arXiv subjects

Mohammed J. Zaki

Publications and source records attributed to Mohammed J. Zaki.

36 records · Page 2Linked to original sources

arXiv2022

Global Self-Attention as a Replacement for Graph Convolution

We propose an extension to the transformer neural network architecture for general-purpose graph learning by adding a dedicated pathway for pairwise structural information, called edge channels. The resultant framework - which we call Edge-augmented Graph Transformer (EGT) - can directly accept, process and output structural information of arbitrary form, which is important for effective learning on graph-structured data. Our model exclusively uses global self-attention as an aggregation mechanism rather than static localized convolutional aggregation. This allows for unconstrained long-range dynamic interactions between nodes. Moreover, the edge channels allow the structural information to evolve from layer to layer, and prediction tasks on edges/links can be performed directly from the output embeddings of these channels. We verify the performance of EGT in a wide range of graph-learning experiments on benchmark datasets, in which it outperforms Convolutional/Message-Passing Graph Neural Networks. EGT sets a new state-of-the-art for the quantum-chemical regression task on the OGB-LSC PCQM4Mv2 dataset containing 3.8 million molecular graphs. Our findings indicate that global self-attention based aggregation can serve as a flexible, adaptive and effective replacement of graph convolution for general-purpose graph learning. Therefore, convolutional local neighborhood aggregation is not an essential inductive bias.

cs.LG↗

arXiv2021

Keyphrase Extraction Using Neighborhood Knowledge Based on Word Embeddings

Keyphrase extraction is the task of finding several interesting phrases in a text document, which provide a list of the main topics within the document. Most existing graph-based models use co-occurrence links as cohesion indicators to model the relationship of syntactic elements. However, a word may have different forms of expression within the document, and may have several synonyms as well. Simply using co-occurrence information cannot capture this information. In this paper, we enhance the graph-based ranking model by leveraging word embeddings as background knowledge to add semantic information to the inter-word graph. Our approach is evaluated on established benchmark datasets and empirical results show that the word embedding neighborhood information improves the model performance.

cs.CL↗

arXiv2021

Can a Fruit Fly Learn Word Embeddings?

The mushroom body of the fruit fly brain is one of the best studied systems in neuroscience. At its core it consists of a population of Kenyon cells, which receive inputs from multiple sensory modalities. These cells are inhibited by the anterior paired lateral neuron, thus creating a sparse high dimensional representation of the inputs. In this work we study a mathematical formalization of this network motif and apply it to learning the correlational structure between words and their context in a corpus of unstructured text, a common natural language processing (NLP) task. We show that this network can learn semantic representations of words and can generate both static and context-dependent word embeddings. Unlike conventional methods (e.g., BERT, GloVe) that use dense representations for word embedding, our algorithm encodes semantic meaning of words and their context in the form of sparse binary hash codes. The quality of the learned representations is evaluated on word similarity analysis, word-sense disambiguation, and document classification. It is shown that not only can the fruit fly network motif achieve performance comparable to existing methods in NLP, but, additionally, it uses only a fraction of the computational resources (shorter training time and smaller memory footprint).

cs.CL↗

arXiv2021

A Framework for Generating Explanations from Temporal Personal Health Data

Whereas it has become easier for individuals to track their personal health data (e.g., heart rate, step count, food log), there is still a wide chasm between the collection of data and the generation of meaningful explanations to help users better understand what their data means to them. With an increased comprehension of their data, users will be able to act upon the newfound information and work towards striving closer to their health goals. We aim to bridge the gap between data collection and explanation generation by mining the data for interesting behavioral findings that may provide hints about a user's tendencies. Our focus is on improving the explainability of temporal personal health data via a set of informative summary templates, or "protoforms." These protoforms span both evaluation-based summaries that help users evaluate their health goals and pattern-based summaries that explain their implicit behaviors. In addition to individual users, the protoforms we use are also designed for population-level summaries. We apply our approach to generate summaries (both univariate and multivariate) from real user data and show that our system can generate interesting and useful explanations.

cs.CL↗

arXiv2021

Personalized Food Recommendation as Constrained Question Answering over a Large-scale Food Knowledge Graph

