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Source author record

Jan-Willem van de Meent

Jan-Willem van de Meent appears in the imported research catalog. Authorship, coauthor and topic links are available while profile ownership is still unclaimed.

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Machine LearningBiological PhysicsArtificial Intelligencecond-mat.softComputer VisionApplicationsBiomoleculeseess.IVeess.SYmath.DGNeurons and Cognitionphysics.class-phphysics.data-anphysics.flu-dynProgramming LanguagesQuantitative MethodsRoboticsSubcellular ProcessesSystems and Control

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Published work

22 published item(s)

preprint2026arXiv

Follow the Mean: Reference-Guided Flow Matching

Existing approaches to controllable generation typically rely on fine-tuning, auxiliary networks, or test-time search. We show that flow matching admits a different control interface: adaptation through examples. For deterministic interpolants, the velocity field is solely governed by a conditional endpoint mean; shifting this mean shifts the flow itself. This yields a simple principle for controllable generation: steer a pretrained model by changing the reference set it follows. We instantiate this idea in two forms. Reference-Mean Guidance is training-free: it computes a closed-form endpoint-mean correction from a reference bank and applies it to a frozen FLUX.2-klein (4B) model, enabling control of color, identity, style, and structure while keeping the prompt, seed, and weights fixed. Semi-Parametric Guidance amortizes the same idea through an explicit mean anchor and learned residual refiner, matching unconditional DiT-B/4 quality on AFHQv2 while allowing the reference set to be swapped at inference time. These results point to a broader direction: generative models that adapt through data, not parameter updates.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Kernel-Gradient Drifting Models

We propose kernel-gradient drifting, a one-step generative modeling framework that replaces the fixed Euclidean displacement direction in drifting models with directions induced by the kernel itself. Standard drifting is attractive because it enables fast, high-quality generation without distilling a large pretrained diffusion model, but its theory is currently understood mainly for Gaussian kernels, where the drift coincides with smoothed score matching and is identifiable. Our gradient-based reformulation exposes this score-based structure for general kernels: the resulting drift is the score difference between kernel-smoothed data and model distributions, yielding identifiability for characteristic kernels and a smoothed-KL descent interpretation of the drifting dynamics. Since kernel gradients are intrinsic tangent vectors, the same construction extends naturally to Riemannian manifolds and to discrete data via the Fisher-Rao geometry of the probability simplex. Across spherical geospatial data, promoter DNA and molecule generation, kernel-gradient drifting enables state-of-the-art one-step generation beyond the Euclidean setting without distillation.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Binding Actions to Objects in World Models

We study the problem of binding actions to objects in object-factored world models using action-attention mechanisms. We propose two attention mechanisms for binding actions to objects, soft attention and hard attention, which we evaluate in the context of structured world models for five environments. Our experiments show that hard attention helps contrastively-trained structured world models to learn to separate individual objects in an object-based grid-world environment. Further, we show that soft attention increases performance of factored world models trained on a robotic manipulation task. The learned action attention weights can be used to interpret the factored world model as the attention focuses on the manipulated object in the environment.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Deriving time-averaged active inference from control principles

Active inference offers a principled account of behavior as minimizing average sensory surprise over time. Applications of active inference to control problems have heretofore tended to focus on finite-horizon or discounted-surprise problems, despite deriving from the infinite-horizon, average-surprise imperative of the free-energy principle. Here we derive an infinite-horizon, average-surprise formulation of active inference from optimal control principles. Our formulation returns to the roots of active inference in neuroanatomy and neurophysiology, formally reconnecting active inference to optimal feedback control. Our formulation provides a unified objective functional for sensorimotor control and allows for reference states to vary over time.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Factored World Models for Zero-Shot Generalization in Robotic Manipulation

World models for environments with many objects face a combinatorial explosion of states: as the number of objects increases, the number of possible arrangements grows exponentially. In this paper, we learn to generalize over robotic pick-and-place tasks using object-factored world models, which combat the combinatorial explosion by ensuring that predictions are equivariant to permutations of objects. Previous object-factored models were limited either by their inability to model actions, or by their inability to plan for complex manipulation tasks. We build on recent contrastive methods for training object-factored world models, which we extend to model continuous robot actions and to accurately predict the physics of robotic pick-and-place. To do so, we use a residual stack of graph neural networks that receive action information at multiple levels in both their node and edge neural networks. Crucially, our learned model can make predictions about tasks not represented in the training data. That is, we demonstrate successful zero-shot generalization to novel tasks, with only a minor decrease in model performance. Moreover, we show that an ensemble of our models can be used to plan for tasks involving up to 12 pick and place actions using heuristic search. We also demonstrate transfer to a physical robot.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Generator Surgery for Compressed Sensing

