Probabilistic Programming

How humans grow and maintain abstract knowledge from the sparse, streaming noisy data of experience is a longstanding challenge in cognitive science. Any computational account must satisfy at least three desiderata: It must be (1) data-efficient and compute-efficient, (2) capture gradations of uncertainty to support intelligent inquiry and information gathering, and (3) be flexible enough to mentally represent the endless range of concepts people can learn and think about. Here we introduce a computational model that captures these three properties, by encoding symbolic knowledge as mental programs that combine natural language with source code, and sequentially inferring mental programs using LLM-guided Bayesian learning algorithms. Across a range of behavioral studies this model successfully reproduces quantitative signatures of human inductive learning and active inquiry, such as anchoring, garden-pathing, and other effects. In contrast, pure LLMs and classic Bayesian models either fail at the underlying task, or do not reproduce human behavior, or succeed only at exorbitant computational cost. These results suggest that one way humans continually grow their knowledge is by mentally representing many hypotheses spanning language-like and program-like representations, then revising those hypotheses to approximate Bayesian updates, while a bottom-up neural mechanism (an LLM) makes inference both tractable and learnable.

Standard probabilistic logic programming frameworks typically rely on grounding logic programs into discrete propositional representations. This operational requirement restricts exact inference to finite domains and discrete probability distributions. In this paper, we introduce Measure-Theoretic Probabilistic Definite Clause Logic (MT-PDCL), a generalized foundational framework that eliminates this finite-domain restriction. By explicitly defining stochastic variables over bounded index domains and equipping the interpretation space with standard Borel $σ$-algebras, MT-PDCL allows logical variables to operate natively over continuous measurable spaces. Building on Continuous Distribution Semantics, MT-PDCL models probabilistic rules as mutually independent causal events. However, rather than aggregating these derivations via finite boolean circuits, declarative entailment is formally defined through exact Lebesgue integration over the continuous measure space. We introduce a continuous immediate consequence operator that unifies the integration of continuous prior distributions with the evaluation of exact continuous observations. We demonstrate that this approach replaces the combinatorial bottleneck of discrete grounding with exact, algebraic, and structurally differentiable inference. While this transition trades discrete combinatorics for the geometric curse of dimensionality, it achieves the expressive power of continuous probabilistic models while preserving the pure declarative syntax of definite clause logic.

Hamiltonian Monte Carlo (HMC) is a successful generic inference method in probabilistic programming, but in its ordinary formulation it needs gradients and finite-dimensional parameter spaces. In Haskell, lazy evaluation lets probabilistic programs express stochastic processes and other non-parametric Bayesian models over implicit infinite-dimensional spaces. This paper develops new formulations of gradient-based HMC for this infinite-dimensional setting, via lazy evaluation. For automatic differentiation, we provide an analysis based on a new notion of "piecewise analytic under cylindrical analytic partition" (PACAP), to show that even if a program is infinite-dimensional and defined lazily, the gradient of the likelihood function is finitely supported. For the Monte Carlo method itself, we develop several HMC variants and a No-U-Turn Sampler that operate over the infinite-dimensional parameter space but are still productive because of lazy evaluation. Experiments cover Gaussian mixture clustering, random walks, and piecewise-constant regression with Poisson-process changepoints.

Probabilistic logic programming is a formalism of statistical relational artificial intelligence that supports causal queries, including interventions from outside the system. When the structure of a probabilistic logic program is learned from data, however, only probabilistic information is used, and a single probability distribution may be compatible with several causal orders. This leads to ambiguity in interventional reasoning, raising the question of when the causal order is uniquely determined by the distribution. Exploiting the relationship between acyclic probabilistic logic programs and Bayesian networks, we derive conditions under which the probabilistic information encoded in a program determines a unique causal order. We also incorporate constraints arising from relational structure by taking into account prescribed sets of causal symmetries induced by the underlying relational vocabulary. The result is a method for verifying when a learned probabilistic logic program supports well-defined intervention semantics.

