We introduce two synthetic likelihood methods for Simulation-Based Inference (SBI), to conduct either amortized or targeted inference from experimental observations when a high-fidelity simulator is available. Both methods learn a conditional energy-based model (EBM) of the likelihood using synthetic data generated by the simulator, conditioned on parameters drawn from a proposal distribution. The learned likelihood can then be combined with any prior to obtain a posterior estimate, from which samples can be drawn using MCMC. Our methods uniquely combine a flexible Energy-Based Model and the minimization of a KL loss: this is in contrast to other synthetic likelihood methods, which either rely on normalizing flows, or minimize score-based objectives; choices that come with known pitfalls. We demonstrate the properties of both methods on a range of synthetic datasets, and apply them to a neuroscience model of the pyloric network in the crab, where our method outperforms prior art for a fraction of the simulation budget.
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Addressing the challenge of scaling-up epidemiological inference to complex and heterogeneous models, we introduce Poisson Approximate Likelihood (PAL) methods. In contrast to the popular ODE approach to compartmental modelling, in which a large population limit is used to motivate a deterministic model, PALs are derived from approximate filtering equations for finite-population, stochastic compartmental models, and the large population limit drives consistency of maximum PAL estimators. Our theoretical results appear to be the first likelihood-based parameter estimation consistency results which apply to a broad class of partially observed stochastic compartmental models and address the large population limit. PALs are simple to implement, involving only elementary arithmetic operations and no tuning parameters, and fast to evaluate, requiring no simulation from the model and having computational cost independent of population size. Through examples we demonstrate how PALs can be used to: fit an age-structured model of influenza, taking advantage of automatic differentiation in Stan; compare over-dispersion mechanisms in a model of rotavirus by embedding PALs within sequential Monte Carlo; and evaluate the role of unit-specific parameters in a meta-population model of measles.
Estimating the mutual information from samples from a joint distribution is a challenging problem in both science and engineering. In this work, we realize a variational bound that generalizes both discriminative and generative approaches. Using this bound, we propose a hybrid method to mitigate their respective shortcomings. Further, we propose Predictive Quantization (PQ): a simple generative method that can be easily combined with discriminative estimators for minimal computational overhead. Our propositions yield a tighter bound on the information thanks to the reduced variance of the estimator. We test our methods on a challenging task of correlated high-dimensional Gaussian distributions and a stochastic process involving a system of free particles subjected to a fixed energy landscape. Empirical results show that hybrid methods consistently improved mutual information estimates when compared to the corresponding discriminative counterpart.
This paper presents a new robust loss function, the T-Loss, for medical image segmentation. The proposed loss is based on the negative log-likelihood of the Student-t distribution and can effectively handle outliers in the data by controlling its sensitivity with a single parameter. This parameter is updated during the backpropagation process, eliminating the need for additional computation or prior information about the level and spread of noisy labels. Our experiments show that the T-Loss outperforms traditional loss functions in terms of dice scores on two public medical datasets for skin lesion and lung segmentation. We also demonstrate the ability of T-Loss to handle different types of simulated label noise, resembling human error. Our results provide strong evidence that the T-Loss is a promising alternative for medical image segmentation where high levels of noise or outliers in the dataset are a typical phenomenon in practice. The project website can be found at //robust-tloss.github.io
Energy-based models (EBMs) are versatile density estimation models that directly parameterize an unnormalized log density. Although very flexible, EBMs lack a specified normalization constant of the model, making the likelihood of the model computationally intractable. Several approximate samplers and variational inference techniques have been proposed to estimate the likelihood gradients for training. These techniques have shown promising results in generating samples, but little attention has been paid to the statistical accuracy of the estimated density, such as determining the relative importance of different classes in a dataset. In this work, we propose a new maximum likelihood training algorithm for EBMs that uses a different type of generative model, normalizing flows (NF), which have recently been proposed to facilitate sampling. Our method fits an NF to an EBM during training so that an NF-assisted sampling scheme provides an accurate gradient for the EBMs at all times, ultimately leading to a fast sampler for generating new data.
In this work, we present a constant-round algorithm for the $2$-ruling set problem in the Congested Clique model. As a direct consequence, we obtain a constant round algorithm in the MPC model with linear space-per-machine and optimal total space. Our results improve on the $O(\log \log \log n)$-round algorithm by [HPS, DISC'14] and the $O(\log \log \Delta)$-round algorithm by [GGKMR, PODC'18]. Our techniques can also be applied to the semi-streaming model to obtain an $O(1)$-pass algorithm. Our main technical contribution is a novel sampling procedure that returns a small subgraph such that almost all nodes in the input graph are adjacent to the sampled subgraph. An MIS on the sampled subgraph provides a $2$-ruling set for a large fraction of the input graph. As a technical challenge, we must handle the remaining part of the graph, which might still be relatively large. We overcome this challenge by showing useful structural properties of the remaining graph and show that running our process twice yields a $2$-ruling set of the original input graph with high probability.
