Recursive calls over recursive data are useful for generating probability distributions, and probabilistic programming allows computations over these distributions to be expressed in a modular and intuitive way. Exact inference is also useful, but unfortunately, existing probabilistic programming languages do not perform exact inference on recursive calls over recursive data, forcing programmers to code many applications manually. We introduce a probabilistic language in which a wide variety of recursion can be expressed naturally, and inference carried out exactly. For instance, probabilistic pushdown automata and their generalizations are easy to express, and polynomial-time parsing algorithms for them are derived automatically. We eliminate recursive data types using program transformations related to defunctionalization and refunctionalization. These transformations are assured correct by a linear type system, and a successful choice of transformations, if there is one, is guaranteed to be found by a greedy algorithm.
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Probabilistic Databases for All
In probabilistic databases the data is uncertain and is modeled by a probability distribution. The central problem in probabilistic databases is query evaluation, which requires performing not only traditional data processing such as joins, projections, unions, but also probabilistic inference in order to compute the probability of each item in the answer. At their core, probabilistic databases are a proposal to integrate logic with probability theory. This paper accompanies a talk given as part of the Gems of PODS series, and describes several results in probabilistic databases, explaining their significance in the broader context of model counting, probabilistic inference, and Statistical Relational Models.
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- PAR ID:
- 10163837
- Date Published:
- Journal Name:
- PODS
- Page Range / eLocation ID:
- 19 to 31
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Recently there has been growing interest in learning probabilistic models that admit poly-time inference called tractable probabilistic models from data. Although they generalize poorly as compared to intractable models, they often yield more accurate estimates at prediction time. In this paper, we seek to further explore this trade-off between generalization performance and inference accuracy by proposing a novel, partially tractable representation called cutset Bayesian networks (CBNs). The main idea in CBNs is to partition the variables into two subsets X and Y, learn a (intractable) Bayesian network that represents P(X) and a tractable conditional model that represents P(Y|X). The hope is that the intractable model will help improve generalization while the tractable model, by leveraging Rao-Blackwellised sampling which combines exact inference and sampling, will help improve the prediction accuracy. To compactly model P(Y|X), we introduce a novel tractable representation called conditional cutset networks (CCNs) in which all conditional probability distributions are represented using calibrated classifiers—classifiers which typically yield higher quality probability estimates than conventional classifiers. We show via a rigorous experimental evaluation that CBNs and CCNs yield more accurate posterior estimates than their tractable as well as intractable counterparts.
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null (Ed.)Probabilistic programming languages aim to describe and automate Bayesian modeling and inference. Modern languages support programmable inference, which allows users to customize inference algorithms by incorporating guide programs to improve inference performance. For Bayesian inference to be sound, guide programs must be compatible with model programs. One pervasive but challenging condition for model-guide compatibility is absolute continuity, which requires that the model and guide programs define probability distributions with the same support. This paper presents a new probabilistic programming language that guarantees absolute continuity, and features general programming constructs, such as branching and recursion. Model and guide programs are implemented as coroutines that communicate with each other to synchronize the set of random variables they sample during their execution. Novel guide types describe and enforce communication protocols between coroutines. If the model and guide are well-typed using the same protocol, then they are guaranteed to enjoy absolute continuity. An efficient algorithm infers guide types from code so that users do not have to specify the types. The new programming language is evaluated with an implementation that includes the type-inference algorithm and a prototype compiler that targets Pyro. Experiments show that our language is capable of expressing a variety of probabilistic models with nontrivial control flow and recursion, and that the coroutine-based computation does not introduce significant overhead in actual Bayesian inference.more » « less
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Weighted model counting and integration (WMC/WMI) are natural problems to which we can reduce many probabilistic inference tasks, e.g., in Bayesian networks, Markov networks, and probabilistic programs. Typically, we are given a first-order formula, where each satisfying assignment is associated with a weight---e.g., a probability of occurrence---and our goal is to compute the total weight of the formula. In this paper, we target exact inference techniques for WMI that leverage the power of satisfiability modulo theories (SMT) solvers to decompose a first-order formula in linear real arithmetic into a set of hyperrectangular regions whose weight is easy to compute. We demonstrate the challenges of hyperrectangular decomposition and present a novel technique that utilizes orthogonal transformations to transform formulas in order to enable efficient inference. Our evaluation demonstrates our technique's ability to improve the time required to achieve exact probability bounds.
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Abstract Probabilistic modeling is fundamental to the statistical analysis of complex data. In addition to forming a coherent description of the data‐generating process, probabilistic models enable parameter inference about given datasets. This procedure is well developed in the Bayesian perspective, in which one infers probability distributions describing to what extent various possible parameters agree with the data. In this paper, we motivate and review probabilistic modeling for adaptive immune receptor repertoire data then describe progress and prospects for future work, from germline haplotyping to adaptive immune system deployment across tissues. The relevant quantities in immune sequence analysis include not only continuous parameters such as gene use frequency but also discrete objects such as B‐cell clusters and lineages. Throughout this review, we unravel the many opportunities for probabilistic modeling in adaptive immune receptor analysis, including settings for which the Bayesian approach holds substantial promise (especially if one is optimistic about new computational methods). From our perspective, the greatest prospects for progress in probabilistic modeling for repertoires concern ancestral sequence estimation for B‐cell receptor lineages, including uncertainty from germline genotype, rearrangement, and lineage development.
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1145/3375395.3389129
