Daily Papers

Modeling dynamical systems and unraveling their underlying structural dependencies is central to many domains in the natural sciences. Various physical systems, such as those arising in cell biology, are inherently high-dimensional and stochastic in nature, and admit only partial, noisy state measurements. Our primary motivating setting is single-cell biology, where destructive measurements yield unpaired population snapshots rather than longitudinal trajectories of the same cells. This poses a significant challenge for addressing the problems of modeling the underlying dynamics and inferring the network structure of these systems. Existing methods are typically tailored either for structure learning or modeling dynamics at the population level, but are limited in their ability to address both problems together. In this work, we address both problems simultaneously: we present StructureFlow, a novel and principled simulation-free training approach for jointly learning the structure and stochastic population dynamics of physical systems. We showcase the utility of StructureFlow for the tasks of structure learning from interventions and dynamical (trajectory) inference of conditional population dynamics. We empirically evaluate our approach on high-dimensional synthetic systems, a set of biologically plausible simulated systems, and an experimental single-cell dataset. We show that StructureFlow can learn the structure of underlying systems while simultaneously modeling their conditional population dynamics --- a key step toward model-based mechanistic understanding of systems behavior.

Closed-loop human-AI systems generate high-dimensional behavioural trajectories whose collective dynamics remain obscure. Using 297,915 learners' adaptive-tutoring histories, we define semantic order variables before model fitting and test them in user-disjoint cohorts. The state exhibits reproducible basin-like flow and operationally defined, state-heterogeneous metastable-like kinetics. A construction-matched null distinguishes normalised-memory relaxation from a reproducible excess field. A four-term conditional mechanism recovers population drift (r = 0.946; learner-bootstrap 95% CI, 0.935-0.955). Predictive event-level self-supervised learning recovers the state and learned-plane flow; null-referenced corrections retain directional, partial-amplitude excess-field structure without full calibration. Shuffled-order training reverses learned-plane flow on ordered trajectories; support-alignment randomisation selectively reduces inward transport. Both axes remain linearly accessible without state supervision. Without cross-model fitting, the models share leading population drift (r = 0.866; learner-bootstrap 95% CI, 0.857-0.875) and persistence ordering; residual directions remain model-specific. These results identify an externally anchored leading-order effective field linking empirical dynamics, an interpretable mechanism and neural computation.

Mean field games (MFGs) have emerged as a powerful framework for modeling interactions in large-scale multi-agent systems. Despite recent advancements in reinforcement learning (RL) for MFGs, existing methods are typically limited to finite spaces or stationary models, hindering their applicability to real-world problems. This paper introduces a novel deep reinforcement learning (DRL) algorithm specifically designed for non-stationary continuous MFGs. The proposed approach builds upon a Fictitious Play (FP) methodology, leveraging DRL for best-response computation and supervised learning for average policy representation. Furthermore, it learns a representation of the time-dependent population distribution using a Conditional Normalizing Flow. To validate the effectiveness of our method, we evaluate it on three different examples of increasing complexity. By addressing critical limitations in scalability and density approximation, this work represents a significant advancement in applying DRL techniques to complex MFG problems, bringing the field closer to real-world multi-agent systems.

We consider a biological population whose environment varies periodically in time, exhibiting two very different "seasons" : one is favorable and the other one is unfavorable. For monotone differential models with concave nonlinearities, we address the following question: the system's period being fixed, under what conditions does there exist a critical duration for the unfavorable season? By "critical duration" we mean that above some threshold, the population cannot sustain and extincts, while below this threshold, the system converges to a unique periodic and positive solution. We term this a "sharp seasonal threshold property" (SSTP, for short). Building upon a previous result, we obtain sufficient conditions for SSTP in any dimension and apply our criterion to a two-dimensional model featuring juvenile and adult populations of insects.

We consider estimating the conditional distribution of a multivariate outcome given covariates when its coordinates may be continuous, binary, categorical, ordinal or rankings, and are conditionally dependent on one another. Different statistical methods have been developed for each outcome type, and most of them target a summary of the conditional distribution, such as the mean of each coordinate, rather than the joint distribution of the outcome vector. We develop generalized engression models, a unified nonparametric distributional regression framework for outcomes of any type. The proposed method builds upon engression, a scoring-rule-based deep generative model, and introduces a data-type-specific link function and a stochastic perturbation that smooths the loss, enabling gradient-based training even with discontinuous links. We establish universal representation results for continuous, discrete and mixed outcomes. In simulations and in two applications, 242 species in a community ecology benchmark and a 17-dimensional mixed-type health outcome, the method matches type-specific models on marginal scores, improves on them on the joint distribution, and matches or exceeds purpose-built state-of-the-art joint species distribution models. Software is available in Python.

We introduce Diffusion World Model (DWM), a conditional diffusion model capable of predicting multistep future states and rewards concurrently. As opposed to traditional one-step dynamics models, DWM offers long-horizon predictions in a single forward pass, eliminating the need for recursive quires. We integrate DWM into model-based value estimation, where the short-term return is simulated by future trajectories sampled from DWM. In the context of offline reinforcement learning, DWM can be viewed as a conservative value regularization through generative modeling. Alternatively, it can be seen as a data source that enables offline Q-learning with synthetic data. Our experiments on the D4RL dataset confirm the robustness of DWM to long-horizon simulation. In terms of absolute performance, DWM significantly surpasses one-step dynamics models with a 44% performance gain, and achieves state-of-the-art performance.

Diffusion models are a class of probabilistic generative models that have been widely used as a prior for image processing tasks like text conditional generation and inpainting. We demonstrate that these models can be adapted to make predictions and provide uncertainty quantification for chaotic dynamical systems. In these applications, diffusion models can implicitly represent knowledge about outliers and extreme events; however, querying that knowledge through conditional sampling or measuring probabilities is surprisingly difficult. Existing methods for conditional sampling at inference time seek mainly to enforce the constraints, which is insufficient to match the statistics of the distribution or compute the probability of the chosen events. To achieve these ends, optimally one would use the conditional score function, but its computation is typically intractable. In this work, we develop a probabilistic approximation scheme for the conditional score function which provably converges to the true distribution as the noise level decreases. With this scheme we are able to sample conditionally on nonlinear userdefined events at inference time, and matches data statistics even when sampling from the tails of the distribution.

We present DEF (\ul{D}iffusion-augmented \ul{E}nsemble \ul{F}orecasting), a novel approach for generating initial condition perturbations. Modern approaches to initial condition perturbations are primarily designed for numerical weather prediction (NWP) solvers, limiting their applicability in the rapidly growing field of machine learning for weather prediction. Consequently, stochastic models in this domain are often developed on a case-by-case basis. We demonstrate that a simple conditional diffusion model can (1) generate meaningful structured perturbations, (2) be applied iteratively, and (3) utilize a guidance term to intuitivey control the level of perturbation. This method enables the transformation of any deterministic neural forecasting system into a stochastic one. With our stochastic extended systems, we show that the model accumulates less error over long-term forecasts while producing meaningful forecast distributions. We validate our approach on the 5.625^circ ERA5 reanalysis dataset, which comprises atmospheric and surface variables over a discretized global grid, spanning from the 1960s to the present. On this dataset, our method demonstrates improved predictive performance along with reasonable spread estimates.

