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Statistical inference in evolutionary models with site-dependence is a long-standing challenge in phylogenetics and computational biology. We consider the problem of approximating marginal sequence likelihoods under dependent-site models of…

Computation · Statistics 2025-11-12 Joseph Mathews , Scott C. Schmidler

Various Markov chain Monte Carlo (MCMC) methods are studied to improve upon random walk Metropolis sampling, for simulation from complex distributions. Examples include Metropolis-adjusted Langevin algorithms, Hamiltonian Monte Carlo, and…

Computation · Statistics 2020-05-19 Zexi Song , Zhiqiang Tan

Markov Chain Monte Carlo (MCMC) requires to evaluate the full data likelihood at different parameter values iteratively and is often computationally infeasible for large data sets. In this paper, we propose to approximate the log-likelihood…

Methodology · Statistics 2020-05-26 Guanyu Hu , HaiYing Wang

Machine translation systems are expected to cope with various types of constraints in many practical scenarios. While neural machine translation (NMT) has achieved strong performance in unconstrained cases, it is non-trivial to impose…

Computation and Language · Computer Science 2022-10-24 Shuo Wang , Peng Li , Zhixing Tan , Zhaopeng Tu , Maosong Sun , Yang Liu

In performing a Bayesian analysis, two difficult problems often emerge. First, in estimating the parameters of some model for the data, the resulting posterior distribution may be multi-modal or exhibit pronounced (curving) degeneracies.…

Instrumentation and Methods for Astrophysics · Physics 2013-12-20 F. Feroz , J. Skilling

Bayesian reasoning in linear mixed-effects models (LMMs) is challenging and often requires advanced sampling techniques like Markov chain Monte Carlo (MCMC). A common approach is to write the model in a probabilistic programming language…

Machine Learning · Computer Science 2025-03-25 Jinlin Lai , Justin Domke , Daniel Sheldon

Markov Chain Monte Carlo (MCMC) algorithms are commonly used for their versatility in sampling from complicated probability distributions. However, as the dimension of the distribution gets larger, the computational costs for a satisfactory…

Cosmology and Nongalactic Astrophysics · Physics 2020-12-01 Hector J. Hortua , Riccardo Volpi , Dimitri Marinelli , Luigi Malago

Recent advances in Markov chain Monte Carlo (MCMC) extend the scope of Bayesian inference to models for which the likelihood function is intractable. Although these developments allow us to estimate model parameters, other basic problems…

Computation · Statistics 2019-12-12 Minh-Ngoc Tran , Marcel Scharth , David Gunawan , Robert Kohn , Scott D. Brown , Guy E. Hawkins

Machine learning models are widely used for real-world applications, such as document analysis and vision. Constrained machine learning problems are problems where learned models have to both be accurate and respect constraints. For…

Machine Learning · Computer Science 2021-12-03 Guillaume Perez , Sebastian Ament , Carla Gomes , Arnaud Lallouet

Recent work shows Large Language Models (LLMs) struggle to understand natural language constraints for various text generation tasks in zero- and few-shot settings. While, in the code domain, there is wide usage of constraints in code…

Software Engineering · Computer Science 2025-03-25 Mehant Kammakomati , Sameer Pimparkhede , Srikanth Tamilselvam , Prince Kumar , Pushpak Bhattacharyya

This paper provides sufficient conditions over the sequence of samples and parameters of an adaptive Markov Chain Monte Carlo (MCMC) algorithm to ensure ergodicity with respect to a target distribution that can have unbounded support. These…

Statistics Theory · Mathematics 2026-02-17 Alexandre Chotard

An algorithm is proposed, analyzed, and tested for solving continuous nonlinear-equality-constrained optimization problems where the objective and constraint functions are defined by expectations or averages over large, finite numbers of…

Optimization and Control · Mathematics 2026-05-14 Frank E. Curtis , Lingjun Guo , Daniel P. Robinson

We design and implement a novel algorithm for computing a multilevel Monte Carlo (MLMC) estimator of the cumulative distribution function of a quantity of interest in problems with random input parameters or initial conditions. Our approach…

Numerical Analysis · Mathematics 2020-08-26 Søren Taverniers , Daniel M. Tartakovsky

Bayesian max-margin models have shown superiority in various practical applications, such as text categorization, collaborative prediction, social network link prediction and crowdsourcing, and they conjoin the flexibility of Bayesian…

Machine Learning · Statistics 2016-10-19 Wenbo Hu , Jun Zhu , Bo Zhang

A non trivial problem that arises in several applications is the estimation of the mean of a truncated normal distribution. In this paper, an iterative deterministic scheme for approximating this mean is proposed. It has been inspired from…

Even after fine-tuning and reinforcement learning, large language models (LLMs) can be difficult, if not impossible, to control reliably with prompts alone. We propose a new inference-time approach to enforcing syntactic and semantic…

Artificial Intelligence · Computer Science 2023-11-28 Alexander K. Lew , Tan Zhi-Xuan , Gabriel Grand , Vikash K. Mansinghka

Sampling problems are widely regarded as the task for which quantum computers can most readily provide a quantum advantage. Leveraging this feature, the quantum-enhanced Markov chain Monte Carlo [Layden, D. et al., Nature 619, 282-287…

Quantum Physics · Physics 2026-02-26 Yuichiro Nakano , Ken N. Okada , Keisuke Fujii

We explore a general framework in Markov chain Monte Carlo (MCMC) sampling where sequential proposals are tried as a candidate for the next state of the Markov chain. This sequential-proposal framework can be applied to various existing…

Computation · Statistics 2019-08-21 Joonha Park , Yves F. Atchadé

In real-world applications of large language models, outputs are often required to be confined: selecting items from predefined product or document sets, generating phrases that comply with safety standards, or conforming to specialized…

Computation and Language · Computer Science 2025-04-15 Haotian Ye , Himanshu Jain , Chong You , Ananda Theertha Suresh , Haowei Lin , James Zou , Felix Yu

Speculative decoding (SD) accelerates language model inference by drafting tokens from a cheap proposal model and verifying them against an expensive target model via rejection sampling. Because rejection truncates the draft block at the…