Building reliable applications that leverage large language models (LLMs) remains a significant challenge. While LLMs offer impressive capabilities across diverse tasks, their outputs often lack accuracy and provide no clear measure of confidence. This uncertainty compounds in flows of multiple calls to LLMs and other tools, making it difficult for developers and end-users to trust the results. This paper introduces a probabilistic language for programming LLM-based flows. It enables developers to quantify and propagate uncertainty throughout the application's flow, and experiment with different inference scaling techniques without adding a single line of code beyond the flow's logic. We present an experimental study to demonstrate this capability, and a case study building a theorem proving agent for the Rocq theorem prover.

Pearl famously argues that causal knowledge enables the prediction of intervention effects. By contrast, purely descriptive knowledge supports only conclusions drawn from observations. His theory of causality, however, is developed exclusively within Bayesian networks and causal models. Consequently, it is largely restricted to acyclic causal relationships, and transferring its ideas to other formalisms risks misinterpretation or inconsistency. This paper brings Pearl's approach to causality into probabilistic logic programming (PLP). To this end, such programs are aligned with philosophical foundations established in prior work that do not rely on temporal notions; that is, all relevant events are assumed to occur simultaneously. A formal causal semantics for these programs, together with a notion of intervention and an implementation, is proposed. It is shown that this semantics coincides with the P-log semantics for stratified ProbLog programs, while the two may differ in the non-stratified case and for other PLP formalisms.

Gradient estimation -- the task of computing the gradient of the expected value of a probabilistic program -- has diverse applications in scientific computing, but is notoriously difficult because of issues such as high-dimensional integration, discrete random choices, and complex stochastic dependencies. This article introduces gradient inference, a new approach to developing sound and efficient gradient estimators for probabilistic programs. Gradient inference rests on a formal reduction from a gradient estimation problem to a closely related probabilistic inference problem, whose solution can be differentiated to obtain a gradient estimator. This inference problem is obtained by applying two powerful statistical operations -- coupling and factorization -- to the input probabilistic program. Our reduction lets us leverage the rich toolkit of probabilistic inference algorithms to design novel gradient estimators that extend and improve upon existing methods. We introduce GradInf, a probabilistic programming system that facilitates the sound and automated implementation of gradient inference. GradInf is centered around programmable source-to-source transformations for coupling and factorizing higher-order probabilistic programs, whose soundness is proven in terms of a denotational semantics. Key to our development is the use of information-flow typing to allow random choices in a probabilistic program to be factored out and partially evaluated, which improves our ability to deploy sophisticated probabilistic inference algorithms. The resulting system offers practitioners a principled framework for designing gradient estimators. We apply GradInf to several challenging case studies, showing that it can express prominent gradient estimators from the literature and enables the construction of new state-of-the-art estimators that outperform the best existing baselines.

Language models increasingly write probabilistic programs (in NumPyro, Stan, or Pyro), but a program that compiles, runs, and passes every unit test can still be \emph{statistically} wrong -- a Gaussian likelihood for heavy-tailed data, a Poisson for over-dispersed counts, an invalid prior support, or a pathological parameterization. The right verifier is therefore not a test suite but the Bayesian workflow itself: posterior predictive checks, simulation-based calibration, sampler diagnostics ($\hat R$, divergences, ESS), and held-out predictive density. We study this calibration oracle along three axes. \textbf{Detection:} on a benchmark of $14$ misspecification types across $10$ model families ($200$ instances), it flags the bug with AUC $0.97$ ($88\%$ at $2\%$ FPR \emph{when handed the correct reference program, an upper bound}) -- and a fully \emph{reference-free} version that uses no correct program reaches $62$--$78\%$ (the upper figure from a small automated model search), versus $0\%$ for a unit-test oracle. \textbf{Repair:} used as feedback in an LLM repair loop across fifteen models, calibration significantly outperforms unit-test feedback -- which is itself \emph{significantly worse than no feedback at all}, a passing test inducing false confidence that suppresses repair -- and improves over no feedback on strong-but-unsaturated models (GPT-5.1 $33{\to}92\%$, Claude $75{\to}100\%$; paired McNemar, $n{=}228$). \textbf{Reality:} on programs LLMs write from scratch for neutral briefs, $15$--$47\%$ of runnable ones are statistically misspecified (unit tests catch none), and calibration-guided repair significantly beats LLM-as-judge review, a Bayesian-workflow checklist, and data-summary self-debug. Across all three, the lesson is the same: for probabilistic programs, correctness is calibration, not compilation.