Food recommendation has become an important means to help guide users to adopt healthy dietary habits. Previous works on food recommendation either i) fail to consider users' explicit requirements, ii) ignore crucial health factors (e.g., allergies and nutrition needs), or iii) do not utilize the rich food knowledge for recommending healthy recipes. To address these limitations, we propose a novel problem formulation for food recommendation, modeling this task as constrained question answering over a large-scale food knowledge base/graph (KBQA). Besides the requirements from the user query, personalized requirements from the user's dietary preferences and health guidelines are handled in a unified way as additional constraints to the QA system. To validate this idea, we create a QA style dataset for personalized food recommendation based on a large-scale food knowledge graph and health guidelines. Furthermore, we propose a KBQA-based personalized food recommendation framework which is equipped with novel techniques for handling negations and numerical comparisons in the queries. Experimental results on the benchmark show that our approach significantly outperforms non-personalized counterparts (average 59.7% absolute improvement across various evaluation metrics), and is able to recommend more relevant and healthier recipes.

cs.CL↗

arXiv2020

Iterative Deep Graph Learning for Graph Neural Networks: Better and Robust Node Embeddings

In this paper, we propose an end-to-end graph learning framework, namely Iterative Deep Graph Learning (IDGL), for jointly and iteratively learning graph structure and graph embedding. The key rationale of IDGL is to learn a better graph structure based on better node embeddings, and vice versa (i.e., better node embeddings based on a better graph structure). Our iterative method dynamically stops when the learned graph structure approaches close enough to the graph optimized for the downstream prediction task. In addition, we cast the graph learning problem as a similarity metric learning problem and leverage adaptive graph regularization for controlling the quality of the learned graph. Finally, combining the anchor-based approximation technique, we further propose a scalable version of IDGL, namely IDGL-Anch, which significantly reduces the time and space complexity of IDGL without compromising the performance. Our extensive experiments on nine benchmarks show that our proposed IDGL models can consistently outperform or match the state-of-the-art baselines. Furthermore, IDGL can be more robust to adversarial graphs and cope with both transductive and inductive learning.

cs.LG↗

arXiv2020

Reinforcement Learning Based Graph-to-Sequence Model for Natural Question Generation

Natural question generation (QG) aims to generate questions from a passage and an answer. Previous works on QG either (i) ignore the rich structure information hidden in text, (ii) solely rely on cross-entropy loss that leads to issues like exposure bias and inconsistency between train/test measurement, or (iii) fail to fully exploit the answer information. To address these limitations, in this paper, we propose a reinforcement learning (RL) based graph-to-sequence (Graph2Seq) model for QG. Our model consists of a Graph2Seq generator with a novel Bidirectional Gated Graph Neural Network based encoder to embed the passage, and a hybrid evaluator with a mixed objective combining both cross-entropy and RL losses to ensure the generation of syntactically and semantically valid text. We also introduce an effective Deep Alignment Network for incorporating the answer information into the passage at both the word and contextual levels. Our model is end-to-end trainable and achieves new state-of-the-art scores, outperforming existing methods by a significant margin on the standard SQuAD benchmark.

cs.CL↗

arXiv2020

GraphFlow: Exploiting Conversation Flow with Graph Neural Networks for Conversational Machine Comprehension

Conversational machine comprehension (MC) has proven significantly more challenging compared to traditional MC since it requires better utilization of conversation history. However, most existing approaches do not effectively capture conversation history and thus have trouble handling questions involving coreference or ellipsis. Moreover, when reasoning over passage text, most of them simply treat it as a word sequence without exploring rich semantic relationships among words. In this paper, we first propose a simple yet effective graph structure learning technique to dynamically construct a question and conversation history aware context graph at each conversation turn. Then we propose a novel Recurrent Graph Neural Network, and based on that, we introduce a flow mechanism to model the temporal dependencies in a sequence of context graphs. The proposed GraphFlow model can effectively capture conversational flow in a dialog, and shows competitive performance compared to existing state-of-the-art methods on CoQA, QuAC and DoQA benchmarks. In addition, visualization experiments show that our proposed model can offer good interpretability for the reasoning process.