Self-sustained neural activity in the absence of ongoing external input is a fundamental feature of nervous system dynamics, yet the conditions under which it can emerge in biophysically grounded network models remain incompletely understood. We studied whether a recurrent network of Hodgkin-Huxley neurons with spike-timing-dependent plasticity and intrinsic stochasticity can maintain autonomous activity after brief transient stimulation. The simulated network comprised 200 neurons (160 excitatory, 40 inhibitory) with 80% connection probability, incorporating excitatory and inhibitory STDP, probabilistic vesicle release, probabilistic synapse formation, receptor variability, and voltage-dependent inhibition. After a brief 200 ms initialization stimulus to 30 excitatory neurons, the network received no further external input. In one 1800 s simulation and two additional 500 s simulations, the network maintained sparse, irregular activity without ongoing drive. In the 1800 s run, 67% of neurons exhibited mean firing rates below 1 Hz, the population mean firing rate was 1.13 +/- 1.34 Hz, participation increased across longer observation windows, and population-mean Fano factors remained near 1-2, consistent with irregular spike timing. Raster activity also showed spontaneous qualitative reorganizations in collective firing patterns over time. These findings suggest that recurrent Hodgkin-Huxley networks with plastic and stochastic synapses can sustain long-duration autonomous activity in a sparse firing regime after brief initialization.

Numerous biological and physical processes can be modeled as systems of interacting entities evolving continuously over time, e.g. the dynamics of communicating cells or physical particles. Learning the dynamics of such systems is essential for predicting the temporal evolution of populations across novel samples and unseen environments. Flow-based models allow for learning these dynamics at the population level - they model the evolution of the entire distribution of samples. However, current flow-based models are limited to a single initial population and a set of predefined conditions which describe different dynamics. We argue that multiple processes in natural sciences have to be represented as vector fields on the Wasserstein manifold of probability densities. That is, the change of the population at any moment in time depends on the population itself due to the interactions between samples. In particular, this is crucial for personalized medicine where the development of diseases and their respective treatment response depends on the microenvironment of cells specific to each patient. We propose Meta Flow Matching (MFM), a practical approach to integrating along these vector fields on the Wasserstein manifold by amortizing the flow model over the initial populations. Namely, we embed the population of samples using a Graph Neural Network (GNN) and use these embeddings to train a Flow Matching model. This gives MFM the ability to generalize over the initial distributions unlike previously proposed methods. We demonstrate the ability of MFM to improve prediction of individual treatment responses on a large scale multi-patient single-cell drug screen dataset.

We incorporate discrete and continuous time Markov processes as building blocks into probabilistic graphical models with latent and observed variables. We introduce the automatic Backward Filtering Forward Guiding (BFFG) paradigm (Mider et al., 2021) for programmable inference on latent states and model parameters. Our starting point is a generative model, a forward description of the probabilistic process dynamics. We backpropagate the information provided by observations through the model to transform the generative (forward) model into a pre-conditional model guided by the data. It approximates the actual conditional model with known likelihood-ratio between the two. The backward filter and the forward change of measure are suitable to be incorporated into a probabilistic programming context because they can be formulated as a set of transformation rules. The guided generative model can be incorporated in different approaches to efficiently sample latent states and parameters conditional on observations. We show applicability in a variety of settings, including Markov chains with discrete state space, interacting particle systems, state space models, branching diffusions and Gamma processes.

Diffusion models are powerful generative models that allow for precise control over the characteristics of the generated samples. While these diffusion models trained on large datasets have achieved success, there is often a need to introduce additional controls in downstream fine-tuning processes, treating these powerful models as pre-trained diffusion models. This work presents a novel method based on reinforcement learning (RL) to add such controls using an offline dataset comprising inputs and labels. We formulate this task as an RL problem, with the classifier learned from the offline dataset and the KL divergence against pre-trained models serving as the reward functions. Our method, CTRL (Conditioning pre-Trained diffusion models with Reinforcement Learning), produces soft-optimal policies that maximize the abovementioned reward functions. We formally demonstrate that our method enables sampling from the conditional distribution with additional controls during inference. Our RL-based approach offers several advantages over existing methods. Compared to classifier-free guidance, it improves sample efficiency and can greatly simplify dataset construction by leveraging conditional independence between the inputs and additional controls. Additionally, unlike classifier guidance, it eliminates the need to train classifiers from intermediate states to additional controls. The code is available at https://github.com/zhaoyl18/CTRL.

High-dimensional count data are common in scientific applications, but most diffusion and flow models are designed for continuous or categorical data, and generation often requires many sequential model evaluations. We propose Count Flow Map, a generative model that learns finite-time transitions directly in count space for one- or few-step generation. Our model directly learns stochastic transitions over finite time intervals, using Poisson births and Binomial deaths to preserve nonnegative integer counts without a predefined maximum. These transition models are trained to match the underlying local birth--death dynamics and to maintain consistency across step sizes. We characterize the connection between local dynamics and finite-time transition consistency and derive a bound on the generation error. After validating Count Flow Map in several simulations, including a high-dimensional, high-count setting, we apply it to single-cell drug perturbation prediction and neural population forecasting, where it captures perturbation responses and supports forecasts of high-activity events with only one or a few model evaluations. Together, these experiments demonstrate that Count Flow Map enables high-quality generation directly in count space across inference budgets, from one-step to few-step generation, using a single trained model.

In-context learning is commonly interpreted as a form of conditional inference, in which the prompt specifies a context and the model's output is treated as an estimate of the corresponding conditional distribution. If this interpretation holds, then LLM estimates should satisfy basic probabilistic identities. In particular, the law of total probability asserts that prior-weighted conditional distributions aggregate into population-level marginals over any valid partition of the population. In this work, we investigate to what extent LLM estimates adhere to this self-consistency principle. We use binary trees as an evaluation scaffold to recursively partition a population into increasingly fine-grained subpopulations. We then prompt LLMs with verbalized subpopulation descriptions in context, aggregate the resulting estimates back into population-level estimates, and compare them across partitions of varying granularity. Applying this protocol across problem domains and state-of-the-art frontier models, we show widespread violations of basic consistency properties. An in-depth study of persona prompting reveals a pattern we call the macro fallacy: estimates reconstructed from more fine-grained subpopulation responses are often better aligned with human reference data than direct population-level estimates. This effect persists across variations in tree structure and estimation task, and can be partially recovered through implicit prompting. Together, these findings suggest that models possess relevant subpopulation knowledge but do not reliably propagate it into aggregate estimates. This gap establishes statistical self-consistency as an unsaturated, reference-free criterion for evaluating LLMs.

Survival analysis, or time-to-event modelling, is a classical statistical problem that has garnered a lot of interest for its practical use in epidemiology, demographics or actuarial sciences. Recent advances on the subject from the point of view of machine learning have been concerned with precise per-individual predictions instead of population studies, driven by the rise of individualized medicine. We introduce here a conditional normalizing flow based estimate of the time-to-event density as a way to model highly flexible and individualized conditional survival distributions. We use a novel hierarchical formulation of normalizing flows to enable efficient fitting of flexible conditional distributions without overfitting and show how the normalizing flow formulation can be efficiently adapted to the censored setting. We experimentally validate the proposed approach on a synthetic dataset as well as four open medical datasets and an example of a common financial problem.

