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Jan 23

Generative Marginalization Models

We introduce marginalization models (MaMs), a new family of generative models for high-dimensional discrete data. They offer scalable and flexible generative modeling with tractable likelihoods by explicitly modeling all induced marginal distributions. Marginalization models enable fast evaluation of arbitrary marginal probabilities with a single forward pass of the neural network, which overcomes a major limitation of methods with exact marginal inference, such as autoregressive models (ARMs). We propose scalable methods for learning the marginals, grounded in the concept of "marginalization self-consistency". Unlike previous methods, MaMs support scalable training of any-order generative models for high-dimensional problems under the setting of energy-based training, where the goal is to match the learned distribution to a given desired probability (specified by an unnormalized (log) probability function such as energy function or reward function). We demonstrate the effectiveness of the proposed model on a variety of discrete data distributions, including binary images, language, physical systems, and molecules, for maximum likelihood and energy-based training settings. MaMs achieve orders of magnitude speedup in evaluating the marginal probabilities on both settings. For energy-based training tasks, MaMs enable any-order generative modeling of high-dimensional problems beyond the capability of previous methods. Code is at https://github.com/PrincetonLIPS/MaM.

  • 3 authors
·
Oct 19, 2023

Plug-and-Play Context Feature Reuse for Efficient Masked Generation

Masked generative models (MGMs) have emerged as a powerful framework for image synthesis, combining parallel decoding with strong bidirectional context modeling. However, generating high-quality samples typically requires many iterative decoding steps, resulting in high inference costs. A straightforward way to speed up generation is by decoding more tokens in each step, thereby reducing the total number of steps. However, when many tokens are decoded simultaneously, the model can only estimate the univariate marginal distributions independently, failing to capture the dependency among them. As a result, reducing the number of steps significantly compromises generation fidelity. In this work, we introduce ReCAP (Reused Context-Aware Prediction), a plug-and-play module that accelerates inference in MGMs by constructing low-cost steps via reusing feature embeddings from previously decoded context tokens. ReCAP interleaves standard full evaluations with lightweight steps that cache and reuse context features, substantially reducing computation while preserving the benefits of fine-grained, iterative generation. We demonstrate its effectiveness on top of three representative MGMs (MaskGIT, MAGE, and MAR), including both discrete and continuous token spaces and covering diverse architectural designs. In particular, on ImageNet256 class-conditional generation, ReCAP achieves up to 2.4x faster inference than the base model with minimal performance drop, and consistently delivers better efficiency-fidelity trade-offs under various generation settings.

  • 4 authors
·
May 25, 2025

Efficient In-Context Learning in Vision-Language Models for Egocentric Videos

Recent advancements in text-only large language models (LLMs) have highlighted the benefit of in-context learning for adapting to new tasks with a few demonstrations. However, extending in-context learning to large vision-language models (VLMs) using a huge amount of naturalistic vision-language data has shown limited success, particularly for egocentric videos, due to high data collection costs. We propose a novel training method Efficient In-context Learning on Egocentric Videos (EILEV), which elicits in-context learning in VLMs for egocentric videos without requiring massive, naturalistic egocentric video datasets. EILEV involves architectural and training data adaptations to allow the model to process contexts interleaved with video clips and narrations, sampling of in-context examples with clusters of similar verbs and nouns, use of data with skewed marginal distributions with a long tail of infrequent verbs and nouns, as well as homonyms and synonyms. Our evaluations show that EILEV-trained models outperform larger VLMs trained on a huge amount of naturalistic data in in-context learning. Furthermore, they can generalize to not only out-of-distribution, but also novel, rare egocentric videos and texts via in-context learning, demonstrating potential for applications requiring cost-effective training, and rapid post-deployment adaptability. Our code and demo are available at https://github.com/yukw777/EILEV.