This project introduces the CRISTAL Method (Coherent Reliable Intentional Synthesis of Truthful Analysis Logic), a neurosymbolic framework for automating complex analysis workflows, with fundamental investment analysis as a primary use case. This domain poses major challenges: high structural uncertainty, noisy and subjective data, tight attention budgets, and the need for justified, reproducible decisions. Human analysts often struggle in this domain due to cognitive biases and limitations, suggesting significant value in automation. But while LLM-based agents have been proposed as analytical aids, their limitations -- poor numerical reasoning, unawareness of uncertainty, and lack of reproducibility -- hinder their effectiveness in this context. CRISTAL addresses these gaps through a principled blend of statistical model synthesis, continuous learning, and active learning. Starting from a natural-language prior knowledge curriculum, CRISTAL builds a dynamic, interpretable probabilistic program that enables full Bayesian inference, including uncertainty quantification and budget-aware data acquisition. CRISTAL continually refines its world model during analysis, leveraging LLMs for code synthesis and learning. We validate CRISTAL on a novel benchmark of synthetic equities with rich financial and textual data. On a company classification task, CRISTAL achieves Bayes-optimal accuracy with just 5 examples and a 5-second budget, outperforming state-of-the-art LLMs that plateau around 40% accuracy even with order-of-magnitude more input data and compute.

Neurosymbolic systems such as DeepProbLog combine neural perception with probabilistic logic, but standard inference is associational. Counterfactual reasoning additionally requires a causal semantics for interventions and evidence. We introduce DeepSWIP, a single-world counterfactual semantics for DeepProbLog programs. Using neural materialization, we reduce fixed-context neural predicates to ordinary ProbLog choices, apply Single World Intervention Programs (SWIPs), and compute counterfactuals by weighted model counting (WMC) over a single transformed program. Under finite grounding and unique-supported-model assumptions, DeepSWIP is exact relative to the learned materialized FCM. The standard quotient-WMC form of ProbLog conditionals identifies active neural probabilities and explains intervention cleaning, calibration sensitivity, and rare-evidence instability. Experiments on MPI3D confirm the transformation against a DeepTwin construction against 12,000 queries, as predicted and a 2.14$\times$ inference speedup from avoiding the Twin's endogenous duplication. A SUMO HOV experiment shows that neural calibration degradation biases plug-in estimates, while a correctly scoped randomized-policy AIPW estimator removes most first-order bias for population mean and ATE estimands. Code is at https://github.com/saibib/deep_SWIP.

Neurosymbolic semantics is fragmented: classical, fuzzy, probabilistic and neural systems each define truth by their own inductive rules. NeSyCat, extending ULLER, subsumes them under a single inductive definition of truth, parametric in a strong monad and an aggregation structure on truth-values. NeSyCat has so far lacked an account of predicates and functions learned by neural networks. We provide NeSyCat Torch as the missing link and interpret computational symbols via neural networks, implementing the framework in probabilistic programming and tensor-based backends. We use the distribution monad for reference semantics and metric evaluation, and complement it by a monad for numerically stable, differentiable training: the lazy log-tensor monad over the log-semiring. For efficient training in batches, we furthermore employ a batch monad. The axioms are the source code: written once in monad-based do-notation, monadic bind performs marginalisation, lazily pruning unneeded branches. On MNIST addition, our HaskTorch, JAX, and PyTorch implementations outperform LTN and DeepProbLog in speed and accuracy, while achieving nearly the accuracy of DeepStochLog. However, unlike DeepStochLog, we stay in a uniform framework that applies to many first-order NeSy approaches. Namely, the construction is parametric in the monad; instantiating it with, e.g., the Giry monad extends the approach to continuous probability (working out a neural representation here is left for future work).

