Directed Acyclic Graphs

This code is copyright (2015) by the University of Hertfordshire and is made available to third parties for research or private study, criticism or review, and for the purpose of reporting the state of the art, under the normal fair use/fair dealing exceptions in Sections 29 and 30 of the Copyright, Designs and Patents Act 1988. Use of the code under this provision is limited to non-commercial use: please contact us if you wish to arrange a licence covering commercial use of the code.This source code implements a unified framework for pre-processing Directed Acyclic Graphs (DAGs) to lookup reachability between two vertices as well as compute the least upper bound of two vertices in constant time. Our framework builds on the adaptive pre-processing algorithm for constant time reachability lookups and extends this to compute the least upper bound of a vertex-pair in constant time. The theoretical details of this work can be found in the research paper which is available at http://uhra.herts.ac.uk/handle/2299/1215

All-Pairs LCA in DAGs: Breaking through the O(n2.5)O(n^{2.5}) barrier

Let $G=(V,E)$ be an $n$-vertex directed acyclic graph (DAG). A lowest common ancestor (LCA) of two vertices $u$ and $v$ is a common ancestor $w$ of $u$ and $v$ such that no descendant of $w$ has the same property. In this paper, we consider the problem of computing an LCA, if any, for all pairs of vertices in a DAG. The fastest known algorithms for this problem exploit fast matrix multiplication subroutines and have running times ranging from $O(n^{2.687})$ [Bender et al.~SODA'01] down to $O(n^{2.615})$ [Kowaluk and Lingas~ICALP'05] and $O(n^{2.569})$ [Czumaj et al.~TCS'07]. Somewhat surprisingly, all those bounds would still be $\Omega(n^{2.5})$ even if matrix multiplication could be solved optimally (i.e., $\omega=2$). This appears to be an inherent barrier for all the currently known approaches, which raises the natural question on whether one could break through the $O(n^{2.5})$ barrier for this problem. In this paper, we answer this question affirmatively: in particular, we present an $\tilde O(n^{2.447})$ ($\tilde O(n^{7/3})$ for $\omega=2$) algorithm for finding an LCA for all pairs of vertices in a DAG, which represents the first improvement on the running times for this problem in the last 13 years. A key tool in our approach is a fast algorithm to partition the vertex set of the transitive closure of $G$ into a collection of $O(\ell)$ chains and $O(n/\ell)$ antichains, for a given parameter $\ell$. As usual, a chain is a path while an antichain is an independent set. We then find, for all pairs of vertices, a \emph{candidate} LCA among the chain and antichain vertices, separately. The first set is obtained via a reduction to min-max matrix multiplication. The computation of the second set can be reduced to Boolean matrix multiplication similarly to previous results on this problem. We finally combine the two solutions together in a careful (non-obvious) manner

Adaptive Constraint Solving for Information Flow Analysis

In program analysis, unknown properties for terms are typically represented symbolically as variables. Bound constraints on these variables can then specify multiple optimisation goals for computer programs and nd application in areas such as type theory, security, alias analysis and resource reasoning. Resolution of bound constraints is a problem steeped in graph theory; interdependencies between the variables is represented as a constraint graph. Additionally, constants are introduced into the system as concrete bounds over these variables and constants themselves are ordered over a lattice which is, once again, represented as a graph. Despite graph algorithms being central to bound constraint solving, most approaches to program optimisation that use bound constraint solving have treated their graph theoretic foundations as a black box. Little has been done to investigate the computational costs or design e cient graph algorithms for constraint resolution. Emerging examples of these lattices and bound constraint graphs, particularly from the domain of language-based security, are showing that these graphs and lattices are structurally diverse and could be arbitrarily large. Therefore, there is a pressing need to investigate the graph theoretic foundations of bound constraint solving. In this thesis, we investigate the computational costs of bound constraint solving from a graph theoretic perspective for Information Flow Analysis (IFA); IFA is a sub- eld of language-based security which veri es whether con dentiality and integrity of classified information is preserved as it is manipulated by a program. We present a novel framework based on graph decomposition for solving the (atomic) bound constraint problem for IFA. Our approach enables us to abstract away from connections between individual vertices to those between sets of vertices in both the constraint graph and an accompanying security lattice which defines ordering over constants. Thereby, we are able to achieve significant speedups compared to state-of-the-art graph algorithms applied to bound constraint solving. More importantly, our algorithms are highly adaptive in nature and seamlessly adapt to the structure of the constraint graph and the lattice. The computational costs of our approach is a function of the latent scope of decomposition in the constraint graph and the lattice; therefore, we enjoy the fastest runtime for every point in the structure-spectrum of these graphs and lattices. While the techniques in this dissertation are developed with IFA in mind, they can be extended to other application of the bound constraints problem, such as type inference and program analysis frameworks which use annotated type systems, where constants are ordered over a lattice