Conditional time series generation plays a critical role in addressing data scarcity and enabling causal analysis in real-world applications. Despite its increasing importance, the field lacks a standardized and systematic benchmarking framework for evaluating generative models across diverse conditions. To address this gap, we introduce the Conditional Time Series Generation Benchmark (ConTSG-Bench). ConTSG-Bench comprises a large-scale, well-aligned dataset spanning diverse conditioning modalities and levels of semantic abstraction, first enabling systematic evaluation of representative generation methods across these dimensions with a comprehensive suite of metrics for generation fidelity and condition adherence. Both the quantitative benchmarking and in-depth analyses of conditional generation behaviors have revealed the traits and limitations of the current approaches, highlighting critical challenges and promising research directions, particularly with respect to precise structural controllability and downstream task utility under complex conditions.

Recent improvements in conditional generative modeling have made it possible to generate high-quality images from language descriptions alone. We investigate whether these methods can directly address the problem of sequential decision-making. We view decision-making not through the lens of reinforcement learning (RL), but rather through conditional generative modeling. To our surprise, we find that our formulation leads to policies that can outperform existing offline RL approaches across standard benchmarks. By modeling a policy as a return-conditional diffusion model, we illustrate how we may circumvent the need for dynamic programming and subsequently eliminate many of the complexities that come with traditional offline RL. We further demonstrate the advantages of modeling policies as conditional diffusion models by considering two other conditioning variables: constraints and skills. Conditioning on a single constraint or skill during training leads to behaviors at test-time that can satisfy several constraints together or demonstrate a composition of skills. Our results illustrate that conditional generative modeling is a powerful tool for decision-making.

Causal discovery aims to uncover the underlying causal relationships given data generated from a system. The goal, however, is not merely to predict causal edges given data, but also to be able to interpret and explain either observed or hypothesized phenomena, such as a particularly large causal effect. We consider this task of conditional causal discovery and cast it as a Bayesian inference problem, in which we target the posterior over causal graphs and parameters conditional on an event such as a causal-effect constraint. Unfortunately, this poses a computational challenge: existing approaches to Bayesian causal discovery struggle when the event has small posterior mass. To address this, we adapt rare-event estimation techniques to perform inference the joint graph-parameter space. Our method gradually drives a particle population toward the constrained region while maintaining samples that approximate the conditional posterior. Empirical evaluation on synthetic graphs validates the accuracy of our approach at small and large scales, and we show in a case study on the Sachs protein dataset how our method can be used to aid scientific exploration by providing pathway-level summaries.

Learning population dynamics from temporally sparse, unpaired distribution snapshots is a fundamental challenge in developmental biology. Recent approaches based on neural differential equations and flow matching can interpolate between observed population snapshots, but may struggle to extrapolate beyond the training horizon and often lack an explicit mechanism for modeling developmental branching. We propose KoopCell, a unified generative framework based on Koopman-Mori-Zwanzig theory that jointly learns representations and predictive linear latent dynamics. Theoretically, using the weak continuity equation, we derive a closed-form least-squares estimator for the Koopman generator from distribution snapshots and establish convergence guarantees under suitable assumptions. To model branching dynamics, we further develop KoopCell-M, which incorporates non-Markovian memory into the latent Koopman dynamics through a Markovian embedding. Experiments on synthetic systems and three scRNA-seq datasets demonstrate the ability of our framework to recover Koopman spectra, model branching through memory, and scale to predicting high-dimensional gene expression distributions, achieving state-of-the-art performance among the evaluated methods.

Diffusion models, a powerful and universal generative AI technology, have achieved tremendous success in computer vision, audio, reinforcement learning, and computational biology. In these applications, diffusion models provide flexible high-dimensional data modeling, and act as a sampler for generating new samples under active guidance towards task-desired properties. Despite the significant empirical success, theory of diffusion models is very limited, potentially slowing down principled methodological innovations for further harnessing and improving diffusion models. In this paper, we review emerging applications of diffusion models, understanding their sample generation under various controls. Next, we overview the existing theories of diffusion models, covering their statistical properties and sampling capabilities. We adopt a progressive routine, beginning with unconditional diffusion models and connecting to conditional counterparts. Further, we review a new avenue in high-dimensional structured optimization through conditional diffusion models, where searching for solutions is reformulated as a conditional sampling problem and solved by diffusion models. Lastly, we discuss future directions about diffusion models. The purpose of this paper is to provide a well-rounded theoretical exposure for stimulating forward-looking theories and methods of diffusion models.

Generative models inspired by dynamical transport of measure -- such as flows and diffusions -- construct a continuous-time map between two probability densities. Conventionally, one of these is the target density, only accessible through samples, while the other is taken as a simple base density that is data-agnostic. In this work, using the framework of stochastic interpolants, we formalize how to couple the base and the target densities. This enables us to incorporate information about class labels or continuous embeddings to construct dynamical transport maps that serve as conditional generative models. We show that these transport maps can be learned by solving a simple square loss regression problem analogous to the standard independent setting. We demonstrate the usefulness of constructing dependent couplings in practice through experiments in super-resolution and in-painting.

Biochemical networks propagate the signals that regulate cellular behaviour, and which routes carry them depends on cellular context: a shift in context rewires the network's effective dynamics. Mechanistic simulators are misspecified here because the effective dynamics emerge from an interaction structure that is only partially known. Model discovery instead learns the dynamics from data, but sparse, correlated measurements poorly identify a full network model. What matters is narrower: the portion the context rewires. We introduce conditionally coarse-grained ODEs (Co^2ODE), which model that portion as a sparse neural or symbolic ODE: a conditional mask selects the markers carrying the rewiring, and a variational autoencoder compresses the remaining markers into a learnt closure term. On single-cell phosphoproteomic data spanning 30 cancer-relevant overexpressions, Co^2ODE compresses a 30-marker panel into a 10-dimensional state while matching the predictive accuracy of a neural ODE fit to the full panel. The closure absorbs what the mask drops, hence the accuracy is insensitive to which markers are kept. Adding a prior score to the loss shifts the selected markers at no cost in fit, indicating the data are not interventional enough to identify the underlying biology.

Conditional Neural Processes (CNPs) are a class of metalearning models popular for combining the runtime efficiency of amortized inference with reliable uncertainty quantification. Many relevant machine learning tasks, such as in spatio-temporal modeling, Bayesian Optimization and continuous control, inherently contain equivariances -- for example to translation -- which the model can exploit for maximal performance. However, prior attempts to include equivariances in CNPs do not scale effectively beyond two input dimensions. In this work, we propose Relational Conditional Neural Processes (RCNPs), an effective approach to incorporate equivariances into any neural process model. Our proposed method extends the applicability and impact of equivariant neural processes to higher dimensions. We empirically demonstrate the competitive performance of RCNPs on a large array of tasks naturally containing equivariances.