State-space models (SSMs) are the standard formalism for Bayesian treatment of dynamical systems, with natural applications in statistics, signal processing, and machine learning. Despite their importance in both theory and application, dynamical systems have proven difficult to incorporate in modern probabilistic programming languages (PPLs), making state-of-the-art methods less accessible to practitioners and introducing friction in following the "Bayesian workflow." We introduce dynestyx, a probabilistic programming library with first-class support for SSMs, including state-of-the-art methods in the estimation of both states and parameters. Through a single, unified interface, users may specify arbitrary priors for discrete-time or continuous-time dynamical systems, perform inference over mixed-effect data, and make state and parameter estimates with principled uncertainty quantification.

Post-training Large Language Models (LLMs) for reasoning typically focuses on deductive tasks such as mathematics and coding where correctness is verifiable. Yet, many real-world reasoning problems are inductive: agents must infer uncertain beliefs from sparse, ambiguous observations. There are challenges to using standard fine-tuning methods for inductive reasoning, including difficulties in curating large-scale, high-quality labeled datasets and in handling targets that are inherently distributional. In this work, we introduce a novel approach, called Program-based Posterior Training (PPT), to address these limitations: we use an LLM to generate diverse open-world scenarios as probabilistic programs, run probabilistic inference to produce distributional target responses to queries, and then fine-tune on these probabilistic soft labels. Using this approach, we fine-tune LLMs on 10,000 programmatically generated scenarios and evaluate on held-out motifs, human-labeled judgments, and external benchmarks. Overall, PPT substantially improves estimation accuracy on held-out inductive tasks, increases alignment with human judgments, and transfers to external benchmarks for estimation and calibration. Additionally, the gains in raw calibration are not subsumed by post-hoc temperature scaling, showing that the models have more deeply internalized uncertainty compared to output rescaling. Together, these results suggest that probabilistic-program-mediated fine-tuning is a promising approach for post-training LLMs to reliably perform approximate inductive inference.

Coding and computation remain major bottlenecks in Markov chain Monte Carlo (MCMC) workflows, especially as modern sampling algorithms have become increasingly complex and existing probabilistic programming systems remain limited in model support, extensibility, and composability. We introduce \textbf{AI4BayesCode}, an extensible LLM-driven system that translates natural-language Bayesian model descriptions into runnable, validated MCMC samplers. To improve reliability, AI4BayesCode adopts a modular design that decomposes models into modular sampling blocks and maps each block to a built-in sampling component, reducing the need to implement complex sampling algorithms from scratch. Reliability is further improved through pre-generation validation of model specifications and post-generation validation of generated sampler code. AI4BayesCode also introduces a novel recursively stateful coding paradigm for MCMC, allowing modular sampling components, potentially developed by different contributors, to be composed coherently within larger MCMC procedures. We develop a benchmark suite to evaluate AI4BayesCode for sampler-generation. Experiments show that AI4BayesCode can implement a wide range of Bayesian models from natural-language descriptions alone. As an open-ended system, its capability can continue to expand with improvements in the underlying AI agent and the addition of new built-in blocks.

LLMs are widely used for code generation and mathematical reasoning tasks where they are required to generate structured output. They either need to reason about code, generate code for a given specification, or reason using programs of thought. The typical approach to code generation is to prompt the model and generate samples until an appropriate program is obtained. Within this process, sampling $n$ programs from the language model requires $n$ GPU compute-intensive generations which becomes prohibitively expensive for larger values of $n$. In this work, we address this limitation by exposing the LLM's distribution within the generated programs themselves. We propose a novel test-time framework we dub probabilistic programs of thought to obtain more samples from the model with fewer LLM generations. Given a program generated by a model and the associated next-token probabilities, we build a probabilistic program that compactly represents exponentially many deterministic programs. Since performing probabilistic reasoning in this probabilistic program is much cheaper, our approach allows sampling new programs without any additional GPU compute and little CPU overhead. We instantiate our approach on benchmarks for code generation, code understanding and mathematical reasoning and report improvements in performance with fewer generations from the LLM.