  • 4 authors
·
Nov 28, 2023

One Transformer Fits All Distributions in Multi-Modal Diffusion at Scale

This paper proposes a unified diffusion framework (dubbed UniDiffuser) to fit all distributions relevant to a set of multi-modal data in one model. Our key insight is -- learning diffusion models for marginal, conditional, and joint distributions can be unified as predicting the noise in the perturbed data, where the perturbation levels (i.e. timesteps) can be different for different modalities. Inspired by the unified view, UniDiffuser learns all distributions simultaneously with a minimal modification to the original diffusion model -- perturbs data in all modalities instead of a single modality, inputs individual timesteps in different modalities, and predicts the noise of all modalities instead of a single modality. UniDiffuser is parameterized by a transformer for diffusion models to handle input types of different modalities. Implemented on large-scale paired image-text data, UniDiffuser is able to perform image, text, text-to-image, image-to-text, and image-text pair generation by setting proper timesteps without additional overhead. In particular, UniDiffuser is able to produce perceptually realistic samples in all tasks and its quantitative results (e.g., the FID and CLIP score) are not only superior to existing general-purpose models but also comparable to the bespoken models (e.g., Stable Diffusion and DALL-E 2) in representative tasks (e.g., text-to-image generation).

  • 10 authors
·
Mar 11, 2023

Your Absorbing Discrete Diffusion Secretly Models the Conditional Distributions of Clean Data

Discrete diffusion models with absorbing processes have shown promise in language modeling. The key quantities to be estimated are the ratios between the marginal probabilities of two transitive states at all timesteps, called the concrete score. In this paper, we reveal that the concrete score in absorbing diffusion can be expressed as conditional probabilities of clean data, multiplied by a time-dependent scalar in an analytic form. Motivated by this finding, we propose reparameterized absorbing discrete diffusion (RADD), a dedicated diffusion model without time-condition that characterizes the time-independent conditional probabilities. Besides its simplicity, RADD can reduce the number of function evaluations (NFEs) by caching the output of the time-independent network when the noisy sample remains unchanged in a sampling interval. Empirically, RADD is up to 3.5 times faster while achieving similar performance with the strongest baseline. Built upon the new perspective of conditional distributions, we further unify absorbing discrete diffusion and any-order autoregressive models (AO-ARMs), showing that the upper bound on the negative log-likelihood for the diffusion model can be interpreted as an expected negative log-likelihood for AO-ARMs. Further, our RADD models achieve SOTA performance among diffusion models on 5 zero-shot language modeling benchmarks (measured by perplexity) at the GPT-2 scale. Our code is available at https://github.com/ML-GSAI/RADD.

  • 7 authors
·
Jun 6, 2024

Bridging the Training-Inference Gap in LLMs by Leveraging Self-Generated Tokens

Language models are often trained to maximize the likelihood of the next token given past tokens in the training dataset. However, during inference time, they are utilized differently, generating text sequentially and auto-regressively by using previously generated tokens as input to predict the next one. Marginal differences in predictions at each step can cascade over successive steps, resulting in different distributions from what the models were trained for and potentially leading to unpredictable behavior. This paper proposes two simple approaches based on model own generation to address this discrepancy between the training and inference time. Our first approach is Batch-Scheduled Sampling, where, during training, we stochastically choose between the ground-truth token from the dataset and the model's own generated token as input to predict the next token. This is done in an offline manner, modifying the context window by interleaving ground-truth tokens with those generated by the model. Our second approach is Reference-Answer-based Correction, where we explicitly incorporate a self-correction capability into the model during training. This enables the model to effectively self-correct the gaps between the generated sequences and the ground truth data without relying on an external oracle model. By incorporating our proposed strategies during training, we have observed an overall improvement in performance compared to baseline methods, as demonstrated by our extensive experiments using summarization, general question-answering, and math question-answering tasks.

  • 7 authors
·
Oct 18, 2024

JEN-1 Composer: A Unified Framework for High-Fidelity Multi-Track Music Generation

With rapid advances in generative artificial intelligence, the text-to-music synthesis task has emerged as a promising direction for music generation from scratch. However, finer-grained control over multi-track generation remains an open challenge. Existing models exhibit strong raw generation capability but lack the flexibility to compose separate tracks and combine them in a controllable manner, differing from typical workflows of human composers. To address this issue, we propose JEN-1 Composer, a unified framework to efficiently model marginal, conditional, and joint distributions over multi-track music via a single model. JEN-1 Composer framework exhibits the capacity to seamlessly incorporate any diffusion-based music generation system, e.g. Jen-1, enhancing its capacity for versatile multi-track music generation. We introduce a curriculum training strategy aimed at incrementally instructing the model in the transition from single-track generation to the flexible generation of multi-track combinations. During the inference, users have the ability to iteratively produce and choose music tracks that meet their preferences, subsequently creating an entire musical composition incrementally following the proposed Human-AI co-composition workflow. Quantitative and qualitative assessments demonstrate state-of-the-art performance in controllable and high-fidelity multi-track music synthesis. The proposed JEN-1 Composer represents a significant advance toward interactive AI-facilitated music creation and composition. Demos will be available at https://jenmusic.ai/audio-demos.