cs.CL↗

arXiv2020

MALOnt: An Ontology for Malware Threat Intelligence

Malware threat intelligence uncovers deep information about malware, threat actors, and their tactics, Indicators of Compromise(IoC), and vulnerabilities in different platforms from scattered threat sources. This collective information can guide decision making in cyber defense applications utilized by security operation centers(SoCs). In this paper, we introduce an open-source malware ontology - MALOnt that allows the structured extraction of information and knowledge graph generation, especially for threat intelligence. The knowledge graph that uses MALOnt is instantiated from a corpus comprising hundreds of annotated malware threat reports. The knowledge graph enables the analysis, detection, classification, and attribution of cyber threats caused by malware. We also demonstrate the annotation process using MALOnt on exemplar threat intelligence reports. A work in progress, this research is part of a larger effort towards auto-generation of knowledge graphs (KGs)for gathering malware threat intelligence from heterogeneous online resources.

cs.CR↗

arXiv2020

Personal Health Knowledge Graphs for Patients

Existing patient data analytics platforms fail to incorporate information that has context, is personal, and topical to patients. For a recommendation system to give a suitable response to a query or to derive meaningful insights from patient data, it should consider personal information about the patient's health history, including but not limited to their preferences, locations, and life choices that are currently applicable to them. In this review paper, we critique existing literature in this space and also discuss the various research challenges that come with designing, building, and operationalizing a personal health knowledge graph (PHKG) for patients.

cs.AI↗

arXiv2019

Deep Iterative and Adaptive Learning for Graph Neural Networks

In this paper, we propose an end-to-end graph learning framework, namely Deep Iterative and Adaptive Learning for Graph Neural Networks (DIAL-GNN), for jointly learning the graph structure and graph embeddings simultaneously. We first cast the graph structure learning problem as a similarity metric learning problem and leverage an adapted graph regularization for controlling smoothness, connectivity and sparsity of the generated graph. We further propose a novel iterative method for searching for a hidden graph structure that augments the initial graph structure. Our iterative method dynamically stops when the learned graph structure approaches close enough to the optimal graph. Our extensive experiments demonstrate that the proposed DIAL-GNN model can consistently outperform or match state-of-the-art baselines in terms of both downstream task performance and computational time. The proposed approach can cope with both transductive learning and inductive learning.

cs.LG↗

arXiv2019

Natural Question Generation with Reinforcement Learning Based Graph-to-Sequence Model

Natural question generation (QG) aims to generate questions from a passage and an answer. In this paper, we propose a novel reinforcement learning (RL) based graph-to-sequence (Graph2Seq) model for QG. Our model consists of a Graph2Seq generator where a novel Bidirectional Gated Graph Neural Network is proposed to embed the passage, and a hybrid evaluator with a mixed objective combining both cross-entropy and RL losses to ensure the generation of syntactically and semantically valid text. The proposed model outperforms previous state-of-the-art methods by a large margin on the SQuAD dataset.

cs.CL↗

arXiv2019

Bidirectional Attentive Memory Networks for Question Answering over Knowledge Bases

When answering natural language questions over knowledge bases (KBs), different question components and KB aspects play different roles. However, most existing embedding-based methods for knowledge base question answering (KBQA) ignore the subtle inter-relationships between the question and the KB (e.g., entity types, relation paths and context). In this work, we propose to directly model the two-way flow of interactions between the questions and the KB via a novel Bidirectional Attentive Memory Network, called BAMnet. Requiring no external resources and only very few hand-crafted features, on the WebQuestions benchmark, our method significantly outperforms existing information-retrieval based methods, and remains competitive with (hand-crafted) semantic parsing based methods. Also, since we use attention mechanisms, our method offers better interpretability compared to other baselines.

cs.CL↗

arXiv2017

KATE: K-Competitive Autoencoder for Text

Autoencoders have been successful in learning meaningful representations from image datasets. However, their performance on text datasets has not been widely studied. Traditional autoencoders tend to learn possibly trivial representations of text documents due to their confounding properties such as high-dimensionality, sparsity and power-law word distributions. In this paper, we propose a novel k-competitive autoencoder, called KATE, for text documents. Due to the competition between the neurons in the hidden layer, each neuron becomes specialized in recognizing specific data patterns, and overall the model can learn meaningful representations of textual data. A comprehensive set of experiments show that KATE can learn better representations than traditional autoencoders including denoising, contractive, variational, and k-sparse autoencoders. Our model also outperforms deep generative models, probabilistic topic models, and even word representation models (e.g., Word2Vec) in terms of several downstream tasks such as document classification, regression, and retrieval.

