We propose an approach for explaining Bayesian network classifiers, which is based on compiling such classifiers into decision functions that have a tractable and symbolic form. We introduce two types of explanations for why a classifier may have classified an instance positively or negatively and suggest algorithms for computing these explanations. The first type of explanation identifies a minimal set of the currently active features that is responsible for the current classification, while the second type of explanation identifies a minimal set of features whose current state (active or not) is sufficient for the classification. We consider in particular the compilation of Naive and Latent-Tree Bayesian network classifiers into Ordered Decision Diagrams (ODDs), providing a context for evaluating our proposal using case studies and experiments based on classifiers from the literature.
Motivation: Haplotype inference is an important step for many types of analyses of genetic variation in the human genome. Traditional approaches for obtaining haplotypes involve collecting genotype information from a population of individuals and then applying a haplotype inference algorithm. The development of high-throughput sequencing technologies allows for an alternative strategy to obtain haplotypes by combining sequence fragments. The problem of ‘haplotype assembly’ is the problem of assembling the two haplotypes for a chromosome given the collection of such fragments, or reads, and their locations in the haplotypes, which are pre-determined by mapping the reads to a reference genome. Errors in reads significantly increase the difficulty of the problem and it has been shown that the problem is NP-hard even for reads of length 2. Existing greedy and stochastic algorithms are not guaranteed to find the optimal solutions for the haplotype assembly problem.Results: In this article, we proposed a dynamic programming algorithm that is able to assemble the haplotypes optimally with time complexity O(m × 2k × n), where m is the number of reads, k is the length of the longest read and n is the total number of SNPs in the haplotypes. We also reduce the haplotype assembly problem into the maximum satisfiability problem that can often be solved optimally even when k is large. Taking advantage of the efficiency of our algorithm, we perform simulation experiments demonstrating that the assembly of haplotypes using reads of length typical of the current sequencing technologies is not practical. However, we demonstrate that the combination of this approach and the traditional haplotype phasing approaches allow us to practically construct haplotypes containing both common and rare variants.Contact: danhe@cs.ucla.edu
We propose an algorithm for compiling Bayesian network classifiers into decision graphs that mimic the input and output behavior of the classifiers. In particular, we compile Bayesian network classifiers into ordered decision graphs, which are tractable and can be exponentially smaller in size than decision trees. This tractability facilitates reasoning about the behavior of Bayesian network classifiers, including the explanation of decisions they make. Our compilation algorithm comes with guarantees on the time of compilation and the size of compiled decision graphs. We apply our compilation algorithm to classifiers from the literature and discuss some case studies in which we show how to automatically explain their decisions and verify properties of their behavior.
We consider the compilation of a binary neural network’s decision function into tractable representations such as Ordered Binary Decision Diagrams (OBDDs) and Sentential Decision Diagrams (SDDs). Obtaining this function as an OBDD/SDD facilitates the explanation and formal verification of a neural network’s behavior. First, we consider the task of verifying the robustness of a neural network, and show how we can compute the expected robustness of a neural network, given an OBDD/SDD representation of it. Next, we consider a more efficient approach for compiling neural networks, based on a pseudo-polynomial time algorithm for compiling a neuron. We then provide a case study in a handwritten digits dataset, highlighting how two neural networks trained from the same dataset can have very high accuracies, yet have very different levels of robustness. Finally, in experiments, we show that it is feasible to obtain compact representations of neural networks as SDDs.
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