Graph Deep Learning: Methods and Applications

The past few years have seen the growing prevalence of deep neural networks on various application domains including image processing, computer vision, speech recognition, machine translation, self-driving cars, game playing, social networks, bioinformatics, and healthcare etc. Due to the broad applications and strong performance, deep learning, a subfield of machine learning and artificial intelligence, is changing everyone\u27s life.Graph learning has been another hot field among the machine learning and data mining communities, which learns knowledge from graph-structured data. Examples of graph learning range from social network analysis such as community detection and link prediction, to relational machine learning such as knowledge graph completion and recommender systems, to mutli-graph tasks such as graph classification and graph generation etc.An emerging new field, graph deep learning, aims at applying deep learning to graphs. To deal with graph-structured data, graph neural networks (GNNs) are invented in recent years which directly take graphs as input and output graph/node representations. Although GNNs have shown superior performance than traditional methods in tasks such as semi-supervised node classification, there still exist a wide range of other important graph learning problems where either GNNs\u27 applicabilities have not been explored or GNNs only have less satisfying performance.In this dissertation, we dive deeper into the field of graph deep learning. By developing new algorithms, architectures and theories, we push graph neural networks\u27 boundaries to a much wider range of graph learning problems. The problems we have explored include: 1) graph classification; 2) medical ontology embedding; 3) link prediction; 4) recommender systems; 5) graph generation; and 6) graph structure optimization.We first focus on two graph representation learning problems: graph classification and medical ontology embedding.For graph classification, we develop a novel deep GNN architecture which aggregates node features through a novel SortPooling layer that replaces the simple summing used in previous works. We demonstrate its state-of-the-art graph classification performance on benchmark datasets. For medical ontology embedding, we propose a novel hierarchical attention propagation model, which uses attention mechanism to learn embeddings of medical concepts from hierarchically-structured medical ontologies such as ICD-9 and CCS. We validate the learned embeddings on sequential procedure/diagnosis prediction tasks with real patient data.Then we investigate GNNs\u27 potential for predicting relations, specifically link prediction and recommender systems. For link prediction, we first develop a theory unifying various traditional link prediction heuristics, and then design a framework to automatically learn suitable heuristics from a given network based on GNNs. Our model shows unprecedented strong link prediction performance, significantly outperforming all traditional methods. For recommender systems, we propose a novel graph-based matrix completion model, which uses a GNN to learn graph structure features from the bipartite graph formed by user and item interactions. Our model not only outperforms various matrix completion baselines, but also demonstrates excellent transfer learning ability -- a model trained on MovieLens can be directly used to predict Douban movie ratings with high performance.Finally, we explore GNNs\u27 applicability to graph generation and graph structure optimization. We focus on a specific type of graphs which usually carry computations on them, namely directed acyclic graphs (DAGs). We develop a variational autoencoder (VAE) for DAGs and prove that it can injectively map computations into a latent space. This injectivity allows us to perform optimization in the continuous latent space instead of the original discrete structure space. We then apply our VAE to two types of DAGs, neural network architectures and Bayesian networks. Experiments show that our model not only generates novel and valid DAGs, but also finds high-quality neural architectures and Bayesian networks through performing Bayesian optimization in its latent space

Unique lowest common ancestors in dags are almost as easy as matrix multiplication

We consider the problem of determining for each pair of vertices of a directed acyclic graph (dag) on n vertices whether or not it has a unique lowest common ancestor, and if so, finding such an ancestor. We show that this problem can be solved in time O(n ω logn), where ω< 2.376 is the exponent of the fastest known algorithm for multiplication of two n×n matrices. We show also that the problem of determining a lowest common ancestor for each pair of vertices of an arbitrary dag on n vertices is solvable in time $widetilde{O}(n^2p+n^{omega})$ , where p is the minimum number of directed paths covering the vertices of the dag. With the help of random bits, we can solve the latter problem in time $widetilde{O}(n^2p)$

EEMCS final report for the causal modeling for air transport safety (CATS) project