Flow matching (FM) has emerged as a powerful framework for learning dynamic transport maps between two empirical distributions. However, less explored is the setting with intermediate observed marginals that can help constrain the flows between the endpoints. This "multimarginal" regime is central to modeling temporal evolution in dynamical systems in many scientific domains that can sample sequential distributions. We tackle this problem with a novel approach that leverages the connection between FM and dynamic optimal transport (OT), softly steering the flow towards the intermediate marginals through potential terms in the dynamic OT action. By extending the conditional FM learning target to incorporate these potentials, we derive an efficient, simulation-free algorithm for multimarginal FM that offers considerable flexibility in the spatiotemporal dynamics of the learned flows. We demonstrate state-of-the-art performance and training efficiency of OT-potential FM (OTP-FM) on diverse single-cell RNA sequencing, oceanographic, and meteorological datasets. Our code is available at https://github.com/Bexorg-Inc/OTP-FM.

Modelling individual decision-making during infectious disease outbreaks is crucial for understanding behavioural dynamics and informing effective public health interventions. Prior work has shown that large language models can simulate realistic human behaviour by generating agent decisions based on demographic prompts and situational context. We build on this foundation with a spatially grounded, agent-based simulation framework that integrates LLM-generated decisions about self-reported influenza-like illness into a census-based synthetic population of agents. Location is treated as a central feature: agents are assigned to spatial units within cities, capturing the spatial distributions of different demographic groups using real-world census data and enabling geographically diverse behavioural modelling. We implement and compare three decision scenarios, independent reasoning, household influence, and message framing, and simulate self-reporting outcomes in San Francisco and Atlanta. Results reveal that income and education are the dominant drivers of reporting rate variation, with smaller but consistent effects from geography, LLM model choice, and message framing. Our framework generates synthetic data that captures both social and geographic heterogeneity, supporting spatial epidemiological modelling and bias-aware behavioural analysis.

Causal inference is often focused on average effects, which can hide important aspects of the effect distributions. Here we consider the entire posterior effects distribution by estimating full counterfactual outcome distributions. We propose a methodology for inference on counterfactual distributions which builds upon the martingale posterior framework of Fong et al. (2023). This provides a highly flexible approach to estimating densities, distribution functions, and derived quantities such as quantiles, which coherently quantifies the epistemic uncertainty on any target estimand of interest. As the predictive recursions are based on an underlying nonparametric model (a Dirichlet process mixture model), our method naturally inherits robustness with respect to restrictive parametric assumptions. In addition, implementation of our method is typically very fast. This approach can be applied to marginal or conditional counterfactual distributions and is easily extended to an instrumental variables setup. Using the concept of almost conditionally identically distributed random variables, we prove convergence of the martingale posterior inference on the counterfactual outcome distributions for the causal models considered in the paper. We illustrate our approach on both simulated and real data. Using the latter, we investigate the effect of zinc lozenges on common cold duration, the impact of vitamin A supplementation on children's survival rates with one-sided non-compliance (analysed in Imbens and Rubin, 1997a) and the effect of job training (LaLonde, 1986).

Model uncertainty and limited data are fundamental challenges to robust management of human intervention in a natural system. These challenges are acutely highlighted by concerns that many ecological systems may contain tipping points, such as Allee population sizes. Before a collapse, we do not know where the tipping points lie, if they exist at all. Hence, we know neither a complete model of the system dynamics nor do we have access to data in some large region of state-space where such a tipping point might exist. We illustrate how a Bayesian Non-Parametric (BNP) approach using a Gaussian Process (GP) prior provides a flexible representation of this inherent uncertainty. We embed GPs in a Stochastic Dynamic Programming (SDP) framework in order to make robust management predictions with both model uncertainty and limited data. We use simulations to evaluate this approach as compared with the standard approach of using model selection to choose from a set of candidate models. We find that model selection erroneously favors models without tipping points -- leading to harvest policies that guarantee extinction. The GPDP performs nearly as well as the true model and significantly outperforms standard approaches. We illustrate this using examples of simulated single-species dynamics, where the standard model selection approach should be most effective, and find that it still fails to account for uncertainty appropriately and leads to population crashes, while management based on the GPDP does not, since it does not underestimate the uncertainty outside of the observed data.

Predicting how a dynamical unit evolves over time - how an individual ages, an epidemic spreads, or a physical system degrades - typically requires dense longitudinal tracking. When only extremely sparse or entirely cross-sectional data is available, inferring individualized, continuous-time trajectories is fundamentally ill-posed. Existing methods force a strict compromise: sequence models (e.g. latent ODEs) require dense longitudinal data, while cross-sectional methods (e.g. optimal transport, flow matching-based) map aggregate populations, losing individual dynamics. In this paper, we demonstrate that this dichotomy can be broken. We introduce CADENCE, a principled probabilistic framework that recovers continuous individual trajectories from isolated snapshots by anchoring latent dynamics to static, individual-level contexts. We provide novel identifiability guarantees for single-timepoint trajectory inference. By combining a score-based spatial encoder (bijective Probability Flow ODE) to eliminate diffeomorphic ambiguities with a Soft Mixture-of-Experts (SMoE) router, we show that individual dynamical parameters and routing function are jointly identifiable. Across a suite of benchmarks spanning physical systems to real-world biological data, CADENCE, trained strictly on extremely sparse snapshots with context structure, matches or exceeds the performance of state-of-the-art sequential models trained on dense, full-trajectory data.

Learning the response of single-cells to various treatments offers great potential to enable targeted therapies. In this context, neural optimal transport (OT) has emerged as a principled methodological framework because it inherently accommodates the challenges of unpaired data induced by cell destruction during data acquisition. However, most existing OT approaches are incapable of conditioning on different treatment contexts (e.g., time, drug treatment, drug dosage, or cell type) and we still lack methods that unanimously show promising generalization performance to unseen treatments. Here, we propose the Conditional Monge Gap which learns OT maps conditionally on arbitrary covariates. We demonstrate its value in predicting single-cell perturbation responses conditional to one or multiple drugs, a drug dosage, or combinations thereof. We find that our conditional models achieve results comparable and sometimes even superior to the condition-specific state-of-the-art on scRNA-seq as well as multiplexed protein imaging data. Notably, by aggregating data across conditions we perform cross-task learning which unlocks remarkable generalization abilities to unseen drugs or drug dosages, widely outperforming other conditional models in capturing heterogeneity (i.e., higher moments) in the perturbed population. Finally, by scaling to hundreds of conditions and testing on unseen drugs, we narrow the gap between structure-based and effect-based drug representations, suggesting a promising path to the successful prediction of perturbation effects for unseen treatments.

While conditional diffusion models are known to have good coverage of the data distribution, they still face limitations in output diversity, particularly when sampled with a high classifier-free guidance scale for optimal image quality or when trained on small datasets. We attribute this problem to the role of the conditioning signal in inference and offer an improved sampling strategy for diffusion models that can increase generation diversity, especially at high guidance scales, with minimal loss of sample quality. Our sampling strategy anneals the conditioning signal by adding scheduled, monotonically decreasing Gaussian noise to the conditioning vector during inference to balance diversity and condition alignment. Our Condition-Annealed Diffusion Sampler (CADS) can be used with any pretrained model and sampling algorithm, and we show that it boosts the diversity of diffusion models in various conditional generation tasks. Further, using an existing pretrained diffusion model, CADS achieves a new state-of-the-art FID of 1.70 and 2.31 for class-conditional ImageNet generation at 256times256 and 512times512 respectively.