  • 4 authors
·
Oct 29, 2023

OTSurv: A Novel Multiple Instance Learning Framework for Survival Prediction with Heterogeneity-aware Optimal Transport

Survival prediction using whole slide images (WSIs) can be formulated as a multiple instance learning (MIL) problem. However, existing MIL methods often fail to explicitly capture pathological heterogeneity within WSIs, both globally -- through long-tailed morphological distributions, and locally through -- tile-level prediction uncertainty. Optimal transport (OT) provides a principled way of modeling such heterogeneity by incorporating marginal distribution constraints. Building on this insight, we propose OTSurv, a novel MIL framework from an optimal transport perspective. Specifically, OTSurv formulates survival predictions as a heterogeneity-aware OT problem with two constraints: (1) global long-tail constraint that models prior morphological distributions to avert both mode collapse and excessive uniformity by regulating transport mass allocation, and (2) local uncertainty-aware constraint that prioritizes high-confidence patches while suppressing noise by progressively raising the total transport mass. We then recast the initial OT problem, augmented by these constraints, into an unbalanced OT formulation that can be solved with an efficient, hardware-friendly matrix scaling algorithm. Empirically, OTSurv sets new state-of-the-art results across six popular benchmarks, achieving an absolute 3.6% improvement in average C-index. In addition, OTSurv achieves statistical significance in log-rank tests and offers high interpretability, making it a powerful tool for survival prediction in digital pathology. Our codes are available at https://github.com/Y-Research-SBU/OTSurv.

  • 5 authors
·
Jun 25, 2025

An Efficient Knowledge Transfer Strategy for Spiking Neural Networks from Static to Event Domain

Spiking neural networks (SNNs) are rich in spatio-temporal dynamics and are suitable for processing event-based neuromorphic data. However, event-based datasets are usually less annotated than static datasets. This small data scale makes SNNs prone to overfitting and limits their performance. In order to improve the generalization ability of SNNs on event-based datasets, we use static images to assist SNN training on event data. In this paper, we first discuss the domain mismatch problem encountered when directly transferring networks trained on static datasets to event data. We argue that the inconsistency of feature distributions becomes a major factor hindering the effective transfer of knowledge from static images to event data. To address this problem, we propose solutions in terms of two aspects: feature distribution and training strategy. Firstly, we propose a knowledge transfer loss, which consists of domain alignment loss and spatio-temporal regularization. The domain alignment loss learns domain-invariant spatial features by reducing the marginal distribution distance between the static image and the event data. Spatio-temporal regularization provides dynamically learnable coefficients for domain alignment loss by using the output features of the event data at each time step as a regularization term. In addition, we propose a sliding training strategy, which gradually replaces static image inputs probabilistically with event data, resulting in a smoother and more stable training for the network. We validate our method on neuromorphic datasets, including N-Caltech101, CEP-DVS, and N-Omniglot. The experimental results show that our proposed method achieves better performance on all datasets compared to the current state-of-the-art methods. Code is available at https://github.com/Brain-Cog-Lab/Transfer-for-DVS.

  • 6 authors
·
Mar 23, 2023

Training-Free Unsupervised Prompt for Vision-Language Models

Prompt learning has become the most effective paradigm for adapting large pre-trained vision-language models (VLMs) to downstream tasks. Recently, unsupervised prompt tuning methods, such as UPL and POUF, directly leverage pseudo-labels as supervisory information to fine-tune additional adaptation modules on unlabeled data. However, inaccurate pseudo labels easily misguide the tuning process and result in poor representation capabilities. In light of this, we propose Training-Free Unsupervised Prompts (TFUP), which maximally preserves the inherent representation capabilities and enhances them with a residual connection to similarity-based prediction probabilities in a training-free and labeling-free manner. Specifically, we integrate both instance confidence and prototype scores to select representative samples, which are used to customize a reliable Feature Cache Model (FCM) for training-free inference. Then, we design a Multi-level Similarity Measure (MSM) that considers both feature-level and semantic-level similarities to calculate the distance between each test image and the cached sample as the weight of the corresponding cached label to generate similarity-based prediction probabilities. In this way, TFUP achieves surprising performance, even surpassing the training-base method on multiple classification datasets. Based on our TFUP, we propose a training-based approach (TFUP-T) to further boost the adaptation performance. In addition to the standard cross-entropy loss, TFUP-T adopts an additional marginal distribution entropy loss to constrain the model from a global perspective. Our TFUP-T achieves new state-of-the-art classification performance compared to unsupervised and few-shot adaptation approaches on multiple benchmarks. In particular, TFUP-T improves the classification accuracy of POUF by 3.3% on the most challenging Domain-Net dataset.