Image recovery from compressive measurements requires a signal prior for the images being reconstructed. Recent work has explored the use of deep generative models with low latent dimension as signal priors for such problems. However, their recovery performance is limited by high representation error. We introduce a method for achieving low representation error using generators as signal priors. Using a pre-trained generator, we remove one or more initial blocks at test time and optimize over the new, higher-dimensional latent space to recover a target image. Experiments demonstrate significantly improved reconstruction quality for a variety of network architectures. This approach also works well for out-of-training-distribution images and is competitive with other state-of-the-art methods. Our experiments show that test-time architectural modifications can greatly improve the recovery quality of generator signal priors for compressed sensing.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Learning Discrete State Abstractions With Deep Variational Inference

Abstraction is crucial for effective sequential decision making in domains with large state spaces. In this work, we propose an information bottleneck method for learning approximate bisimulations, a type of state abstraction. We use a deep neural encoder to map states onto continuous embeddings. We map these embeddings onto a discrete representation using an action-conditioned hidden Markov model, which is trained end-to-end with the neural network. Our method is suited for environments with high-dimensional states and learns from a stream of experience collected by an agent acting in a Markov decision process. Through this learned discrete abstract model, we can efficiently plan for unseen goals in a multi-goal Reinforcement Learning setting. We test our method in simplified robotic manipulation domains with image states. We also compare it against previous model-based approaches to finding bisimulations in discrete grid-world-like environments. Source code is available at https://github.com/ondrejba/discrete_abstractions.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Amortized Population Gibbs Samplers with Neural Sufficient Statistics

We develop amortized population Gibbs (APG) samplers, a class of scalable methods that frames structured variational inference as adaptive importance sampling. APG samplers construct high-dimensional proposals by iterating over updates to lower-dimensional blocks of variables. We train each conditional proposal by minimizing the inclusive KL divergence with respect to the conditional posterior. To appropriately account for the size of the input data, we develop a new parameterization in terms of neural sufficient statistics. Experiments show that APG samplers can train highly structured deep generative models in an unsupervised manner, and achieve substantial improvements in inference accuracy relative to standard autoencoding variational methods.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Deep Markov Spatio-Temporal Factorization

We introduce deep Markov spatio-temporal factorization (DMSTF), a generative model for dynamical analysis of spatio-temporal data. Like other factor analysis methods, DMSTF approximates high dimensional data by a product between time dependent weights and spatially dependent factors. These weights and factors are in turn represented in terms of lower dimensional latents inferred using stochastic variational inference. The innovation in DMSTF is that we parameterize weights in terms of a deep Markovian prior extendable with a discrete latent, which is able to characterize nonlinear multimodal temporal dynamics, and perform multidimensional time series forecasting. DMSTF learns a low dimensional spatial latent to generatively parameterize spatial factors or their functional forms in order to accommodate high spatial dimensionality. We parameterize the corresponding variational distribution using a bidirectional recurrent network in the low-level latent representations. This results in a flexible family of hierarchical deep generative factor analysis models that can be extended to perform time series clustering or perform factor analysis in the presence of a control signal. Our experiments, which include simulated and real-world data, demonstrate that DMSTF outperforms related methodologies in terms of predictive performance for unseen data, reveals meaningful clusters in the data, and performs forecasting in a variety of domains with potentially nonlinear temporal transitions.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Nested Reasoning About Autonomous Agents Using Probabilistic Programs

As autonomous agents become more ubiquitous, they will eventually have to reason about the plans of other agents, which is known as theory of mind reasoning. We develop a planning-as-inference framework in which agents perform nested simulation to reason about the behavior of other agents in an online manner. As a concrete application of this framework, we use probabilistic programs to model a high-uncertainty variant of pursuit-evasion games in which an agent must make inferences about the other agents' plans to craft counter-plans. Our probabilistic programs incorporate a variety of complex primitives such as field-of-view calculations and path planners, which enable us to model quasi-realistic scenarios in a computationally tractable manner. We perform extensive experimental evaluations which establish a variety of rational behaviors and quantify how allocating computation across levels of nesting affects the variance of our estimators.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Query-Focused EHR Summarization to Aid Imaging Diagnosis

Electronic Health Records (EHRs) provide vital contextual information to radiologists and other physicians when making a diagnosis. Unfortunately, because a given patient's record may contain hundreds of notes and reports, identifying relevant information within these in the short time typically allotted to a case is very difficult. We propose and evaluate models that extract relevant text snippets from patient records to provide a rough case summary intended to aid physicians considering one or more diagnoses. This is hard because direct supervision (i.e., physician annotations of snippets relevant to specific diagnoses in medical records) is prohibitively expensive to collect at scale. We propose a distantly supervised strategy in which we use groups of International Classification of Diseases (ICD) codes observed in 'future' records as noisy proxies for 'downstream' diagnoses. Using this we train a transformer-based neural model to perform extractive summarization conditioned on potential diagnoses. This model defines an attention mechanism that is conditioned on potential diagnoses (queries) provided by the diagnosing physician. We train (via distant supervision) and evaluate variants of this model on EHR data from Brigham and Women's Hospital in Boston and MIMIC-III (the latter to facilitate reproducibility). Evaluations performed by radiologists demonstrate that these distantly supervised models yield better extractive summaries than do unsupervised approaches. Such models may aid diagnosis by identifying sentences in past patient reports that are clinically relevant to a potential diagnosis.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Black-Box Policy Search with Probabilistic Programs

