Efficient sampling for Bayesian inference of conjunctive Bayesian networks

Motivation: Cancer development is driven by the accumulation of advantageous mutations and subsequent clonal expansion of cells harbouring these mutations, but the order in which mutations occur remains poorly understood. Advances in genome sequencing and the soon-arriving flood of cancer genome data produced by large cancer sequencing consortia hold the promise to elucidate cancer progression. However, new computational methods are needed to analyse these large datasets. Results: We present a Bayesian inference scheme for Conjunctive Bayesian Networks, a probabilistic graphical model in which mutations accumulate according to partial order constraints and cancer genotypes are observed subject to measurement noise. We develop an efficient MCMC sampling scheme specifically designed to overcome local optima induced by dependency structures. We demonstrate the performance advantage of our sampler over traditional approaches on simulated data and show the advantages of adopting a Bayesian perspective when reanalyzing cancer datasets and comparing our results to previous maximum-likelihood-based approaches. Availability: An R package including the sampler and examples is available at http://www.cbg.ethz.ch/software/bayes-cbn. Contacts: [email protected]

Efficient computational strategies to learn the structure of probabilistic graphical models of cumulative phenomena

Structural learning of Bayesian Networks (BNs) is a NP-hard problem, which is further complicated by many theoretical issues, such as the I-equivalence among different structures. In this work, we focus on a specific subclass of BNs, named Suppes-Bayes Causal Networks (SBCNs), which include specific structural constraints based on Suppes' probabilistic causation to efficiently model cumulative phenomena. Here we compare the performance, via extensive simulations, of various state-of-the-art search strategies, such as local search techniques and Genetic Algorithms, as well as of distinct regularization methods. The assessment is performed on a large number of simulated datasets from topologies with distinct levels of complexity, various sample size and different rates of errors in the data. Among the main results, we show that the introduction of Suppes' constraints dramatically improve the inference accuracy, by reducing the solution space and providing a temporal ordering on the variables. We also report on trade-offs among different search techniques that can be efficiently employed in distinct experimental settings. This manuscript is an extended version of the paper "Structural Learning of Probabilistic Graphical Models of Cumulative Phenomena" presented at the 2018 International Conference on Computational Science

The Libra Toolkit for Probabilistic Models

The Libra Toolkit is a collection of algorithms for learning and inference with discrete probabilistic models, including Bayesian networks, Markov networks, dependency networks, and sum-product networks. Compared to other toolkits, Libra places a greater emphasis on learning the structure of tractable models in which exact inference is efficient. It also includes a variety of algorithms for learning graphical models in which inference is potentially intractable, and for performing exact and approximate inference. Libra is released under a 2-clause BSD license to encourage broad use in academia and industry

Logical Abstractions for Noisy Variational Quantum Algorithm Simulation

Due to the unreliability and limited capacity of existing quantum computer prototypes, quantum circuit simulation continues to be a vital tool for validating next generation quantum computers and for studying variational quantum algorithms, which are among the leading candidates for useful quantum computation. Existing quantum circuit simulators do not address the common traits of variational algorithms, namely: 1) their ability to work with noisy qubits and operations, 2) their repeated execution of the same circuits but with different parameters, and 3) the fact that they sample from circuit final wavefunctions to drive a classical optimization routine. We present a quantum circuit simulation toolchain based on logical abstractions targeted for simulating variational algorithms. Our proposed toolchain encodes quantum amplitudes and noise probabilities in a probabilistic graphical model, and it compiles the circuits to logical formulas that support efficient repeated simulation of and sampling from quantum circuits for different parameters. Compared to state-of-the-art state vector and density matrix quantum circuit simulators, our simulation approach offers greater performance when sampling from noisy circuits with at least eight to 20 qubits and with around 12 operations on each qubit, making the approach ideal for simulating near-term variational quantum algorithms. And for simulating noise-free shallow quantum circuits with 32 qubits, our simulation approach offers a $66\times$ reduction in sampling cost versus quantum circuit simulation techniques based on tensor network contraction.Comment: ASPLOS '21, April 19-23, 2021, Virtual, US

Augmenting Deep Learning Performance in an Evidential Multiple Classifier System

International audienceThe main objective of this work is to study the applicability of ensemble methods in the context of deep learning with limited amounts of labeled data. We exploit an ensemble of neural networks derived using Monte Carlo dropout, along with an ensemble of SVM classifiers which owes its effectiveness to the hand-crafted features used as inputs and to an active learning procedure. In order to leverage each classifier's respective strengths, we combine them in an evidential framework, which models specifically their imprecision and uncertainty. The application we consider in order to illustrate the interest of our Multiple Classifier System is pedestrian detection in high-density crowds, which is ideally suited for its difficulty, cost of labeling and intrinsic imprecision of annotation data. We show that the fusion resulting from the effective modeling of uncertainty allows for performance improvement, and at the same time, for a deeper interpretation of the result in terms of commitment of the decision