Causal Discovery for Relational Domains: Representation, Reasoning, and Learning

Many domains are currently experiencing the growing trend to record and analyze massive, observational data sets with increasing complexity. A commonly made claim is that these data sets hold potential to transform their corresponding domains by providing previously unknown or unexpected explanations and enabling informed decision-making. However, only knowledge of the underlying causal generative process, as opposed to knowledge of associational patterns, can support such tasks. Most methods for traditional causal discovery—the development of algorithms that learn causal structure from observational data—are restricted to representations that require limiting assumptions on the form of the data. Causal discovery has almost exclusively been applied to directed graphical models of propositional data that assume a single type of entity with independence among instances. However, most real-world domains are characterized by systems that involve complex interactions among multiple types of entities. Many state-of-the-art methods in statistics and machine learning that address such complex systems focus on learning associational models, and they are oftentimes mistakenly interpreted as causal. The intersection between causal discovery and machine learning in complex systems is small. The primary objective of this thesis is to extend causal discovery to such complex systems. Specifically, I formalize a relational representation and model that can express the causal and probabilistic dependencies among the attributes of interacting, heterogeneous entities. I show that the traditional method for reasoning about statistical independence from model structure fails to accurately derive conditional independence facts from relational models. I introduce a new theory—relational d-separation—and a novel, lifted representation—the abstract ground graph—that supports a sound, complete, and computationally efficient method for algorithmically deriving conditional independencies from probabilistic models of relational data. The abstract ground graph representation also presents causal implications that enable the detection of causal direction for bivariate relational dependencies without parametric assumptions. I leverage these implications and the theoretical framework of relational d-separation to develop a sound and complete algorithm—the relational causal discovery (RCD) algorithm—that learns causal structure from relational data

Co-regularised support vector regression

We consider a semi-supervised learning scenario for regression, where only few labelled examples, many unlabelled instances and different data representations (multiple views) are available. For this setting, we extend support vector regression with a co-regularisation term and obtain co-regularised support vector regression (CoSVR). In addition to labelled data, co-regularisation includes information from unlabelled examples by ensuring that models trained on different views make similar predictions. Ligand affinity prediction is an important real-world problem that fits into this scenario. The characterisation of the strength of protein-ligand bonds is a crucial step in the process of drug discovery and design. We introduce variants of the base CoSVR algorithm and discuss their theoretical and computational properties. For the CoSVR function class we provide a theoretical bound on the Rademacher complexity. Finally, we demonstrate the usefulness of CoSVR for the affinity prediction task and evaluate its performance empirically on different protein-ligand datasets. We show that CoSVR outperforms co-regularised least squares regression as well as existing state-of-the-art approaches for affinity prediction

Toward Data-Driven Discovery of Software Vulnerabilities

Over the years, Software Engineering, as a discipline, has recognized the potential for engineers to make mistakes and has incorporated processes to prevent such mistakes from becoming exploitable vulnerabilities. These processes span the spectrum from using unit/integration/fuzz testing, static/dynamic/hybrid analysis, and (automatic) patching to discover instances of vulnerabilities to leveraging data mining and machine learning to collect metrics that characterize attributes indicative of vulnerabilities. Among these processes, metrics have the potential to uncover systemic problems in the product, process, or people that could lead to vulnerabilities being introduced, rather than identifying specific instances of vulnerabilities. The insights from metrics can be used to support developers and managers in making decisions to improve the product, process, and/or people with the goal of engineering secure software. Despite empirical evidence of metrics\u27 association with historical software vulnerabilities, their adoption in the software development industry has been limited. The level of granularity at which the metrics are defined, the high false positive rate from models that use the metrics as explanatory variables, and, more importantly, the difficulty in deriving actionable intelligence from the metrics are often cited as factors that inhibit metrics\u27 adoption in practice. Our research vision is to assist software engineers in building secure software by providing a technique that generates scientific, interpretable, and actionable feedback on security as the software evolves. In this dissertation, we present our approach toward achieving this vision through (1) systematization of vulnerability discovery metrics literature, (2) unsupervised generation of metrics-informed security feedback, and (3) continuous developer-in-the-loop improvement of the feedback. We systematically reviewed the literature to enumerate metrics that have been proposed and/or evaluated to be indicative of vulnerabilities in software and to identify the validation criteria used to assess the decision-informing ability of these metrics. In addition to enumerating the metrics, we implemented a subset of these metrics as containerized microservices. We collected the metric values from six large open-source projects and assessed metrics\u27 generalizability across projects, application domains, and programming languages. We then used an unsupervised approach from literature to compute threshold values for each metric and assessed the thresholds\u27 ability to classify risk from historical vulnerabilities. We used the metrics\u27 values, thresholds, and interpretation to provide developers natural language feedback on security as they contributed changes and used a survey to assess their perception of the feedback. We initiated an open dialogue to gain an insight into their expectations from such feedback. In response to developer comments, we assessed the effectiveness of an existing vulnerability discovery approach—static analysis—and that of vulnerability discovery metrics in identifying risk from vulnerability contributing commits