Reinforcement Learning from Human Feedback has emerged as a standard for aligning diffusion models. However, we identify a fundamental limitation in the standard DPO formulation because it relies on the Bradley-Terry model to aggregate diverse evaluation axes like aesthetic quality and semantic alignment into a single scalar reward. This aggregation creates a reward conflict where the model is forced to unlearn desirable features of a specific dimension if they appear in a globally non-preferred sample. To address this issue, we propose Multi Reward Conditional DPO (MCDPO). This method resolves reward conflicts by introducing a disentangled Bradley-Terry objective. MCDPO explicitly injects a preference outcome vector as a condition during training, which allows the model to learn the correct optimization direction for each reward axis independently within a single network. We further introduce dimensional reward dropout to ensure balanced optimization across dimensions. Extensive experiments on Stable Diffusion 1.5 and SDXL demonstrate that MCDPO achieves superior performance on benchmarks. Notably, our conditional framework enables dynamic and multiple-axis control at inference time using Classifier Free Guidance to amplify specific reward dimensions without additional training or external reward models.

Learning accurate predictive models of real-world dynamic phenomena (e.g., climate, biological) remains a challenging task. One key issue is that the data generated by both natural and artificial processes often comprise time series that are irregularly sampled and/or contain missing observations. In this work, we propose the Neural Continuous-Discrete State Space Model (NCDSSM) for continuous-time modeling of time series through discrete-time observations. NCDSSM employs auxiliary variables to disentangle recognition from dynamics, thus requiring amortized inference only for the auxiliary variables. Leveraging techniques from continuous-discrete filtering theory, we demonstrate how to perform accurate Bayesian inference for the dynamic states. We propose three flexible parameterizations of the latent dynamics and an efficient training objective that marginalizes the dynamic states during inference. Empirical results on multiple benchmark datasets across various domains show improved imputation and forecasting performance of NCDSSM over existing models.

A core goal of computational social science is to discover interpretable differences in how language varies across outcomes of interest, such as political affiliation or instructional quality. Recent LLM-based hypothesis generation methods describe such differences in natural language, but select for globally discriminative patterns without accounting for covariates that shape the data based on researchers' domain knowledge. When covariates are ignored, selected patterns can reflect confounds rather than differences of substantive interest. We introduce conditional hypothesis generation, a framework that incorporates researcher-specified covariates to steer hypothesis discovery toward differences that hold within relevant subgroups. Two challenges arise: the target subgroup may be underrepresented (stratum imbalance), and the direction of a difference may reverse across subgroups (sign reversal). We propose two econometrics-inspired methods: one introduces feature--covariate interactions to detect sign reversals, and the other applies within-stratum demeaning and inverse-frequency reweighting to equalize underrepresented strata. Synthetic experiments show each method outperforms global baselines in its targeted setting, and expert evaluation on two real-world datasets confirms that covariate-aware generation surfaces more useful hypotheses within relevant subgroups.

When do language diffusion models memorize their training data, and how to quantitatively assess their true generative regime? We address these questions by showing that Uniform-based Discrete Diffusion Models (UDDMs) fundamentally behave as Associative Memories (AMs) with emergent creative capabilities. The core idea of an AM is to reliably recover stored data points as memories by establishing distinct basins of attraction around them. Historically, models like Hopfield networks use an explicit energy function to guarantee these stable attractors. We broaden this perspective by leveraging the observation that energy is not strictly necessary, as basins of attraction can also be formed via conditional likelihood maximization. By evaluating token recovery of training and test examples, we identify in UDDMs a sharp memorization-to-generalization transition governed by the size of the training dataset: as it increases, basins around training examples shrink and basins around unseen test examples expand, until both later converge to the same level. Crucially, we can detect this transition using only the conditional entropy of predicted token sequences: memorization is characterized by vanishing conditional entropy, while in the generalization regime the conditional entropy of most tokens remains finite. Thus, conditional entropy offers a practical probe for the memorization-to-generalization transition in deployed models.

We develop a data-driven information-theoretic framework for sharp partial identification of causal effects under unmeasured confounding. Existing approaches often rely on restrictive assumptions, such as bounded or discrete outcomes; require external inputs (for example, instrumental variables, proxies, or user-specified sensitivity parameters); necessitate full structural causal model specifications; or focus solely on population-level averages while neglecting covariate-conditional effects. We overcome all four limitations simultaneously by establishing novel information-theoretic, data-driven divergence bounds. Our key theoretical contribution shows that the f-divergence between the observational distribution P(Y | A = a, X = x) and the interventional distribution P(Y | do(A = a), X = x) is upper bounded by a function of the propensity score alone. This result enables sharp partial identification of conditional causal effects directly from observational data, without requiring external sensitivity parameters, auxiliary variables, full structural specifications, or outcome boundedness assumptions. For practical implementation, we develop a semiparametric estimator satisfying Neyman orthogonality (Chernozhukov et al., 2018), which ensures root-n consistent inference even when nuisance functions are estimated via flexible machine learning methods. Simulation studies and real-world data applications, implemented in the GitHub repository (https://github.com/yonghanjung/Information-Theretic-Bounds), demonstrate that our framework provides tight and valid causal bounds across a wide range of data-generating processes.

Many social and environmental phenomena are associated with macroscopic changes in the built environment, captured by satellite imagery on a global scale and with daily temporal resolution. While widely used for prediction, these images and especially image sequences remain underutilized for causal inference, especially in the context of randomized controlled trials (RCTs), where causal identification is established by design. In this paper, we develop and compare a set of general tools for analyzing Conditional Average Treatment Effects (CATEs) from temporal satellite data that can be applied to any RCT where geographical identifiers are available. Through a simulation study, we analyze different modeling strategies for estimating CATE in sequences of satellite images. We find that image sequence representation models with more parameters generally yield a greater ability to detect heterogeneity. To explore the role of model and data choice in practice, we apply the approaches to two influential RCTs -- Banerjee et al. (2015), a poverty study in Cusco, Peru, and Bolsen et al. (2014), a water conservation experiment in Georgia, USA. We benchmark our image sequence models against image-only, tabular-only, and combined image-tabular data sources, summarizing practical implications for investigators in a multivariate analysis. Land cover classifications over satellite images facilitate interpretation of what image features drive heterogeneity. We also show robustness to data and model choice of satellite-based generalization of the RCT results to larger geographical areas outside the original. Overall, this paper shows how satellite sequence data can be incorporated into the analysis of RCTs, and provides evidence about the implications of data, model, and evaluation metric choice for causal analysis.

We introduce a novel score-based diffusion framework named Twigs that incorporates multiple co-evolving flows for enriching conditional generation tasks. Specifically, a central or trunk diffusion process is associated with a primary variable (e.g., graph structure), and additional offshoot or stem processes are dedicated to dependent variables (e.g., graph properties or labels). A new strategy, which we call loop guidance, effectively orchestrates the flow of information between the trunk and the stem processes during sampling. This approach allows us to uncover intricate interactions and dependencies, and unlock new generative capabilities. We provide extensive experiments to demonstrate strong performance gains of the proposed method over contemporary baselines in the context of conditional graph generation, underscoring the potential of Twigs in challenging generative tasks such as inverse molecular design and molecular optimization.