stat.ML↗

arXiv2015

Arabesque: A System for Distributed Graph Mining - Extended version

Distributed data processing platforms such as MapReduce and Pregel have substantially simplified the design and deployment of certain classes of distributed graph analytics algorithms. However, these platforms do not represent a good match for distributed graph mining problems, as for example finding frequent subgraphs in a graph. Given an input graph, these problems require exploring a very large number of subgraphs and finding patterns that match some "interestingness" criteria desired by the user. These algorithms are very important for areas such as social net- works, semantic web, and bioinformatics. In this paper, we present Arabesque, the first distributed data processing platform for implementing graph mining algorithms. Arabesque automates the process of exploring a very large number of subgraphs. It defines a high-level filter-process computational model that simplifies the development of scalable graph mining algorithms: Arabesque explores subgraphs and passes them to the application, which must simply compute outputs and decide whether the subgraph should be further extended. We use Arabesque's API to produce distributed solutions to three fundamental graph mining problems: frequent subgraph mining, counting motifs, and finding cliques. Our implementations require a handful of lines of code, scale to trillions of subgraphs, and represent in some cases the first available distributed solutions.

cs.DC↗

arXiv2013

DAGGER: A Scalable Index for Reachability Queries in Large Dynamic Graphs

With the ubiquity of large-scale graph data in a variety of application domains, querying them effectively is a challenge. In particular, reachability queries are becoming increasingly important, especially for containment, subsumption, and connectivity checks. Whereas many methods have been proposed for static graph reachability, many real-world graphs are constantly evolving, which calls for dynamic indexing. In this paper, we present a fully dynamic reachability index over dynamic graphs. Our method, called DAGGER, is a light-weight index based on interval labeling, that scales to million node graphs and beyond. Our extensive experimental evaluation on real-world and synthetic graphs confirms its effectiveness over baseline methods.

cs.DB↗

arXiv2012

BitPath -- Label Order Constrained Reachability Queries over Large Graphs

In this paper we focus on the following constrained reachability problem over edge-labeled graphs like RDF -- "given source node x, destination node y, and a sequence of edge labels (a, b, c, d), is there a path between the two nodes such that the edge labels on the path satisfy a regular expression "*a.*b.*c.*d.*". A "*" before "a" allows any other edge label to appear on the path before edge "a". "a.*" forces at least one edge with label "a". ".*" after "a" allows zero or more edge labels after "a" and before "b". Our query processing algorithm uses simple divide-and-conquer and greedy pruning procedures to limit the search space. However, our graph indexing technique -- based on "compressed bit-vectors" -- allows indexing large graphs which otherwise would have been infeasible. We have evaluated our approach on graphs with more than 22 million edges and 6 million nodes -- much larger compared to the datasets used in the contemporary work on path queries.

cs.DB↗

arXiv2012

Mining Attribute-structure Correlated Patterns in Large Attributed Graphs

In this work, we study the correlation between attribute sets and the occurrence of dense subgraphs in large attributed graphs, a task we call structural correlation pattern mining. A structural correlation pattern is a dense subgraph induced by a particular attribute set. Existing methods are not able to extract relevant knowledge regarding how vertex attributes interact with dense subgraphs. Structural correlation pattern mining combines aspects of frequent itemset and quasi-clique mining problems. We propose statistical significance measures that compare the structural correlation of attribute sets against their expected values using null models. Moreover, we evaluate the interestingness of structural correlation patterns in terms of size and density. An efficient algorithm that combines search and pruning strategies in the identification of the most relevant structural correlation patterns is presented. We apply our method for the analysis of three real-world attributed graphs: a collaboration, a music, and a citation network, verifying that it provides valuable knowledge in a feasible time.

cs.DB↗