Artifact Lifecycle Discovery

Artifact-centric modeling is a promising approach for modeling business processes based on the so-called business artifacts - key entities driving the company's operations and whose lifecycles define the overall business process. While artifact-centric modeling shows significant advantages, the overwhelming majority of existing process mining methods cannot be applied (directly) as they are tailored to discover monolithic process models. This paper addresses the problem by proposing a chain of methods that can be applied to discover artifact lifecycle models in Guard-Stage-Milestone notation. We decompose the problem in such a way that a wide range of existing (non-artifact-centric) process discovery and analysis methods can be reused in a flexible manner. The methods presented in this paper are implemented as software plug-ins for ProM, a generic open-source framework and architecture for implementing process mining tools

Ensembles of Randomized Time Series Shapelets Provide Improved Accuracy while Reducing Computational Costs

Shapelets are discriminative time series subsequences that allow generation of interpretable classification models, which provide faster and generally better classification than the nearest neighbor approach. However, the shapelet discovery process requires the evaluation of all possible subsequences of all time series in the training set, making it extremely computation intensive. Consequently, shapelet discovery for large time series datasets quickly becomes intractable. A number of improvements have been proposed to reduce the training time. These techniques use approximation or discretization and often lead to reduced classification accuracy compared to the exact method. We are proposing the use of ensembles of shapelet-based classifiers obtained using random sampling of the shapelet candidates. Using random sampling reduces the number of evaluated candidates and consequently the required computational cost, while the classification accuracy of the resulting models is also not significantly different than that of the exact algorithm. The combination of randomized classifiers rectifies the inaccuracies of individual models because of the diversity of the solutions. Based on the experiments performed, it is shown that the proposed approach of using an ensemble of inexpensive classifiers provides better classification accuracy compared to the exact method at a significantly lesser computational cost

Cache Hierarchy Inspired Compression: a Novel Architecture for Data Streams

We present an architecture for data streams based on structures typically found in web cache hierarchies. The main idea is to build a meta level analyser from a number of levels constructed over time from a data stream. We present the general architecture for such a system and an application to classification. This architecture is an instance of the general wrapper idea allowing us to reuse standard batch learning algorithms in an inherently incremental learning environment. By artificially generating data sources we demonstrate that a hierarchy containing a mixture of models is able to adapt over time to the source of the data. In these experiments the hierarchies use an elementary performance based replacement policy and unweighted voting for making classification decisions

Higher-Order Process Modeling: Product-Lining, Variability Modeling and Beyond

We present a graphical and dynamic framework for binding and execution of business) process models. It is tailored to integrate 1) ad hoc processes modeled graphically, 2) third party services discovered in the (Inter)net, and 3) (dynamically) synthesized process chains that solve situation-specific tasks, with the synthesis taking place not only at design time, but also at runtime. Key to our approach is the introduction of type-safe stacked second-order execution contexts that allow for higher-order process modeling. Tamed by our underlying strict service-oriented notion of abstraction, this approach is tailored also to be used by application experts with little technical knowledge: users can select, modify, construct and then pass (component) processes during process execution as if they were data. We illustrate the impact and essence of our framework along a concrete, realistic (business) process modeling scenario: the development of Springer's browser-based Online Conference Service (OCS). The most advanced feature of our new framework allows one to combine online synthesis with the integration of the synthesized process into the running application. This ability leads to a particularly flexible way of implementing self-adaption, and to a particularly concise and powerful way of achieving variability not only at design time, but also at runtime.Comment: In Proceedings Festschrift for Dave Schmidt, arXiv:1309.455

An Overview of the Use of Neural Networks for Data Mining Tasks

In the recent years the area of data mining has experienced a considerable demand for technologies that extract knowledge from large and complex data sources. There is a substantial commercial interest as well as research investigations in the area that aim to develop new and improved approaches for extracting information, relationships, and patterns from datasets. Artificial Neural Networks (NN) are popular biologically inspired intelligent methodologies, whose classification, prediction and pattern recognition capabilities have been utilised successfully in many areas, including science, engineering, medicine, business, banking, telecommunication, and many other fields. This paper highlights from a data mining perspective the implementation of NN, using supervised and unsupervised learning, for pattern recognition, classification, prediction and cluster analysis, and focuses the discussion on their usage in bioinformatics and financial data analysis tasks