Conditional generative models are increasingly used for scientific prediction beyond the direct training support. Yet scientific questions often concern whether one intervention changes the effect of another. Such interactions can be of primary interest while explaining little of the total variation, allowing models to appear accurate overall without recovering the relevant scientific effect. It remains unclear how these models learn interactions and when these successfully extrapolate to unseen conditions. We therefore study interaction recovery in flow-matching models using a physiological time-series simulator, drug dose-response data, combinatorial cell perturbations, and molecular conformer generations, where we separate recovery from hallucinated interaction structure. In the controlled setting, individual effects are learned much earlier than interactions and models hallucinate interactions where none exist. Across settings, we find qualitatively different generalization problems, with successful prediction depending on whether condition structure continues from observed to held-out targets. When it does, interactions are recoverable. If not, models can generate plausible responses while missing the interaction. We furthermore find that hallucinations increase as targets become less identifiable, and that successful interaction recovery in output space can fail under nonlinear readouts. Finally, we show that aggregate fidelity metrics can conceal whether models learn and extrapolate interactions.

Crowd counting is a fundamental problem in crowd analysis which is typically accomplished by estimating a crowd density map and summing over the density values. However, this approach suffers from background noise accumulation and loss of density due to the use of broad Gaussian kernels to create the ground truth density maps. This issue can be overcome by narrowing the Gaussian kernel. However, existing approaches perform poorly when trained with ground truth density maps with broad kernels. To deal with this limitation, we propose using conditional diffusion models to predict density maps, as diffusion models show high fidelity to training data during generation. With that, we present CrowdDiff that generates the crowd density map as a reverse diffusion process. Furthermore, as the intermediate time steps of the diffusion process are noisy, we incorporate a regression branch for direct crowd estimation only during training to improve the feature learning. In addition, owing to the stochastic nature of the diffusion model, we introduce producing multiple density maps to improve the counting performance contrary to the existing crowd counting pipelines. We conduct extensive experiments on publicly available datasets to validate the effectiveness of our method. CrowdDiff outperforms existing state-of-the-art crowd counting methods on several public crowd analysis benchmarks with significant improvements.

Accurate epidemic forecasting is crucial for outbreak preparedness, but existing data-driven models are often brittle. Typically trained on a single pathogen, they struggle with data scarcity during new outbreaks and fail under distribution shifts caused by viral evolution or interventions. However, decades of surveillance data and the design of various compartmental models from diverse diseases offer an untapped source of transferable knowledge. To leverage the collective lessons from history, we propose CAPE, the first open-source pre-trained model for epidemic forecasting. Unlike existing time series foundation models that overlook epidemiological challenges, CAPE models epidemic dynamics as mixtures of latent compartmental population states, termed compartmental prototypes. It models a flexible dictionary of compartment prototypes directly from a large collection of simulation data, enabling each outbreak to be expressed as a time-varying mixture that links observed infections to latent population states. To promote robust generalization, CAPE adopts the next-token-prediction paradigm during pre-training with lightweight epidemic-aware regularization that aligns the learned prototypes with epidemiological semantics. On a comprehensive benchmark spanning 17 diseases, CAPE significantly outperforms strong baselines with zero-shot forecasting. This work represents a principled step toward pre-trained epidemic models that are both transferable and epidemiologically grounded. We provide our code in: https://github.com/nuuuh/CAPE.

Conditional diffusion models are powerful generative models that can leverage various types of conditional information, such as class labels, segmentation masks, or text captions. However, in many real-world scenarios, conditional information may be noisy or unreliable due to human annotation errors or weak alignment. In this paper, we propose the Coherence-Aware Diffusion (CAD), a novel method that integrates coherence in conditional information into diffusion models, allowing them to learn from noisy annotations without discarding data. We assume that each data point has an associated coherence score that reflects the quality of the conditional information. We then condition the diffusion model on both the conditional information and the coherence score. In this way, the model learns to ignore or discount the conditioning when the coherence is low. We show that CAD is theoretically sound and empirically effective on various conditional generation tasks. Moreover, we show that leveraging coherence generates realistic and diverse samples that respect conditional information better than models trained on cleaned datasets where samples with low coherence have been discarded.

Datasets scraped from the internet have been critical to the successes of large-scale machine learning. Yet, this very success puts the utility of future internet-derived datasets at potential risk, as model outputs begin to replace human annotations as a source of supervision. In this work, we first formalize a system where interactions with one model are recorded as history and scraped as training data in the future. We then analyze its stability over time by tracking changes to a test-time bias statistic (e.g. gender bias of model predictions). We find that the degree of bias amplification is closely linked to whether the model's outputs behave like samples from the training distribution, a behavior which we characterize and define as consistent calibration. Experiments in three conditional prediction scenarios - image classification, visual role-labeling, and language generation - demonstrate that models that exhibit a sampling-like behavior are more calibrated and thus more stable. Based on this insight, we propose an intervention to help calibrate and stabilize unstable feedback systems. Code is available at https://github.com/rtaori/data_feedback.

The population dynamics of molecules, cells, and organisms are governed by a number of unknown forces. In the last decade, population dynamics have predominantly been modeled with Wasserstein gradient flows. However, since gradient flows minimize free energy, they fail to capture important dynamical properties, such as periodicity. In this work, we propose a change in perspective by considering dynamics that minimize a population-level action under a damped Wasserstein Lagrangian. By deriving the corresponding Hamiltonian equations of motion, we formalize Wasserstein Lagrangian Mechanics, a structured class of second-order dynamics that encompasses classical mechanics, quantum mechanics, and gradient flows. We then propose WLM as the first algorithm that learns these second-order dynamics from observed marginals, without specifying the Lagrangian. By directly learning the population mechanics, WLM can both forecast and interpolate unseen marginals, and outperforms existing gradient flow and flow matching methods across a wide range of dynamics, including vortex dynamics, embryonic development, and flocking.

Robust generalization under distribution shift remains a key challenge for conditional generative modeling: conditional flow-based methods often fit the training conditions well but fail to extrapolate to unseen ones. We introduce SP-FM, a shortest-path flow-matching framework that improves out-of-distribution (OOD) generalization by conditioning both the base distribution and the flow field on the condition. Specifically, SP-FM learns a condition-dependent base distribution parameterized as a flexible, learnable mixture, together with a condition-dependent vector field trained via shortest-path flow matching. Conditioning the base allows the model to adapt its starting distribution across conditions, enabling smooth interpolation and more reliable extrapolation beyond the observed training range. We provide theoretical insights into the resulting conditional transport and show how mixture-conditioned bases enhance robustness under shift. Empirically, SP-FM is effective across heterogeneous domains, including predicting responses to unseen perturbations in single-cell transcriptomics and modeling treatment effects in high-content microscopy--based drug screening. Overall, SP-FM provides a simple yet effective plug-in strategy for improving conditional generative modeling and OOD generalization across diverse domains.

We explore a data-driven approach for learning to optimize neural networks. We construct a dataset of neural network checkpoints and train a generative model on the parameters. In particular, our model is a conditional diffusion transformer that, given an initial input parameter vector and a prompted loss, error, or return, predicts the distribution over parameter updates that achieve the desired metric. At test time, it can optimize neural networks with unseen parameters for downstream tasks in just one update. We find that our approach successfully generates parameters for a wide range of loss prompts. Moreover, it can sample multimodal parameter solutions and has favorable scaling properties. We apply our method to different neural network architectures and tasks in supervised and reinforcement learning.

