arXiv subjects

Francisco Vargas

Publications and source records attributed to Francisco Vargas.

At least 19 recordsLinked to original sources

arXiv2026

Free energy Estimation on Any State Space

Free energy estimation is a fundamental yet challenging problem, from physics to statistics. Classical approaches rely on thermodynamic transformations, ranging from direct estimation, quasistatic integration, to finite-time averaging. Recent work [He and Du et al., 2025] learns neural transports to significantly accelerate the efficiency in the finite-time regime. In this paper, we generalize this framework to arbitrary state spaces. Building on this view, we develop a generalized neural transport learning approach for efficient estimation. Experiments validate the effectiveness and efficiency of the proposed method beyond continuous settings, extending to discrete and multimodal spaces as well as autoregressive settings. Beyond free energy estimation, we establish algebraic identities and reveal a group-theoretic structure linking infinitesimal time reversal and generalized Doob's $h$-transforms, showing that their compositions form a generalized dihedral group.

stat.ML↗

arXiv2026

CMAD: Cooperative Multi-Agent Diffusion via Stochastic Optimal Control

Continuous-time generative models have achieved remarkable success in image restoration and synthesis. However, controlling the composition of multiple pre-trained models remains an open challenge. Current approaches largely treat composition as an algebraic composition of probability densities, such as via products or mixtures of experts. This perspective assumes the target distribution is known explicitly, which is almost never the case. In this work, we propose a different paradigm that formulates compositional generation as a cooperative Stochastic Optimal Control problem. Rather than combining probability densities, we treat pre-trained diffusion models as interacting agents whose diffusion trajectories are jointly steered, via optimal control, toward a shared objective defined on their aggregated output. We validate our framework on conditional MNIST generation and compare it against a naïve inference-time DPS-style baseline replacing learned cooperative control with per-step gradient guidance.

cs.LG↗

arXiv2026

RNE: plug-and-play diffusion inference-time control and energy-based training

Diffusion models generate data by removing noise gradually, which corresponds to the time-reversal of a noising process. However, access to only the denoising kernels is often insufficient. In many applications, we need the knowledge of the marginal densities along the generation trajectory, which enables tasks such as inference-time control. To address this gap, in this paper, we introduce the Radon-Nikodym Estimator (RNE). Based on the concept of the \textit{density ratio} between path distributions, it reveals a fundamental connection between marginal densities and transition kernels, providing a flexible plug-and-play framework that unifies (1) diffusion density estimation, (2) inference-time control, and (3) energy-based diffusion training under a single perspective. Experiments demonstrate that RNE delivers strong results in inference-time control applications, such as annealing and model composition, with promising inference-time scaling performance, and achieves a simple yet efficient regularisation for training energy-based diffusion models. Additionally, our proposed RNE is modality-agnostic and applicable not only to continuous diffusion models but also to their discrete diffusion counterparts.

cs.LG↗

arXiv2026

Accelerated Parallel Tempering via Neural Transports

Markov Chain Monte Carlo (MCMC) algorithms are essential tools in computational statistics for sampling from unnormalised probability distributions, but can be fragile when targeting high-dimensional, multimodal, or complex target distributions. Parallel Tempering (PT) enhances MCMC's sample efficiency through annealing and parallel computation, propagating samples from tractable reference distributions to intractable targets via state swapping across interpolating distributions. The effectiveness of PT is limited by the often minimal overlap between adjacent distributions in challenging problems, which requires increasing the computational resources to compensate. We introduce a framework that accelerates PT by leveraging neural samplers -- including normalising flows, diffusion models, and controlled diffusions -- to reduce the required overlap. Our approach utilises neural samplers in parallel, circumventing the computational burden of neural samplers while preserving the asymptotic consistency of classical PT. We demonstrate theoretically and empirically on a variety of multimodal sampling problems that our method improves sample quality, reduces the computational cost compared to classical PT, and enables efficient free energy/normalising constant estimation.

stat.ML↗

arXiv2026

CREPE: Controlling Diffusion with Replica Exchange

Inference-time control of diffusion models aims to steer model outputs to satisfy new constraints without retraining. Previous approaches have mostly relied on heuristic guidance or have been coupled with Sequential Monte Carlo (SMC) for bias correction. In this paper, we propose a flexible alternative based on replica exchange, an algorithm designed initially for sampling problems. We refer to this method as CREPE (Controlling with REPlica Exchange). Unlike SMC, CREPE: (1) generates particles sequentially, (2) maintains high diversity in the generated samples after a burn-in period, and (3) enables online refinement or early termination. We demonstrate its versatility across various tasks, including temperature annealing, reward-tilting, model composition and classifier-free guidance debiasing, with competitive performance compared to prior SMC methods.