In this work, we introduce a ``score-based assessment'' framework for estimating the transferability of pre-trained speech models (PSMs) for fine-tuning target tasks. We leverage upon two representation theories, Bayesian likelihood estimation and optimal transport, to generate rank scores for the PSM candidates using the extracted representations. Our framework efficiently computes transferability scores without actual fine-tuning of candidate models or layers by making a temporal independent hypothesis. We evaluate some popular supervised speech models (e.g., Conformer RNN-Transducer) and self-supervised speech models (e.g., HuBERT) in cross-layer and cross-model settings using public data. Experimental results show a high Spearman's rank correlation and low $p$-value between our estimation framework and fine-tuning ground truth. Our proposed transferability framework requires less computational time and resources, making it a resource-saving and time-efficient approach for tuning speech foundation models.
Inverse problems, i.e., estimating parameters of physical models from experimental data, are ubiquitous in science and engineering. The Bayesian formulation is the gold standard because it alleviates ill-posedness issues and quantifies epistemic uncertainty. Since analytical posteriors are not typically available, one resorts to Markov chain Monte Carlo sampling or approximate variational inference. However, inference needs to be rerun from scratch for each new set of data. This drawback limits the applicability of the Bayesian formulation to real-time settings, e.g., health monitoring of engineered systems, and medical diagnosis. The objective of this paper is to develop a methodology that enables real-time inference by learning the Bayesian inverse map, i.e., the map from data to posteriors. Our approach is as follows. We represent the posterior distribution using a parameterization based on deep neural networks. Next, we learn the network parameters by amortized variational inference method which involves maximizing the expectation of evidence lower bound over all possible datasets compatible with the model. We demonstrate our approach by solving examples a set of benchmark problems from science and engineering. Our results show that the posterior estimates of our approach are in agreement with the corresponding ground truth obtained by Markov chain Monte Carlo. Once trained, our approach provides the posterior parameters of observation just at the cost of a forward pass of the neural network.
Transport maps can ease the sampling of distributions with non-trivial geometries by transforming them into distributions that are easier to handle. The potential of this approach has risen with the development of Normalizing Flows (NF) which are maps parameterized with deep neural networks trained to push a reference distribution towards a target. NF-enhanced samplers recently proposed blend (Markov chain) Monte Carlo methods with either (i) proposal draws from the flow or (ii) a flow-based reparametrization. In both cases, the quality of the learned transport conditions performance. The present work clarifies for the first time the relative strengths and weaknesses of these two approaches. Our study concludes that multimodal targets can be reliably handled with flow-based proposals up to moderately high dimensions. In contrast, methods relying on reparametrization struggle with multimodality but are more robust otherwise in high-dimensional settings and under poor training. To further illustrate the influence of target-proposal adequacy, we also derive a new quantitative bound for the mixing time of the Independent Metropolis-Hastings sampler.
Joint Bayesian Inference of Graphical Structure and Parameters with a Single Generative Flow Network
Generative Flow Networks (GFlowNets), a class of generative models over discrete and structured sample spaces, have been previously applied to the problem of inferring the marginal posterior distribution over the directed acyclic graph (DAG) of a Bayesian Network, given a dataset of observations. Based on recent advances extending this framework to non-discrete sample spaces, we propose in this paper to approximate the joint posterior over not only the structure of a Bayesian Network, but also the parameters of its conditional probability distributions. We use a single GFlowNet whose sampling policy follows a two-phase process: the DAG is first generated sequentially one edge at a time, and then the corresponding parameters are picked once the full structure is known. Since the parameters are included in the posterior distribution, this leaves more flexibility for the local probability models of the Bayesian Network, making our approach applicable even to non-linear models parametrized by neural networks. We show that our method, called JSP-GFN, offers an accurate approximation of the joint posterior, while comparing favorably against existing methods on both simulated and real data.
Image segmentation is an important component of many image understanding systems. It aims to group pixels in a spatially and perceptually coherent manner. Typically, these algorithms have a collection of parameters that control the degree of over-segmentation produced. It still remains a challenge to properly select such parameters for human-like perceptual grouping. In this work, we exploit the diversity of segments produced by different choices of parameters. We scan the segmentation parameter space and generate a collection of image segmentation hypotheses (from highly over-segmented to under-segmented). These are fed into a cost minimization framework that produces the final segmentation by selecting segments that: (1) better describe the natural contours of the image, and (2) are more stable and persistent among all the segmentation hypotheses. We compare our algorithm's performance with state-of-the-art algorithms, showing that we can achieve improved results. We also show that our framework is robust to the choice of segmentation kernel that produces the initial set of hypotheses.
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