  • 7 authors
·
Apr 25, 2024

PUFM++: Point Cloud Upsampling via Enhanced Flow Matching

Recent advances in generative modeling have demonstrated strong promise for high-quality point cloud upsampling. In this work, we present PUFM++, an enhanced flow-matching framework for reconstructing dense and accurate point clouds from sparse, noisy, and partial observations. PUFM++ improves flow matching along three key axes: (i) geometric fidelity, (ii) robustness to imperfect input, and (iii) consistency with downstream surface-based tasks. We introduce a two-stage flow-matching strategy that first learns a direct, straight-path flow from sparse inputs to dense targets, and then refines it using noise-perturbed samples to approximate the terminal marginal distribution better. To accelerate and stabilize inference, we propose a data-driven adaptive time scheduler that improves sampling efficiency based on interpolation behavior. We further impose on-manifold constraints during sampling to ensure that generated points remain aligned with the underlying surface. Finally, we incorporate a recurrent interface network~(RIN) to strengthen hierarchical feature interactions and boost reconstruction quality. Extensive experiments on synthetic benchmarks and real-world scans show that PUFM++ sets a new state of the art in point cloud upsampling, delivering superior visual fidelity and quantitative accuracy across a wide range of tasks. Code and pretrained models are publicly available at https://github.com/Holmes-Alan/Enhanced_PUFM.

  • 4 authors
·
Dec 24, 2025

Identifying and Solving Conditional Image Leakage in Image-to-Video Diffusion Model

Diffusion models have obtained substantial progress in image-to-video (I2V) generation. However, such models are not fully understood. In this paper, we report a significant but previously overlooked issue in I2V diffusion models (I2V-DMs), namely, conditional image leakage. I2V-DMs tend to over-rely on the conditional image at large time steps, neglecting the crucial task of predicting the clean video from noisy inputs, which results in videos lacking dynamic and vivid motion. We further address this challenge from both inference and training aspects by presenting plug-and-play strategies accordingly. First, we introduce a training-free inference strategy that starts the generation process from an earlier time step to avoid the unreliable late-time steps of I2V-DMs, as well as an initial noise distribution with optimal analytic expressions (Analytic-Init) by minimizing the KL divergence between it and the actual marginal distribution to effectively bridge the training-inference gap. Second, to mitigate conditional image leakage during training, we design a time-dependent noise distribution for the conditional image, which favors high noise levels at large time steps to sufficiently interfere with the conditional image. We validate these strategies on various I2V-DMs using our collected open-domain image benchmark and the UCF101 dataset. Extensive results demonstrate that our methods outperform baselines by producing videos with more dynamic and natural motion without compromising image alignment and temporal consistency. The project page: https://cond-image-leak.github.io/.

  • 6 authors
·
Jun 22, 2024

A likelihood approach to nonparametric estimation of a singular distribution using deep generative models

We investigate statistical properties of a likelihood approach to nonparametric estimation of a singular distribution using deep generative models. More specifically, a deep generative model is used to model high-dimensional data that are assumed to concentrate around some low-dimensional structure. Estimating the distribution supported on this low-dimensional structure, such as a low-dimensional manifold, is challenging due to its singularity with respect to the Lebesgue measure in the ambient space. In the considered model, a usual likelihood approach can fail to estimate the target distribution consistently due to the singularity. We prove that a novel and effective solution exists by perturbing the data with an instance noise, which leads to consistent estimation of the underlying distribution with desirable convergence rates. We also characterize the class of distributions that can be efficiently estimated via deep generative models. This class is sufficiently general to contain various structured distributions such as product distributions, classically smooth distributions and distributions supported on a low-dimensional manifold. Our analysis provides some insights on how deep generative models can avoid the curse of dimensionality for nonparametric distribution estimation. We conduct a thorough simulation study and real data analysis to empirically demonstrate that the proposed data perturbation technique improves the estimation performance significantly.

