Data mining and knowledge discovery: a guided approach base on monotone boolean functions

This dissertation deals with an important problem in Data Mining and Knowledge Discovery (DM & KD), and Information Technology (IT) in general. It addresses the problem of efficiently learning monotone Boolean functions via membership queries to oracles. The monotone Boolean function can be thought of as a phenomenon, such as breast cancer or a computer crash, together with a set of predictor variables. The oracle can be thought of as an entity that knows the underlying monotone Boolean function, and provides a Boolean response to each query. In practice, it may take the shape of a human expert, or it may be the outcome of performing tasks such as running experiments or searching large databases. Monotone Boolean functions have a general knowledge representation power and are inherently frequent in applications. A key goal of this dissertation is to demonstrate the wide spectrum of important real-life applications that can be analyzed by using the new proposed computational approaches. The applications of breast cancer diagnosis, computer crashing, college acceptance policies, and record linkage in databases are here used to demonstrate this point and illustrate the algorithmic details. Monotone Boolean functions have the added benefit of being intuitive. This property is perhaps the most important in learning environments, especially when human interaction is involved, since people tend to make better use of knowledge they can easily interpret, understand, validate, and remember. The main goal of this dissertation is to design new algorithms that can minimize the average number of queries used to completely reconstruct monotone Boolean functions defined on a finite set of vectors V = {0,1}^n. The optimal query selections are found via a recursive algorithm in exponential time (in the size of V). The optimality conditions are then summarized in the simple form of evaluative criteria, which are near optimal and only take polynomial time to compute. Extensive unbiased empirical results show that the evaluative criterion approach is far superior to any of the existing methods. In fact, the reduction in average number of queries increases exponentially with the number of variables n, and faster than exponentially with the oracle\u27s error rate

Detecting controlling nodes of boolean regulatory networks

Boolean models of regulatory networks are assumed to be tolerant to perturbations. That qualitatively implies that each function can only depend on a few nodes. Biologically motivated constraints further show that functions found in Boolean regulatory networks belong to certain classes of functions, for example, the unate functions. It turns out that these classes have specific properties in the Fourier domain. That motivates us to study the problem of detecting controlling nodes in classes of Boolean networks using spectral techniques. We consider networks with unbalanced functions and functions of an average sensitivity less than 23k, where k is the number of controlling variables for a function. Further, we consider the class of 1-low networks which include unate networks, linear threshold networks, and networks with nested canalyzing functions. We show that the application of spectral learning algorithms leads to both better time and sample complexity for the detection of controlling nodes compared with algorithms based on exhaustive search. For a particular algorithm, we state analytical upper bounds on the number of samples needed to find the controlling nodes of the Boolean functions. Further, improved algorithms for detecting controlling nodes in large-scale unate networks are given and numerically studied

GPURepair: Automated Repair of GPU Kernels

This paper presents a tool for repairing errors in GPU kernels written in CUDA or OpenCL due to data races and barrier divergence. Our novel extension to prior work can also remove barriers that are deemed unnecessary for correctness. We implement these ideas in our tool called GPURepair, which uses GPUVerify as the verification oracle for GPU kernels. We also extend GPUVerify to support CUDA Cooperative Groups, allowing GPURepair to perform inter-block synchronization for CUDA kernels. To the best of our knowledge, GPURepair is the only tool that can propose a fix for intra-block data races and barrier divergence errors for both CUDA and OpenCL kernels and the only tool that fixes inter-block data races for CUDA kernels. We perform extensive experiments on about 750 kernels and provide a comparison with prior work. We demonstrate the superiority of GPURepair through its capability to fix more kernels and its unique ability to remove redundant barriers and handle inter-block data races.Comment: 19 pages, 1 algorithm, 3 figures, 22nd International Conference on Verification Model Checking and Abstract Interpretation (VMCAI 2021

Model Checking a Temporal Logic via Program Verification

openThe thesis explores the possibility of viewing Model Checking as an instance of program verification in order to allow for the reuse of the vast theory and toolset of Abstract Interpretation in the setting of Model Checking. Model Checking is a formal verification technique used to analyse the correctness of software systems, based on a representation of the system as a formal model, such as a finite-state machine or a transition system, and on a representation of the properties it must satisfy as temporal logic formulae. On the other hand, Abstract Interpretation is a program analysis method, based on the idea of extracting properties of programs by (over-)approximating their semantics over a so-called abstract domain, typically a complete lattice, whose elements represent program properties. The thesis focuses on ACTL, the universal fragment of the temporal logic CTL, which can describe properties of executions which are universally quantified. It shows how properties expressed in ACTL can be mapped into programs written in a suitable programming language, whose semantics consists of counterexamples to the validity of the formula. Then such a program is analysed by Abstract Interpretation over some abstract domain, exploiting the idea of local completeness as put forward in some recent work, combining lower- and under-approximations.The thesis explores the possibility of viewing Model Checking as an instance of program verification in order to allow for the reuse of the vast theory and toolset of Abstract Interpretation in the setting of Model Checking. Model Checking is a formal verification technique used to analyse the correctness of software systems, based on a representation of the system as a formal model, such as a finite-state machine or a transition system, and on a representation of the properties it must satisfy as temporal logic formulae. On the other hand, Abstract Interpretation is a program analysis method, based on the idea of extracting properties of programs by (over-)approximating their semantics over a so-called abstract domain, typically a complete lattice, whose elements represent program properties. The thesis focuses on ACTL, the universal fragment of the temporal logic CTL, which can describe properties of executions which are universally quantified. It shows how properties expressed in ACTL can be mapped into programs written in a suitable programming language, whose semantics consists of counterexamples to the validity of the formula. Then such a program is analysed by Abstract Interpretation over some abstract domain, exploiting the idea of local completeness as put forward in some recent work, combining lower- and under-approximations

Specifying Graph Languages with Type Graphs

We investigate three formalisms to specify graph languages, i.e. sets of graphs, based on type graphs. First, we are interested in (pure) type graphs, where the corresponding language consists of all graphs that can be mapped homomorphically to a given type graph. In this context, we also study languages specified by restriction graphs and their relation to type graphs. Second, we extend this basic approach to a type graph logic and, third, to type graphs with annotations. We present decidability results and closure properties for each of the formalisms.Comment: (v2): -Fixed some typos -Added more reference

Validity-Guided Synthesis of Reactive Systems from Assume-Guarantee Contracts

Automated synthesis of reactive systems from specifications has been a topic of research for decades. Recently, a variety of approaches have been proposed to extend synthesis of reactive systems from proposi- tional specifications towards specifications over rich theories. We propose a novel, completely automated approach to program synthesis which reduces the problem to deciding the validity of a set of forall-exists formulas. In spirit of IC3 / PDR, our problem space is recursively refined by blocking out regions of unsafe states, aiming to discover a fixpoint that describes safe reactions. If such a fixpoint is found, we construct a witness that is directly translated into an implementation. We implemented the algorithm on top of the JKind model checker, and exercised it against contracts written using the Lustre specification language. Experimental results show how the new algorithm outperforms JKinds already existing synthesis procedure based on k-induction and addresses soundness issues in the k-inductive approach with respect to unrealizable results.Comment: 18 pages, 5 figures, 2 table