This document reports on the work realized by the DIAM in relation to the completion of the CATS model as presented in Figure 1.6 and tries to explain some of the steps taken for its completion. The project spans over a period of time of three years. Intermediate reports have been presented throughout the project’s progress. These are presented in Appendix 1. In this report the continuous‐discrete distribution‐free BBNs are briefly discussed. The human reliability models developed for dealing with dependence in the model variables are described and the software application UniNet is presente

Provably and Practically Efficient Race Detection for Task-Parallel Code

Parallel systems are pervasive nowadays. Specifically, modern computers have embraced multicore architectures due to the difficulties of exploiting higher clock speeds on single-core CPUs. However, parallel programming is challenging. Determinacy race, in particular, is a common pitfall when writing task-parallel code. It can easily lead to non-deterministic behavior of the parallel program and therefore a determinacy race is often considered as a bug. Unfortunately, such bugs are hard to debug because they do not necessarily produce obvious failures in every single execution. To ease the debugging process of determinacy races in task-parallel code, this dissertation proposes several provably and practically efficient parallel race detection algorithms. Unlike prior works mostly target fork-join parallelism, we focus on less structured but important programming paradigms – pipeline parallelism and futures. In addition, we build an efficient runtime system for scheduling futures, which is not only a facility to study the race detection problem for futures but also useful in practice. Finally, this dissertation investigates mechanisms that optimize the access history of race detectors, which provides significant additional boost to the performance

Advanced Modelling Strategies: Challenges and pitfalls in robust causal inference with observational data

Advanced Modelling Strategies: Challenges and pitfalls in robust causal inference with observational data summarises the lecture notes prepared for a four-day workshop sponsored by the Society for Social Medicine and hosted by the Leeds Institute for Data Analytics (LIDA) at the University of Leeds on 17th-20th July 2017

Scheduling techniques to improve the worst-case execution time of real-time parallel applications on heterogeneous platforms

The key to providing high performance and energy-efficient execution for hard real-time applications is the time predictable and efficient usage of heterogeneous multiprocessors. However, schedulability analysis of parallel applications executed on unrelated heterogeneous multiprocessors is challenging and has not been investigated adequately by earlier works. The unrelated model is suitable to represent many of the multiprocessor platforms available today because a task (i.e., sequential code) may exhibit a different work-case-execution-time (WCET) on each type of processor on an unrelated heterogeneous multiprocessors platform. A parallel application can be realistically modeled as a directed acyclic graph (DAG), where the nodes are sequential tasks and the edges are dependencies among the tasks. This thesis considers a sporadic DAG model which is used broadly to analyze and verify the real-time requirements of parallel applications. A global work-conserving scheduler can efficiently utilize an unrelated platform by executing the tasks of a DAG on different processor types. However, it is challenging to compute an upper bound on the worst-case schedule length of the DAG, called makespan, which is used to verify whether the deadline of a DAG is met or not. There are two main challenges. First, because of the heterogeneity of the processors, the WCET for each task of the DAG depends on which processor the task is executing on during actual runtime. Second, timing anomalies are the main obstacle to compute the makespan even for the simpler case when all the processors are of the same type, i.e., homogeneous multiprocessors. To that end, this thesis addresses the following problem: How we can schedule multiple sporadic DAGs on unrelated multiprocessors such that all the DAGs meet their deadlines. Initially, the thesis focuses on homogeneous multiprocessors that is a special case of unrelated multiprocessors to understand and tackle the main challenge of timing anomalies. A novel timing-anomaly-free scheduler is proposed which can be used to compute the makespan of a DAG just by simulating the execution of the tasks based on this proposed scheduler. A set of representative task-based parallel OpenMP applications from the BOTS benchmark suite are modeled as DAGs to investigate the timing behavior of real-world applications. A simulation framework is developed to evaluate the proposed method. Furthermore, the thesis targets unrelated multiprocessors and proposes a global scheduler to execute the tasks of a single DAG to an unrelated multiprocessors platform. Based on the proposed scheduler, methods to compute the makespan of a single DAG are introduced. A set of representative parallel applications from the BOTS benchmark suite are modeled as DAGs that execute on unrelated multiprocessors. Furthermore, synthetic DAGs are generated to examine additional structures of parallel applications and various platform capabilities. A simulation framework that simulates the execution of the tasks of a DAG on an unrelated multiprocessor platform is introduced to assess the effectiveness of the proposed makespan computations. Finally, based on the makespan computation of a single DAG this thesis presents the design and schedulability analysis of global and federated scheduling of sporadic DAGs that execute on unrelated multiprocessors