use, sensible out of the box model behaviour, standardized dataset ingestion, and output generation. This paper discusses the design principles behind this framework with practical examples. We show Karate Club's efficiency with respect to learning performance on a wide range of real world clustering problems, classification tasks and support evidence with regards to its competitive speed.