In this work, we explore how probabilistic programs can be used to represent policies in sequential decision problems. In this formulation, a probabilistic program is a black-box stochastic simulator for both the problem domain and the agent. We relate classic policy gradient techniques to recently introduced black-box variational methods which generalize to probabilistic program inference. We present case studies in the Canadian traveler problem, Rock Sample, and a benchmark for optimal diagnosis inspired by Guess Who. Each study illustrates how programs can efficiently represent policies using moderate numbers of parameters.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Inducing Interpretable Representations with Variational Autoencoders

We develop a framework for incorporating structured graphical models in the \emph{encoders} of variational autoencoders (VAEs) that allows us to induce interpretable representations through approximate variational inference. This allows us to both perform reasoning (e.g. classification) under the structural constraints of a given graphical model, and use deep generative models to deal with messy, high-dimensional domains where it is often difficult to model all the variation. Learning in this framework is carried out end-to-end with a variational objective, applying to both unsupervised and semi-supervised schemes.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Probabilistic structure discovery in time series data

Existing methods for structure discovery in time series data construct interpretable, compositional kernels for Gaussian process regression models. While the learned Gaussian process model provides posterior mean and variance estimates, typically the structure is learned via a greedy optimization procedure. This restricts the space of possible solutions and leads to over-confident uncertainty estimates. We introduce a fully Bayesian approach, inferring a full posterior over structures, which more reliably captures the uncertainty of the model.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

A physical perspective on cytoplasmic streaming (invited)

Organisms show a remarkable range of sizes, yet the dimensions of a single cell rarely exceed $100$ $μ$m. While the physical and biological origins of this constraint remain poorly understood, exceptions to this rule give valuable insights. A well-known counterexample is the aquatic plant $Chara$, whose cells can exceed $10$ cm in length and $1$ mm in diameter. Two spiraling bands of molecular motors at the cell periphery drive the cellular fluid up and down at speeds up to $100$ $μ$m/s, motion that has been hypothesized to mitigate the slowness of metabolite transport on these scales and to aid in homeostasis. This is the most organized instance of a broad class of continuous motions known as "cytoplasmic streaming", found in a wide range of eukaryotic organisms - algae, plants, amoebae, nematodes, and flies - often in unusually large cells. In this overview of the physics of this phenomenon, we examine the interplay between streaming, transport and cell size, and discuss the possible role of self-organization phenomena in establishing the observed patterns of streaming.

0 citations0 reviewsNo code linkedOpen access
preprint2015arXiv

Particle Gibbs with Ancestor Sampling for Probabilistic Programs

Particle Markov chain Monte Carlo techniques rank among current state-of-the-art methods for probabilistic program inference. A drawback of these techniques is that they rely on importance resampling, which results in degenerate particle trajectories and a low effective sample size for variables sampled early in a program. We here develop a formalism to adapt ancestor resampling, a technique that mitigates particle degeneracy, to the probabilistic programming setting. We present empirical results that demonstrate nontrivial performance gains.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

Multiple Lac-mediated loops revealed by Bayesian statistics and tethered particle motion

The bacterial transcription factor LacI loops DNA by binding to two separate locations on the DNA simultaneously. Despite being one of the best-studied model systems for transcriptional regulation, the number and conformations of loop structures accessible to LacI remain unclear, though the importance of multiple co-existing loops has been implicated in interactions between LacI and other cellular regulators of gene expression. To probe this issue, we have developed a new analysis method for tethered particle motion, a versatile and commonly-used in vitro single-molecule technique. Our method, vbTPM, performs variational Bayesian inference in hidden Markov models. It learns the number of distinct states (i.e., DNA-protein conformations) directly from tethered particle motion data with better resolution than existing methods, while easily correcting for common experimental artifacts. Studying short (roughly 100 bp) LacI-mediated loops, we provide evidence for three distinct loop structures, more than previously reported in single-molecule studies. Moreover, our results confirm that changes in LacI conformation and DNA binding topology both contribute to the repertoire of LacI-mediated loops formed in vitro, and provide qualitatively new input for models of looping and transcriptional regulation. We expect vbTPM to be broadly useful for probing complex protein-nucleic acid interactions.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