  • 4 authors
·
May 9, 2021

Weighted least-squares approximation with determinantal point processes and generalized volume sampling

We consider the problem of approximating a function from L^2 by an element of a given m-dimensional space V_m, associated with some feature map varphi, using evaluations of the function at random points x_1,dots,x_n. After recalling some results on optimal weighted least-squares using independent and identically distributed points, we consider weighted least-squares using projection determinantal point processes (DPP) or volume sampling. These distributions introduce dependence between the points that promotes diversity in the selected features varphi(x_i). We first provide a generalized version of volume-rescaled sampling yielding quasi-optimality results in expectation with a number of samples n = O(mlog(m)), that means that the expected L^2 error is bounded by a constant times the best approximation error in L^2. Also, further assuming that the function is in some normed vector space H continuously embedded in L^2, we further prove that the approximation is almost surely bounded by the best approximation error measured in the H-norm. This includes the cases of functions from L^infty or reproducing kernel Hilbert spaces. Finally, we present an alternative strategy consisting in using independent repetitions of projection DPP (or volume sampling), yielding similar error bounds as with i.i.d. or volume sampling, but in practice with a much lower number of samples. Numerical experiments illustrate the performance of the different strategies.

  • 2 authors
·
Dec 21, 2023

A Flexible Parametric Modelling Framework for Survival Analysis

We introduce a general, flexible, parametric survival modelling framework which encompasses key shapes of hazard function (constant, increasing, decreasing, up-then-down, down-then-up), various common survival distributions (log-logistic, Burr type XII, Weibull, Gompertz), and includes defective distributions (i.e., cure models). This generality is achieved using four basic distributional parameters: two scale-type parameters and two shape parameters. Generalising to covariate dependence, the scale-type regression components correspond to accelerated failure time (AFT) and proportional hazards (PH) models. Therefore, this general formulation unifies the most popular survival models which allows us to consider the practical value of possible modelling choices for survival data. Furthermore, in line with our proposed flexible baseline distribution, we advocate the use of multi-parameter regression in which more than one distributional parameter depends on covariates - rather than the usual convention of having a single covariate-dependent (scale) parameter. While many choices are available, we suggest introducing covariates through just one or other of the two scale parameters, which covers AFT and PH models, in combination with a `power' shape parameter, which allows for more complex non-AFT/non-PH effects, while the other shape parameter remains covariate-independent, and handles automatic selection of the baseline distribution. We explore inferential issues in simulations, both with and without a covariate, with particular focus on evidence concerning the need, or otherwise, to include both AFT and PH parameters. We illustrate the efficacy of our modelling framework by investigating differences between treatment groups using data from a lung cancer study and a melanoma study. Censoring is accommodated throughout.

  • 3 authors
·
Jan 10, 2019

Regression Discontinuity Design with Distribution-Valued Outcomes

This article introduces Regression Discontinuity Design (RDD) with Distribution-Valued Outcomes (R3D), extending the standard RDD framework to settings where the outcome is a distribution rather than a scalar. Such settings arise when treatment is assigned at a higher level of aggregation than the outcome-for example, when a subsidy is allocated based on a firm-level revenue cutoff while the outcome of interest is the distribution of employee wages within the firm. Since standard RDD methods cannot accommodate such two-level randomness, I propose a novel approach based on random distributions. The target estimand is a "local average quantile treatment effect", which averages across random quantiles. To estimate this target, I introduce two related approaches: one that extends local polynomial regression to random quantiles and another based on local Fr\'echet regression, a form of functional regression. For both estimators, I establish asymptotic normality and develop uniform, debiased confidence bands together with a data-driven bandwidth selection procedure. Simulations validate these theoretical properties and show existing methods to be biased and inconsistent in this setting. I then apply the proposed methods to study the effects of gubernatorial party control on within-state income distributions in the US, using a close-election design. The results suggest a classic equality-efficiency tradeoff under Democratic governorship, driven by reductions in income at the top of the distribution.