cs.LG↗

arXiv2026

Mirror Bridges Between Probability Measures

Resampling from a target measure whose density is unknown is a fundamental problem in mathematical statistics and machine learning. A setting that dominates the machine learning literature consists of learning a map from an easy-to-sample prior, such as the Gaussian distribution, to a target measure. Under this model, samples from the prior are pushed forward to generate a new sample on the target measure, which is often difficult to sample from directly. A related problem of particular interest is that of generating a new sample proximate to or otherwise conditioned on a given input sample. In this paper, we propose a new model called the mirror bridge to solve this problem of conditional resampling. Our key observation is that solving the Schrödinger bridge problem between a distribution and itself provides a natural way to produce new samples, giving in-distribution variations of an input data point. We demonstrate how to efficiently estimate the solution of this largely overlooked version of the Schrödinger bridge problem. We show that our proposed method leads to significant algorithmic simplifications over existing alternatives, in addition to providing control over in-distribution variation. Empirically, we demonstrate how these benefits can be leveraged to produce proximal samples in a number of application domains.

cs.LG↗

arXiv2026

Iterative Importance Fine-tuning of Diffusion Models

Diffusion models are an important tool for generative modelling, serving as effective priors in applications such as imaging and protein design. A key challenge in applying diffusion models for downstream tasks is efficiently sampling from resulting posterior distributions, which can be addressed using Doob's $h$-transform. This work introduces a self-supervised algorithm for fine-tuning diffusion models by learning the optimal control, enabling amortised conditional sampling. Our method iteratively refines the control using a synthetic dataset resampled with path-based importance weights. We demonstrate the effectiveness of this framework on class-conditional sampling, inverse problems and reward fine-tuning for text-to-image diffusion models.

cs.LG↗

arXiv2026

FEAT: Free energy Estimators with Adaptive Transport

We present Free energy Estimators with Adaptive Transport (FEAT), a novel framework for free energy estimation -- a critical challenge across scientific domains. FEAT leverages learned transports implemented via stochastic interpolants and provides consistent, minimum-variance estimators based on escorted Jarzynski equality and controlled Crooks theorem, alongside variational upper and lower bounds on free energy differences. Unifying equilibrium and non-equilibrium methods under a single theoretical framework, FEAT establishes a principled foundation for neural free energy calculations. Experimental validation on toy examples, molecular simulations, and quantum field theory demonstrates improvements over existing learning-based methods. Our PyTorch implementation is available at https://github.com/jiajunhe98/FEAT.

stat.ML↗

arXiv2025

Sampling from Energy distributions with Target Concrete Score Identity

We introduce the Target Concrete Score Identity Sampler (TCSIS), a method for sampling from unnormalized densities on discrete state spaces by learning the reverse dynamics of a Continuous-Time Markov Chain (CTMC). Our approach builds on a forward in time CTMC with a uniform noising kernel and relies on the proposed Target Concrete Score Identity, which relates the concrete score, the ratio of marginal probabilities of two states, to a ratio of expectations of Boltzmann factors under the forward uniform diffusion kernel. This formulation enables Monte Carlo estimation of the concrete score without requiring samples from the target distribution or computation of the partition function. We approximate the concrete score with a neural network and propose two algorithms: Self-Normalized TCSIS and Unbiased TCSIS. Finally, we demonstrate the effectiveness of TCSIS on problems from statistical physics.

cs.LG↗

arXiv2025

Gradient Variance Reveals Failure Modes in Flow-Based Generative Models

Rectified Flows learn ODE vector fields whose trajectories are straight between source and target distributions, enabling near one-step inference. We show that this straight-path objective conceals fundamental failure modes: under deterministic training, low gradient variance drives memorization of arbitrary training pairings, even when interpolant lines between pairs intersect. To analyze this mechanism, we study Gaussian-to-Gaussian transport and use the loss gradient variance across stochastic and deterministic regimes to characterize which vector fields optimization favors in each setting. We then show that, in a setting where all interpolating lines intersect, applying Rectified Flow yields the same specific pairings at inference as during training. More generally, we prove that a memorizing vector field exists even when training interpolants intersect, and that optimizing the straight-path objective converges to this ill-defined field. At inference, deterministic integration reproduces the exact training pairings. We validate our findings empirically on the CelebA dataset, confirming that deterministic interpolants induce memorization, while the injection of small noise restores generalization.