Longitudinal observational data are often subject to informative missingness. For example, in healthcare research using electronic health records, covariates and outcomes are measured only when patients interact with the healthcare system. Whether these data are observed usually depends on the unobserved variable values themselves, introducing a common form of data missing not at random. We develop identification and estimation methods for the effects of longitudinal modified treatment policies under a self-censoring model which explicitly models this dependence. We consider effects of treatments that can be modified only at measurement times (e.g., interactions with the heathcare system). We study two settings: one in which the observed history suffices for treatment confounding control, and another in which confounder control requires covariate values that were not measured at missed visits. In both settings, we combine longitudinal causal identification with shadow-variable conditional moment restrictions to obtain recursive identification formulas for the counterfactual outcome mean. We derive gradients of the pathwise derivatives and second-order remainder expansions, and use these results to construct estimators that accommodate machine learning for nuisance-function estimation. Under suitable product-rate conditions and cross-fitting, the estimators are asymptotically linear and permit root-n inference, including simultaneous inference across outcome times. We also describe conditional-moment learning and ensemble approaches for estimating the nuisance functions required by our approach, together with a pool-and-smooth strategy that borrows information across sparsely measured outcomes.

To measure the difference between two probability distributions, referred to as the source and target, respectively, we exploit both the chain rule and Bayes' theorem to construct conditional transport (CT), which is constituted by both a forward component and a backward one. The forward CT is the expected cost of moving a source data point to a target one, with their joint distribution defined by the product of the source probability density function (PDF) and a source-dependent conditional distribution, which is related to the target PDF via Bayes' theorem. The backward CT is defined by reversing the direction. The CT cost can be approximated by replacing the source and target PDFs with their discrete empirical distributions supported on mini-batches, making it amenable to implicit distributions and stochastic gradient descent-based optimization. When applied to train a generative model, CT is shown to strike a good balance between mode-covering and mode-seeking behaviors and strongly resist mode collapse. On a wide variety of benchmark datasets for generative modeling, substituting the default statistical distance of an existing generative adversarial network with CT is shown to consistently improve the performance. PyTorch code is provided.

Conditional Text Generation has drawn much attention as a topic of Natural Language Generation (NLG) which provides the possibility for humans to control the properties of generated contents. Current conditional generation models cannot handle emerging conditions due to their joint end-to-end learning fashion. When a new condition added, these techniques require full retraining. In this paper, we present a new framework named Pre-train and Plug-in Variational Auto-Encoder (PPVAE) towards flexible conditional text generation. PPVAE decouples the text generation module from the condition representation module to allow "one-to-many" conditional generation. When a fresh condition emerges, only a lightweight network needs to be trained and works as a plug-in for PPVAE, which is efficient and desirable for real-world applications. Extensive experiments demonstrate the superiority of PPVAE against the existing alternatives with better conditionality and diversity but less training effort.

Recent advancements in generative modeling have made it possible to generate high-quality content from context information, but a key question remains: how to teach models to know when to generate content? To answer this question, this study proposes a novel event generative model that draws its statistical intuition from marked temporal point processes, and offers a clean, flexible, and computationally efficient solution for a wide range of applications involving multi-dimensional marks. We aim to capture the distribution of the point process without explicitly specifying the conditional intensity or probability density. Instead, we use a conditional generator that takes the history of events as input and generates the high-quality subsequent event that is likely to occur given the prior observations. The proposed framework offers a host of benefits, including exceptional efficiency in learning the model and generating samples, as well as considerable representational power to capture intricate dynamics in multi- or even high-dimensional event space. Our numerical results demonstrate superior performance compared to other state-of-the-art baselines.

Developing efficient multi-objective optimization methods to compute the Pareto set of optimal compromises between conflicting objectives remains a key challenge, especially for large-scale and expensive problems. To bridge this gap, we introduce SPREAD, a generative framework based on Denoising Diffusion Probabilistic Models (DDPMs). SPREAD first learns a conditional diffusion process over points sampled from the decision space and then, at each reverse diffusion step, refines candidates via a sampling scheme that uses an adaptive multiple gradient descent-inspired update for fast convergence alongside a Gaussian RBF-based repulsion term for diversity. Empirical results on multi-objective optimization benchmarks, including offline and Bayesian surrogate-based settings, show that SPREAD matches or exceeds leading baselines in efficiency, scalability, and Pareto front coverage.

Many of society's most pressing challenges, from pandemic response to supply chain disruptions to climate adaptation, emerge from the collective behavior of millions of autonomous agents making decisions over time. Large Population Models (LPMs) offer an approach to understand these complex systems by simulating entire populations with realistic behaviors and interactions at unprecedented scale. LPMs extend traditional modeling approaches through three key innovations: computational methods that efficiently simulate millions of agents simultaneously, mathematical frameworks that learn from diverse real-world data streams, and privacy-preserving communication protocols that bridge virtual and physical environments. This allows researchers to observe how agent behavior aggregates into system-level outcomes and test interventions before real-world implementation. While current AI advances primarily focus on creating "digital humans" with sophisticated individual capabilities, LPMs develop "digital societies" where the richness of interactions reveals emergent phenomena. By bridging individual agent behavior and population-scale dynamics, LPMs offer a complementary path in AI research illuminating collective intelligence and providing testing grounds for policies and social innovations before real-world deployment. We discuss the technical foundations and some open problems here. LPMs are implemented by the AgentTorch framework (github.com/AgentTorch/AgentTorch)

In recent years, diffusion models have gained popularity for their ability to generate higher-quality images in comparison to GAN models. However, like any other large generative models, these models require a huge amount of data, computational resources, and meticulous tuning for successful training. This poses a significant challenge, rendering it infeasible for most individuals. As a result, the research community has devised methods to leverage pre-trained unconditional diffusion models with additional guidance for the purpose of conditional image generative. These methods enable conditional image generations on diverse inputs and, most importantly, circumvent the need for training the diffusion model. In this paper, our objective is to reduce the time-required and computational overhead introduced by the addition of guidance in diffusion models -- while maintaining comparable image quality. We propose a set of methods based on our empirical analysis, demonstrating a reduction in computation time by approximately threefold.

Inferring cellular dynamics from unpaired single-cell snapshots requires modeling both state transitions and population growth or death. Unbalanced dynamic optimal transport (UDOT) addresses this by penalizing growth along transport paths, making the choice of growth penalty a key way to encode biological priors on proliferation and apoptosis. However, existing UDOT solvers either rely on computationally expensive NeuralODE simulations or depend on analytical solutions of conditional paths, restricting their efficiency solely to quadratic penalties, i.e. Wasserstein-Fisher-Rao (WFR) geodesics. To enable an efficient UDOT solver for general growth penalties, we first show that concave growth penalties lead to degenerate solutions where growth and transport are separated. We then introduce Simulation-free Unbalanced Dynamic Optimal transport (SUDO), a simulation-free framework for UDOT with general non-quadratic convex growth penalties. SUDO learns the conditional paths and transport costs, solves the induced semi-coupling problem, and subsequently leverages unbalanced flow matching to achieve a simulation-free solution. On WFR benchmarks, SUDO matches the accuracy of efficient, analytical solution-driven algorithms while outperforming simulation-based methods in computational speed. Beyond WFR, SUDO supports asymmetric penalties that encode proliferation-dominant priors and produce more plausible trajectories and growth estimates on synthetic and single-cell datasets.