  • 1 authors
·
Apr 4, 2025

An Efficient Tester-Learner for Halfspaces

We give the first efficient algorithm for learning halfspaces in the testable learning model recently defined by Rubinfeld and Vasilyan (2023). In this model, a learner certifies that the accuracy of its output hypothesis is near optimal whenever the training set passes an associated test, and training sets drawn from some target distribution -- e.g., the Gaussian -- must pass the test. This model is more challenging than distribution-specific agnostic or Massart noise models where the learner is allowed to fail arbitrarily if the distributional assumption does not hold. We consider the setting where the target distribution is Gaussian (or more generally any strongly log-concave distribution) in d dimensions and the noise model is either Massart or adversarial (agnostic). For Massart noise, our tester-learner runs in polynomial time and outputs a hypothesis with (information-theoretically optimal) error opt + epsilon for any strongly log-concave target distribution. For adversarial noise, our tester-learner obtains error O(opt) + epsilon in polynomial time when the target distribution is Gaussian; for strongly log-concave distributions, we obtain O(opt) + epsilon in quasipolynomial time. Prior work on testable learning ignores the labels in the training set and checks that the empirical moments of the covariates are close to the moments of the base distribution. Here we develop new tests of independent interest that make critical use of the labels and combine them with the moment-matching approach of Gollakota et al. (2023). This enables us to simulate a variant of the algorithm of Diakonikolas et al. (2020) for learning noisy halfspaces using nonconvex SGD but in the testable learning setting.

  • 4 authors
·
Feb 28, 2023

The Slepian model based independent interval approximation of persistency and zero-level exceedance distributions

In physics and engineering literature, the distribution of the excursion-above-zero time distribution (exceedance distribution) for a stationary Gaussian process has been approximated by a stationary switching process with independently distributed switching times. The approach matched the covariance of the clipped Gaussian process with the one for the stationary switching process and the distribution of the latter was used as the so-called independent interval approximation (IIA). The approach successfully assessed the persistency exponent for many physically important processes but left an unanswered question when such an approach leads to a mathematically meaningful and proper exceedance distribution. Here we address this question by proposing an alternative matching of the expected values of the clipped Slepian process and the corresponding switched process initiated at the origin. The method has allowed resolving the mathematical correctness of the matching method for a large subclass of the Gaussian processes with monotonic covariance, for which we provide a sufficient condition for the validity of the IIA. Within this class, the IIA produces a valid distribution for the excursion time and is represented in an explicit stochastic form that connects directly to the covariance of the underlying Gaussian process. We compare the excursion level distributions as well as the corresponding persistency exponents obtained through the IIA method with numerically computed exact distributions, and the simulated distribution for several important Gaussian models. We also argue that for stationary Gaussian processes with a non-monotonic covariance, the IIA fails and should not be used.

  • 2 authors
·
Jan 3, 2024

TabEBM: A Tabular Data Augmentation Method with Distinct Class-Specific Energy-Based Models

Data collection is often difficult in critical fields such as medicine, physics, and chemistry. As a result, classification methods usually perform poorly with these small datasets, leading to weak predictive performance. Increasing the training set with additional synthetic data, similar to data augmentation in images, is commonly believed to improve downstream classification performance. However, current tabular generative methods that learn either the joint distribution p(x, y) or the class-conditional distribution p(x mid y) often overfit on small datasets, resulting in poor-quality synthetic data, usually worsening classification performance compared to using real data alone. To solve these challenges, we introduce TabEBM, a novel class-conditional generative method using Energy-Based Models (EBMs). Unlike existing methods that use a shared model to approximate all class-conditional densities, our key innovation is to create distinct EBM generative models for each class, each modelling its class-specific data distribution individually. This approach creates robust energy landscapes, even in ambiguous class distributions. Our experiments show that TabEBM generates synthetic data with higher quality and better statistical fidelity than existing methods. When used for data augmentation, our synthetic data consistently improves the classification performance across diverse datasets of various sizes, especially small ones. Code is available at https://github.com/andreimargeloiu/TabEBM.

  • 4 authors
·
Sep 24, 2024

Von Mises Mixture Distributions for Molecular Conformation Generation

Molecules are frequently represented as graphs, but the underlying 3D molecular geometry (the locations of the atoms) ultimately determines most molecular properties. However, most molecules are not static and at room temperature adopt a wide variety of geometries or conformations. The resulting distribution on geometries p(x) is known as the Boltzmann distribution, and many molecular properties are expectations computed under this distribution. Generating accurate samples from the Boltzmann distribution is therefore essential for computing these expectations accurately. Traditional sampling-based methods are computationally expensive, and most recent machine learning-based methods have focused on identifying modes in this distribution rather than generating true samples. Generating such samples requires capturing conformational variability, and it has been widely recognized that the majority of conformational variability in molecules arises from rotatable bonds. In this work, we present VonMisesNet, a new graph neural network that captures conformational variability via a variational approximation of rotatable bond torsion angles as a mixture of von Mises distributions. We demonstrate that VonMisesNet can generate conformations for arbitrary molecules in a way that is both physically accurate with respect to the Boltzmann distribution and orders of magnitude faster than existing sampling methods.