cs.LG↗

arXiv2025

Debiasing Guidance for Discrete Diffusion with Sequential Monte Carlo

Discrete diffusion models are a class of generative models that produce samples from an approximated data distribution within a discrete state space. Often, there is a need to target specific regions of the data distribution. Current guidance methods aim to sample from a distribution with mass proportional to $p_0(x_0) p(ζ|x_0)^α$ but fail to achieve this in practice. We introduce a Sequential Monte Carlo algorithm that generates unbiasedly from this target distribution, utilising the learnt unconditional and guided process. We validate our approach on low-dimensional distributions, controlled images and text generations. For text generation, our method provides strong control while maintaining low perplexity compared to guidance-based approaches.

cs.LG↗

arXiv2025

The impact of fine tuning in LLaMA on hallucinations for named entity extraction in legal documentation

The extraction of information about traffic accidents from legal documents is crucial for quantifying insurance company costs. Extracting entities such as percentages of physical and/or psychological disability and the involved compensation amounts is a challenging process, even for experts, due to the subtle arguments and reasoning in the court decision. A two-step procedure is proposed: first, segmenting the document identifying the most relevant segments, and then extracting the entities. For text segmentation, two methodologies are compared: a classic method based on regular expressions and a second approach that divides the document into blocks of n-tokens, which are then vectorized using multilingual models for semantic searches (text-embedding-ada-002/MiniLM-L12-v2 ). Subsequently, large language models (LLaMA-2 7b, 70b, LLaMA-3 8b, and GPT-4 Turbo) are applied with prompting to the selected segments for entity extraction. For the LLaMA models, fine-tuning is performed using LoRA. LLaMA-2 7b, even with zero temperature, shows a significant number of hallucinations in extractions which are an important contention point for named entity extraction. This work shows that these hallucinations are substantially reduced after finetuning the model. The performance of the methodology based on segment vectorization and subsequent use of LLMs significantly surpasses the classic method which achieves an accuracy of 39.5%. Among open-source models, LLaMA-2 70B with finetuning achieves the highest accuracy 79.4%, surpassing its base version 61.7%. Notably, the base LLaMA-3 8B model already performs comparably to the finetuned LLaMA-2 70B model, achieving 76.6%, highlighting the rapid progress in model development. Meanwhile, GPT-4 Turbo achieves the highest accuracy at 86.1%.

cs.CL↗

arXiv2025

Path Integral Optimiser: Global Optimisation via Neural Schrödinger-Föllmer Diffusion

We present an early investigation into the use of neural diffusion processes for global optimisation, focusing on Zhang et al.'s Path Integral Sampler. One can use the Boltzmann distribution to formulate optimization as solving a Schrödinger bridge sampling problem, then apply Girsanov's theorem with a simple (single-point) prior to frame it in stochastic control terms, and compute the solution's integral terms via a neural approximation (a Fourier MLP). We provide theoretical bounds for this optimiser, results on toy optimisation tasks, and a summary of the stochastic theory motivating the model. Ultimately, we found the optimiser to display promising per-step performance at optimisation tasks between 2 and 1,247 dimensions, but struggle to explore higher-dimensional spaces when faced with a 15.9k parameter model, indicating a need for work on adaptation in such environments.

cs.LG↗

arXiv2025

DEFT: Efficient Fine-Tuning of Diffusion Models by Learning the Generalised $h$-transform

Generative modelling paradigms based on denoising diffusion processes have emerged as a leading candidate for conditional sampling in inverse problems. In many real-world applications, we often have access to large, expensively trained unconditional diffusion models, which we aim to exploit for improving conditional sampling. Most recent approaches are motivated heuristically and lack a unifying framework, obscuring connections between them. Further, they often suffer from issues such as being very sensitive to hyperparameters, being expensive to train or needing access to weights hidden behind a closed API. In this work, we unify conditional training and sampling using the mathematically well-understood Doob's h-transform. This new perspective allows us to unify many existing methods under a common umbrella. Under this framework, we propose DEFT (Doob's h-transform Efficient FineTuning), a new approach for conditional generation that simply fine-tunes a very small network to quickly learn the conditional $h$-transform, while keeping the larger unconditional network unchanged. DEFT is much faster than existing baselines while achieving state-of-the-art performance across a variety of linear and non-linear benchmarks. On image reconstruction tasks, we achieve speedups of up to 1.6$\times$, while having the best perceptual quality on natural images and reconstruction performance on medical images. Further, we also provide initial experiments on protein motif scaffolding and outperform reconstruction guidance methods.