Stylistic Clusters and the Syrian/South Syrian Tradition of First-Millennium BCE Levantine Ivory Carving: A Machine Learning Approach

Thousands of first-millennium BCE ivory carvings have been excavated from Neo-Assyrian sites in Mesopotamia (primarily Nimrud, Khorsabad, and Arslan Tash) hundreds of miles from their Levantine production contexts. At present, their specific manufacture dates and workshop localities are unknown. Relying on subjective, visual methods, scholars have grappled with their classification and regional attribution for over a century. This study combines visual approaches with machine-learning techniques to offer data-driven perspectives on the classification and attribution of this early Iron Age corpus. The study sample consisted of 162 sculptures of female figures. We have developed an algorithm that clusters the ivories based on a combination of descriptive and anthropometric data. The resulting categories, which are based on purely statistical criteria, show good agreement with conventional art historical classifications, while revealing new perspectives, especially with regard to the contested Syrian/South Syrian/Intermediate tradition. Specifically, we have identified that objects of the Syrian/South Syrian/Intermediate tradition may be more closely related to Phoenician objects than to North Syrian objects; we offer a reconsideration of a subset of Phoenician objects, and we confirm Syrian/South Syrian/Intermediate stylistic subgroups that might distinguish networks of acquisition among the sites of Nimrud, Khorsabad, Arslan Tash and the Levant. We have also identified which features are most significant in our cluster assignments and might thereby be most diagnostic of regional carving traditions. In short, our study both corroborates traditional visual classification methods and demonstrates how machine-learning techniques may be employed to reveal complementary information not accessible through the exclusively visual analysis of an archaeological corpus.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

Tempering by Subsampling

In this paper we demonstrate that tempering Markov chain Monte Carlo samplers for Bayesian models by recursively subsampling observations without replacement can improve the performance of baseline samplers in terms of effective sample size per computation. We present two tempering by subsampling algorithms, subsampled parallel tempering and subsampled tempered transitions. We provide an asymptotic analysis of the computational cost of tempering by subsampling, verify that tempering by subsampling costs less than traditional tempering, and demonstrate both algorithms on Bayesian approaches to learning the mean of a high dimensional multivariate Normal and estimating Gaussian process hyperparameters.

0 citations0 reviewsNo code linkedOpen access
preprint2013arXiv

Hierarchically-coupled hidden Markov models for learning kinetic rates from single-molecule data

We address the problem of analyzing sets of noisy time-varying signals that all report on the same process but confound straightforward analyses due to complex inter-signal heterogeneities and measurement artifacts. In particular we consider single-molecule experiments which indirectly measure the distinct steps in a biomolecular process via observations of noisy time-dependent signals such as a fluorescence intensity or bead position. Straightforward hidden Markov model (HMM) analyses attempt to characterize such processes in terms of a set of conformational states, the transitions that can occur between these states, and the associated rates at which those transitions occur; but require ad-hoc post-processing steps to combine multiple signals. Here we develop a hierarchically coupled HMM that allows experimentalists to deal with inter-signal variability in a principled and automatic way. Our approach is a generalized expectation maximization hyperparameter point estimation procedure with variational Bayes at the level of individual time series that learns an single interpretable representation of the overall data generating process.

0 citations0 reviewsNo code linkedOpen access
preprint2010arXiv

Polymer rheology simulations at the meso- and macroscopic scale

We show that simulations of polymer rheology at a fluctuating mesoscopic scale and at the macroscopic scale where flow instabilities occur can be achieved at the same time with dissipative particle dynamics (DPD) technique.} We model the visco-elasticity of polymer liquids by introducing a finite fraction of dumbbells in the standard DPD fluid. The stretching and tumbling statistics of these dumbbells is in agreement with what is known for isolated polymers in shear flows. At the same time, the model exhibits behaviour reminiscent of drag reduction in the turbulent state: as the polymer fraction increases, the onset of turbulence in plane Couette flow is pushed to higher Reynolds numbers. The method opens up the possibility to model nontrivial rheological conditions with ensuing coarse grained polymer statistics.

0 citations0 reviewsNo code linkedOpen access
preprint2009arXiv

Measurement of Cytoplasmic Streaming in Chara Corallina by Magnetic Resonance Velocimetry

In aquatic plants such as the Characean algae, the force generation that drives cyclosis is localized within the cytoplasm, yet produces fluid flows throughout the vacuole. For this to occur the tonoplast must transmit hydrodynamic shear efficiently. Here, using magnetic resonance velocimetry, we present the first whole-cell measurements of the cross-sectional longitudinal velocity field in Chara corallina and show that it is in quantitative agreement with a recent theoretical analysis of rotational cytoplasmic streaming driven by bidirectional helical forcing in the cytoplasm, with direct shear transmission by the tonoplast.

0 citations0 reviewsNo code linkedOpen access