  • 3 authors
·
Jun 12, 2023

Denotational validation of higher-order Bayesian inference

We present a modular semantic account of Bayesian inference algorithms for probabilistic programming languages, as used in data science and machine learning. Sophisticated inference algorithms are often explained in terms of composition of smaller parts. However, neither their theoretical justification nor their implementation reflects this modularity. We show how to conceptualise and analyse such inference algorithms as manipulating intermediate representations of probabilistic programs using higher-order functions and inductive types, and their denotational semantics. Semantic accounts of continuous distributions use measurable spaces. However, our use of higher-order functions presents a substantial technical difficulty: it is impossible to define a measurable space structure over the collection of measurable functions between arbitrary measurable spaces that is compatible with standard operations on those functions, such as function application. We overcome this difficulty using quasi-Borel spaces, a recently proposed mathematical structure that supports both function spaces and continuous distributions. We define a class of semantic structures for representing probabilistic programs, and semantic validity criteria for transformations of these representations in terms of distribution preservation. We develop a collection of building blocks for composing representations. We use these building blocks to validate common inference algorithms such as Sequential Monte Carlo and Markov Chain Monte Carlo. To emphasize the connection between the semantic manipulation and its traditional measure theoretic origins, we use Kock's synthetic measure theory. We demonstrate its usefulness by proving a quasi-Borel counterpart to the Metropolis-Hastings-Green theorem.

  • 10 authors
·
Nov 8, 2017

Generative Distribution Embeddings

Many real-world problems require reasoning across multiple scales, demanding models which operate not on single data points, but on entire distributions. We introduce generative distribution embeddings (GDE), a framework that lifts autoencoders to the space of distributions. In GDEs, an encoder acts on sets of samples, and the decoder is replaced by a generator which aims to match the input distribution. This framework enables learning representations of distributions by coupling conditional generative models with encoder networks which satisfy a criterion we call distributional invariance. We show that GDEs learn predictive sufficient statistics embedded in the Wasserstein space, such that latent GDE distances approximately recover the W_2 distance, and latent interpolation approximately recovers optimal transport trajectories for Gaussian and Gaussian mixture distributions. We systematically benchmark GDEs against existing approaches on synthetic datasets, demonstrating consistently stronger performance. We then apply GDEs to six key problems in computational biology: learning representations of cell populations from lineage-tracing data (150K cells), predicting perturbation effects on single-cell transcriptomes (1M cells), predicting perturbation effects on cellular phenotypes (20M single-cell images), modeling tissue-specific DNA methylation patterns (253M sequences), designing synthetic yeast promoters (34M sequences), and spatiotemporal modeling of viral protein sequences (1M sequences).

  • 5 authors
·
May 23, 2025

MLE convergence speed to information projection of exponential family: Criterion for model dimension and sample size -- complete proof version--

For a parametric model of distributions, the closest distribution in the model to the true distribution located outside the model is considered. Measuring the closeness between two distributions with the Kullback-Leibler (K-L) divergence, the closest distribution is called the "information projection." The estimation risk of the maximum likelihood estimator (MLE) is defined as the expectation of K-L divergence between the information projection and the predictive distribution with plugged-in MLE. Here, the asymptotic expansion of the risk is derived up to n^{-2}-order, and the sufficient condition on the risk for the Bayes error rate between the true distribution and the information projection to be lower than a specified value is investigated. Combining these results, the "p-n criterion" is proposed, which determines whether the MLE is sufficiently close to the information projection for the given model and sample. In particular, the criterion for an exponential family model is relatively simple and can be used for a complex model with no explicit form of normalizing constant. This criterion can constitute a solution to the sample size or model acceptance problem. Use of the p-n criteria is demonstrated for two practical datasets. The relationship between the results and information criteria is also studied.