cs.LG↗

arXiv2025

Transport meets Variational Inference: Controlled Monte Carlo Diffusions

Connecting optimal transport and variational inference, we present a principled and systematic framework for sampling and generative modelling centred around divergences on path space. Our work culminates in the development of the \emph{Controlled Monte Carlo Diffusion} sampler (CMCD) for Bayesian computation, a score-based annealing technique that crucially adapts both forward and backward dynamics in a diffusion model. On the way, we clarify the relationship between the EM-algorithm and iterative proportional fitting (IPF) for Schr{ö}dinger bridges, deriving as well a regularised objective that bypasses the iterative bottleneck of standard IPF-updates. Finally, we show that CMCD has a strong foundation in the Jarzinsky and Crooks identities from statistical physics, and that it convincingly outperforms competing approaches across a wide array of experiments.

stat.ML↗

arXiv2025

No Trick, No Treat: Pursuits and Challenges Towards Simulation-free Training of Neural Samplers

We consider the sampling problem, where the aim is to draw samples from a distribution whose density is known only up to a normalization constant. Recent breakthroughs in generative modeling to approximate a high-dimensional data distribution have sparked significant interest in developing neural network-based methods for this challenging problem. However, neural samplers typically incur heavy computational overhead due to simulating trajectories during training. This motivates the pursuit of simulation-free training procedures of neural samplers. In this work, we propose an elegant modification to previous methods, which allows simulation-free training with the help of a time-dependent normalizing flow. However, it ultimately suffers from severe mode collapse. On closer inspection, we find that nearly all successful neural samplers rely on Langevin preconditioning to avoid mode collapsing. We systematically analyze several popular methods with various objective functions and demonstrate that, in the absence of Langevin preconditioning, most of them fail to adequately cover even a simple target. Finally, we draw attention to a strong baseline by combining the state-of-the-art MCMC method, Parallel Tempering (PT), with an additional generative model to shed light on future explorations of neural samplers.

cs.LG↗

arXiv2024

Kernelized Concept Erasure

The representation space of neural models for textual data emerges in an unsupervised manner during training. Understanding how those representations encode human-interpretable concepts is a fundamental problem. One prominent approach for the identification of concepts in neural representations is searching for a linear subspace whose erasure prevents the prediction of the concept from the representations. However, while many linear erasure algorithms are tractable and interpretable, neural networks do not necessarily represent concepts in a linear manner. To identify non-linearly encoded concepts, we propose a kernelization of a linear minimax game for concept erasure. We demonstrate that it is possible to prevent specific non-linear adversaries from predicting the concept. However, the protection does not transfer to different nonlinear adversaries. Therefore, exhaustively erasing a non-linearly encoded concept remains an open problem.

cs.LG↗

arXiv2024

Improving Antibody Design with Force-Guided Sampling in Diffusion Models

Antibodies, crucial for immune defense, primarily rely on complementarity-determining regions (CDRs) to bind and neutralize antigens, such as viruses. The design of these CDRs determines the antibody's affinity and specificity towards its target. Generative models, particularly denoising diffusion probabilistic models (DDPMs), have shown potential to advance the structure-based design of CDR regions. However, only a limited dataset of bound antibody-antigen structures is available, and generalization to out-of-distribution interfaces remains a challenge. Physics based force-fields, which approximate atomic interactions, offer a coarse but universal source of information to better mold designs to target interfaces. Integrating this foundational information into diffusion models is, therefore, highly desirable. Here, we propose a novel approach to enhance the sampling process of diffusion models by integrating force field energy-based feedback. Our model, DiffForce, employs forces to guide the diffusion sampling process, effectively blending the two distributions. Through extensive experiments, we demonstrate that our method guides the model to sample CDRs with lower energy, enhancing both the structure and sequence of the generated antibodies.

q-bio.QM↗