23 papers · ranked by Valyu relevance
Vaishak Belle
Probabilistic planning attempts to incorporate stochastic models directly into the planning process, which is the problem of synthesizing a sequence of actions that achieves some objective for a putative agent. Probabilistic programming has rapidly emerged as a key paradigm to integrate probabilistic concepts with…
Jan-Willem van de Meent, Brooks Paige, Hongseok Yang, Frank Wood
2 an interface between program executions and an inference controller. This document closes with a chapter on advanced topics which we believe to be, at the time of writing, interesting directions for probabilistic programming research; directions that point towards a tight integration with deep neural network research…
Steven Holtzen, Todd Millstein, Guy Van den Broeck
Abstraction is a fundamental tool for reasoning about complex systems. Program abstraction has been utilized to great effect for analyzing deterministic programs. At the heart of program abstraction is the relationship between a concrete program, which is difficult to analyze, and an abstract program, which is more…
Viktor Senderov, Jan Kudlicka, Daniel Lundén, Viktor Palmkvist + 4 more
We present TreePPL, a language for probabilistic modeling and inference in statistical phylogenetics. Specifically, TreePPL is a domain-specific universal probabilistic programming language (PPL), particularly designed for describing phylogenetic models. The core idea is to express the model as a computer program…
Malte Rørmose Damgaard, Rasmus Pedersen, Thomas Bak
Title: Summary Inspired by the “cognitive hourglass” model presented by the researchers behind the cognitive architecture called Sigma, we propose a framework for developing cognitive architectures for cognitive robotics. The main purpose of the proposed framework is to ease development of cognitive architectures by…
Fredrik Ronquist, Jan Kudlicka, Viktor Senderov, Johannes Borgström + 5 more
Statistical phylogenetic analysis currently relies on complex, dedicated software packages, making it difficult for evolutionary biologists to explore new models and inference strategies. Recent years have seen more generic solutions based on probabilistic graphical models, but this formalism can only partly express…
Yura Perov
This abstract extends on the previous work [21, 22] on program induction [16] using probabilistic programming. It describes possible further steps to extend that work, such that, ultimately, automatic probabilistic program synthesis can generalise over any reasonable set of inputs and outputs, in particular in regard…
Abdul Karim Obeid, Peter D. Bruza, Peter Wittek, Marco Barbieri
This article explores how probabilistic programming can be used to simulate quantum correlations in an EPR experimental setting. Probabilistic programs are based on standard probability which cannot produce quantum correlations. In order to address this limitation, a hypergraph formalism was programmed which both…
Daniel Lundén, David Broman, Fredrik Ronquist, Lawrence M. Murray
Probabilistic programming is a programming paradigm for expressing flexible probabilistic models. Implementations of probabilistic programming languages employ a variety of inference algorithms, where sequential Monte Carlo methods are commonly used. A problem with current state-of-the-art implementations using…
Ichiro Hasuo, Yuichiro Oyabu, Clovis Eberhart, Kohei Suenaga + 2 more
'Kenta Cho' 'Shin-ya Katsumata'] We introduce a novel sampling algorithm for Bayesian inference on imperative probabilistic programs. It features a hierarchical architecture that separates control flows from data: the top-level samples a control flow, and the bottom level samples data values along the control flow…
Andreas Stuhlmüller, Noah D. Goodman
We describe a dynamic programming algorithm for computing the marginal distribution of discrete probabilistic programs. This algorithm takes a functional interpreter for an arbitrary probabilistic programming language and turns it into an efficient marginalizer. Because direct caching of sub-distributions is impossible…
Majd Abdallah, Valentin Iovene, Gaston Zanitti, Demian Wassermann
Inferring reliable brain-behavior associations requires synthesizing evidence from thousands of functional neuroimaging studies through meta-analysis. However, existing meta-analysis tools are limited to investigating simple neuroscience concepts and expressing a restricted range of questions. Here, we expand the scope…
Nina Baldy, Marmaduke Woodman, Viktor Jirsa, Meysam Hashemi
Understanding the intricate dynamics of brain activities necessitates models that incorporate causality and nonlinearity. Dynamic Causal Modelling (DCM) presents a statistical framework that embraces causal relationships among brain regions and their responses to experimental manipulations, such as stimulation. In this…
Yura Perov
This thesis describes work on two applications of probabilistic programming: the learning of probabilistic program code given specifications, in particular program code of one-dimensional samplers; and the facilitation of sequential Monte Carlo inference with help of data-driven proposals. The latter is presented with…
Kenton Murray, Jayant Krishnamurthy
We present probabilistic neural programs, a framework for program induction that permits flexible specification of both a computational model and inference algorithm while simultaneously enabling the use of deep neural networks. Probabilistic neural programs combine a computation graph for specifying a neural network…
Parisa Kordjamshidi, Dan Roth, Kristian Kersting
Data-driven approaches are becoming increasingly common as problem-solving tools in many areas of science and technology. In most cases, machine learning models are the key component of these solutions. Often, a solution involves multiple learning models, along with significant levels of reasoning with the models'…
Lucian Chan, Geoffrey Hutchison, Garrett Morris
Generating low-energy molecular conformers is a key task for many areas of computational chemistry, molecular modeling and cheminformatics. Most current conformer generation methods primarily focus on generating geometrically diverse conformers rather than finding the most probable or energetically lowest minima. Here…
Authors not listed
Solving optimization problems, especially for nonlinear and constrained systems, is a challenge. Decades of specialized algorithms have been developed for general and special cases of root finding, minimization (including constraints), for parameter estimation, and mapping connected spaces. These approaches typically…
Krishna Rijal, Pankaj Mehta
The Gillespie algorithm is commonly used to simulate and analyze complex chemical reaction networks. Here, we leverage recent breakthroughs in deep learning to develop a fully differentiable variant of the Gillespie algorithm. The differentiable Gillespie algorithm (DGA) approximates discontinuous operations in the…
Authors not listed
Step-by-step thinking is essential in all domains of chemical sciences and engineering. While machine learning tools are broadly used, algorithms that automate reasoning are far less common. We elaborate on seven categories of human reasoning activities and connect each to applications in chemical science and…
Authors not listed
Bayesian optimization (BO) has become increasingly important for experimental optimization across scientific domains, yet implementing BO pipelines requires significant programming expertise and familiarity with specialized frameworks. This creates a barrier for domain experts who could benefit from BO but lack the…
Sterling Baird, Jason R. Hall, Taylor D. Sparks
Would you rather search for a line inside a cube or a point inside a square? This type of solution degeneracy often exists in physics-based simulations and wet-lab experiments, but constraining these degeneracies is often unsupported or difficult to implement in many optimization packages, requiring additional time and…
Sterling Baird, Jason R. Hall, Taylor D. Sparks
Would you rather search for a line inside a cube or a point inside a square? Physics-based simulations and wet-lab experiments often have symmetries (degeneracies) that allow reducing problem dimensionality or search space, but constraining these degeneracies is often unsupported or difficult to implement in many…