  • 1 authors
·
May 19, 2021

Distribution Transformers: Fast Approximate Bayesian Inference With On-The-Fly Prior Adaptation

While Bayesian inference provides a principled framework for reasoning under uncertainty, its widespread adoption is limited by the intractability of exact posterior computation, necessitating the use of approximate inference. However, existing methods are often computationally expensive, or demand costly retraining when priors change, limiting their utility, particularly in sequential inference problems such as real-time sensor fusion. To address these challenges, we introduce the Distribution Transformer -- a novel architecture that can learn arbitrary distribution-to-distribution mappings. Our method can be trained to map a prior to the corresponding posterior, conditioned on some dataset -- thus performing approximate Bayesian inference. Our novel architecture represents a prior distribution as a (universally-approximating) Gaussian Mixture Model (GMM), and transforms it into a GMM representation of the posterior. The components of the GMM attend to each other via self-attention, and to the datapoints via cross-attention. We demonstrate that Distribution Transformers both maintain flexibility to vary the prior, and significantly reduces computation times-from minutes to milliseconds-while achieving log-likelihood performance on par with or superior to existing approximate inference methods across tasks such as sequential inference, quantum system parameter inference, and Gaussian Process predictive posterior inference with hyperpriors.

  • 4 authors
·
Feb 4, 2025

Machine Learning with Multitype Protected Attributes: Intersectional Fairness through Regularisation

Ensuring equitable treatment (fairness) across protected attributes (such as gender or ethnicity) is a critical issue in machine learning. Most existing literature focuses on binary classification, but achieving fairness in regression tasks-such as insurance pricing or hiring score assessments-is equally important. Moreover, anti-discrimination laws also apply to continuous attributes, such as age, for which many existing methods are not applicable. In practice, multiple protected attributes can exist simultaneously; however, methods targeting fairness across several attributes often overlook so-called "fairness gerrymandering", thereby ignoring disparities among intersectional subgroups (e.g., African-American women or Hispanic men). In this paper, we propose a distance covariance regularisation framework that mitigates the association between model predictions and protected attributes, in line with the fairness definition of demographic parity, and that captures both linear and nonlinear dependencies. To enhance applicability in the presence of multiple protected attributes, we extend our framework by incorporating two multivariate dependence measures based on distance covariance: the previously proposed joint distance covariance (JdCov) and our novel concatenated distance covariance (CCdCov), which effectively address fairness gerrymandering in both regression and classification tasks involving protected attributes of various types. We discuss and illustrate how to calibrate regularisation strength, including a method based on Jensen-Shannon divergence, which quantifies dissimilarities in prediction distributions across groups. We apply our framework to the COMPAS recidivism dataset and a large motor insurance claims dataset.

  • 5 authors
·
Sep 9, 2025

On the statistical theory of self-gravitating collisionless dark matter flow: Scale and redshift variation of velocity and density distributions

This paper studies the scale and redshift variation of density and velocity distributions in self-gravitating collisionless dark matter flow by a halo-based non-projection approach. All particles are divided into halo and out-of-halo particles for redshift variation of distributions. Without projecting particle fields onto a structured grid, the scale variation is analyzed by identifying all particle pairs on different scales r. We demonstrate that: i) Delaunay tessellation can be used to reconstruct the density field. The density correlation, spectrum, and dispersion functions were obtained, modeled, and compared with the N-body simulation; ii) the velocity distributions are symmetric on both small and large scales and are non-symmetric with a negative skewness on intermediate scales due to the inverse energy cascade at a constant rate varepsilon_u; iii) On small scales, the even order moments of pairwise velocity Delta u_L follow a two-thirds law (-varepsilon_ur)^{2/3}, while the odd order moments follow a linear scaling langle(Delta u_L)^{2n+1}rangle=(2n+1)langle(Delta u_L)^{2n}ranglelangleDelta u_Lrangler; iv) The scale variation of the velocity distributions was studied for longitudinal velocities u_L or u_L^{'}, pairwise velocity (velocity difference) Delta u_L=u_L^{'}-u_L and velocity sum Sigma u_L=u^{'}_L+u_L. Fully developed velocity fields are never Gaussian on any scale, despite that they can initially be Gaussian; v) On small scales, u_L and Sigma u_L can be modeled by a X distribution to maximize the system entropy; vi) On large scales, Delta u_L and Sigma u_L can be modeled by a logistic or a X distribution; vii) the redshift variation of the velocity distributions follows the evolution of the X distribution involving a shape parameter alpha(z) decreasing with time.

  • 1 authors
·
Feb 14, 2022