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Probabilistic models over strings have played a key role in developing methods allowing indels to be treated as phylogenetically informative events. There is an extensive literature on using automata and transducers on phylogenies to do…

Populations and Evolution · Quantitative Biology 2013-07-15 Alexandre Bouchard-Côté

Probabilistic graphical models (PGMs) are powerful tools for representing statistical dependencies through graphs in high-dimensional systems. However, they are limited to pairwise interactions. In this work, we propose the simplicial…

Machine Learning · Statistics 2025-10-16 Lorenzo Marinucci , Gabriele D'Acunto , Paolo Di Lorenzo , Sergio Barbarossa

Interpreting data with mathematical models is an important aspect of real-world industrial and applied mathematical modeling. Often we are interested to understand the extent to which a particular set of data informs and constrains model…

Methodology · Statistics 2025-03-06 Matthew J Simpson , Ruth E Baker

Models with intractable normalizing functions arise frequently in statistics. Common examples of such models include exponential random graph models for social networks and Markov point processes for ecology and disease modeling. Inference…

Computation · Statistics 2018-08-03 Jaewoo Park , Murali Haran

Neural network design has utilized flexible nonlinear processes which can mimic biological systems, but has suffered from a lack of traceability in the resulting network. Graphical probabilistic models ground network design in probabilistic…

Machine Learning · Computer Science 2015-06-19 Kenric P. Nelson , Madalina Barbu , Brian J. Scannell

This article presents a type-based analysis for deriving upper bounds on the expected execution cost of probabilistic programs. The analysis is naturally compositional, parametric in the cost model, and supports higher order functions and…

Programming Languages · Computer Science 2020-09-23 Di Wang , David M Kahn , Jan Hoffmann

We describe a probabilistic (generative) view of affinity matrices along with inference algorithms for a subclass of problems associated with data clustering. This probabilistic view is helpful in understanding different models and…

Machine Learning · Computer Science 2012-12-12 Romer Rosales , Brendan J. Frey

Decision theories offer principled methods for making choices under various types of uncertainty. Algorithms that implement these theories have been successfully applied to a wide range of real-world problems, including materials and drug…

Machine Learning · Computer Science 2026-05-26 Agustinus Kristiadi

The graphical lasso is a widely used algorithm for fitting undirected Gaussian graphical models. However, for inference on functionals of edge values in the learned graph, standard tools lack formal statistical guarantees, such as control…

Methodology · Statistics 2025-04-01 Sofia Guglielmini , Gerda Claeskens , Snigdha Panigrahi

We describe a general framework for probabilistic modeling of complex scenes and inference from ambiguous observations. The approach is motivated by applications in image analysis and is based on the use of priors defined by stochastic…

Computer Vision and Pattern Recognition · Computer Science 2019-08-14 Jeroen Chua , Pedro F. Felzenszwalb

Inference amortization methods share information across multiple posterior-inference problems, allowing each to be carried out more efficiently. Generally, they require the inversion of the dependency structure in the generative model, as…

Machine Learning · Statistics 2018-11-30 Stefan Webb , Adam Golinski , Robert Zinkov , N. Siddharth , Tom Rainforth , Yee Whye Teh , Frank Wood

Graphical models are widely used in diverse application domains to model the conditional dependencies amongst a collection of random variables. In this paper, we consider settings where the graph structure is covariate-dependent, and…

Machine Learning · Statistics 2025-04-24 Jiahe Lin , Yikai Zhang , George Michailidis

Log-linear models are the popular workhorses of analyzing contingency tables. A log-linear parameterization of an interaction model can be more expressive than a direct parameterization based on probabilities, leading to a powerful way of…

Machine Learning · Statistics 2015-08-06 Henrik Nyman , Johan Pensar , Timo Koski , Jukka Corander

We present a new probabilistic modelling framework based on the recent notion of normal factor graph (NFG). We show that the proposed NFG models and their transformations unify some existing models such as factor graphs, convolutional…

Information Theory · Computer Science 2012-09-17 Ali Al-Bashabsheh , Yongyi Mao

Machine learning (ML) has emerged as a powerful tool for tackling complex regression and classification tasks, yet its success often hinges on the quality of training data. This study introduces an ML paradigm inspired by domain knowledge…

Machine Learning · Computer Science 2025-01-10 Mohsen Rashki

Inferring a graphical model or network from observational data from a large number of variables is a well studied problem in machine learning and computational statistics. In this paper we consider a version of this problem that is relevant…

Methodology · Statistics 2013-12-06 Andy Dahl , Victoria Hore , Valentina Iotchkova , Jonathan Marchini

We present new algorithms for inference in credal networks --- directed acyclic graphs associated with sets of probabilities. Credal networks are here interpreted as encoding strong independence relations among variables. We first present a…

Artificial Intelligence · Computer Science 2013-01-07 Jose Carlos Ferreira da Rocha , Fabio Gagliardi Cozman

Inferring the causal structure of a set of random variables from a finite sample of the joint distribution is an important problem in science. Recently, methods using additive noise models have been suggested to approach the case of…

Machine Learning · Statistics 2012-07-24 Jonas Peters , Dominik Janzing , Bernhard Schölkopf

Many collective systems exist in nature far from equilibrium, ranging from cellular sheets up to flocks of birds. These systems reflect a form of active matter, whereby individual material components have internal energy. Under specific…

Soft Condensed Matter · Physics 2023-04-17 Namid R. Stillman , Silke Henkes , Roberto Mayor , Gilles Louppe

When quantitative models are used to support decision-making on complex and important topics, understanding a model's ``reasoning'' can increase trust in its predictions, expose hidden biases, or reduce vulnerability to adversarial attacks.…

Machine Learning · Computer Science 2019-07-09 Dimitris Bertsimas , Arthur Delarue , Patrick Jaillet , Sebastien Martin