Current controllable diffusion models typically rely on fixed architectures that modify intermediate activations to inject guidance conditioned on a new modality. This approach uses a static conditioning strategy for a dynamic, multi-stage denoising process, limiting the model's ability to adapt its response as the generation evolves from coarse structure to fine detail. We introduce TC-LoRA (Temporally Modulated Conditional LoRA), a new paradigm that enables dynamic, context-aware control by conditioning the model's weights directly. Our framework uses a hypernetwork to generate LoRA adapters on-the-fly, tailoring weight modifications for the frozen backbone at each diffusion step based on time and the user's condition. This mechanism enables the model to learn and execute an explicit, adaptive strategy for applying conditional guidance throughout the entire generation process. Through experiments on various data domains, we demonstrate that this dynamic, parametric control significantly enhances generative fidelity and adherence to spatial conditions compared to static, activation-based methods. TC-LoRA establishes an alternative approach in which the model's conditioning strategy is modified through a deeper functional adaptation of its weights, allowing control to align with the dynamic demands of the task and generative stage.

Recent advances in diffusion models have shown remarkable potential in the conditional generation of novel molecules. These models can be guided in two ways: (i) explicitly, through additional features representing the condition, or (ii) implicitly, using a property predictor. However, training property predictors or conditional diffusion models requires an abundance of labeled data and is inherently challenging in real-world applications. We propose a novel approach that attenuates the limitations of acquiring large labeled datasets by leveraging domain knowledge from quantum chemistry as a non-differentiable oracle to guide an unconditional diffusion model. Instead of relying on neural networks, the oracle provides accurate guidance in the form of estimated gradients, allowing the diffusion process to sample from a conditional distribution specified by quantum chemistry. We show that this results in more precise conditional generation of novel and stable molecular structures. Our experiments demonstrate that our method: (1) significantly reduces atomic forces, enhancing the validity of generated molecules when used for stability optimization; (2) is compatible with both explicit and implicit guidance in diffusion models, enabling joint optimization of molecular properties and stability; and (3) generalizes effectively to molecular optimization tasks beyond stability optimization.

Practitioners frequently aim to infer an unobserved population trajectory using sample snapshots at multiple time points. For instance, in single-cell sequencing, scientists would like to learn how gene expression evolves over time. But sequencing any cell destroys that cell. So we cannot access any cell's full trajectory, but we can access snapshot samples from many cells. Stochastic differential equations are commonly used to analyze systems with full individual-trajectory access; since here we have only sample snapshots, these methods are inapplicable. The deep learning community has recently explored using Schr\"odinger bridges (SBs) and their extensions to estimate these dynamics. However, these methods either (1) interpolate between just two time points or (2) require a single fixed reference dynamic within the SB, which is often just set to be Brownian motion. But learning piecewise from adjacent time points can fail to capture long-term dependencies. And practitioners are typically able to specify a model class for the reference dynamic but not the exact values of the parameters within it. So we propose a new method that (1) learns the unobserved trajectories from sample snapshots across multiple time points and (2) requires specification only of a class of reference dynamics, not a single fixed one. In particular, we suggest an iterative projection method inspired by Schr\"odinger bridges; we alternate between learning a piecewise SB on the unobserved trajectories and using the learned SB to refine our best guess for the dynamics within the reference class. We demonstrate the advantages of our method via a well-known simulated parametric model from ecology, simulated and real data from systems biology, and real motion-capture data.

Social simulation offers the social sciences an experimental instrument that the real world cannot supply, and generative agents have transformed it by acting as silicon samples that unite agent-based modeling with real behavioral data. Existing platforms verify collective behavior, align simulated populations with real societies in cross-sections, and employ autonomous agents for the research process. However, two social science requirements remain without systematic support: intervention in the content of a simulation and the researcher's control over the process that produces it. We present SocioVerse2, which extends SocioVerse 1.0 into a human-AI co-evolutionary paradigm built from two loops and one infrastructure. The longitudinal simulation loop simulates the target population with evolving environments and forks counterfactual branches via interventions. The controllable research loop takes the study itself as an editable state and updates state versions via controllable editing. The social science agentic infrastructure carries both loops through composable skills with researcher checkpoints, a population service over five persona pools, and an environment service over 21 real-world signal sources with point-in-time guarantees. We validate SocioVerse2 across three case families and seven case studies, from reproducing canonical agent-based models to modeling policy processes on real records and nowcasting macro-economic indices beyond the response model's knowledge cutoff. With the human-AI co-evolutionary paradigm, these cases go beyond system demonstrations to become substantive studies that investigate frontier questions in their respective disciplines. Code, data services, and a workbench are released as open-source resources.

Conditional visual generation has witnessed remarkable progress with the advent of diffusion models (DMs), especially in tasks like control-to-image generation. However, challenges such as expensive computational cost, high inference latency, and difficulties of integration with large language models (LLMs) have necessitated exploring alternatives to DMs. This paper introduces ControlVAR, a novel framework that explores pixel-level controls in visual autoregressive (VAR) modeling for flexible and efficient conditional generation. In contrast to traditional conditional models that learn the conditional distribution, ControlVAR jointly models the distribution of image and pixel-level conditions during training and imposes conditional controls during testing. To enhance the joint modeling, we adopt the next-scale AR prediction paradigm and unify control and image representations. A teacher-forcing guidance strategy is proposed to further facilitate controllable generation with joint modeling. Extensive experiments demonstrate the superior efficacy and flexibility of ControlVAR across various conditional generation tasks against popular conditional DMs, \eg, ControlNet and T2I-Adaptor. Code: https://github.com/lxa9867/ControlVAR.

We introduce a new predator-prey model by replacing the growth and predation constant by a square matrix, and the population density as a population vector. The classical Lotka-Volterra model describes a population that either modulates or converges. Stability analysis of such models have been extensively studied by the works of Merdan (https://doi.org/10.1016/j.chaos.2007.06.062). The new model adds complexity by introducing an age group structure where the population of each age group evolves as prescribed by the Leslie matrix. The added complexity changes the behavior of the model such that the population either displays roughly an exponential growth or decay. We first provide an exact equation that describes a time evolution and use analytic techniques to obtain an approximate growth factor. We also discuss the variants of the Leslie model, i.e., the complex value predator-prey model and the competitive model. We then prove the Last Species Standing theorem that determines the dominant population in the large time limit. The recursive structure of the model denies the application of simple regression. We discuss a machine learning scheme that allows an admissible fit for the population evolution of Paramecium Aurelia and Paramecium Caudatum. Another potential avenue to simplify the computation is to use the machinery of quantum operators. We demonstrate the potential of this approach by computing the Hamiltonian of a simple Leslie system.

This chapter provides a pedagogical introduction and overview of spatial and temporal correlation and fluctuation effects resulting from the fundamentally stochastic kinetics underlying chemical reactions and the dynamics of populations or epidemics. After reviewing the assumptions and mean-field type approximations involved in the construction of chemical rate equations for uniform reactant densities, we first discuss spatial clustering in birth-death systems, where non-linearities are introduced through either density-limiting pair reactions, or equivalently via local imposition of finite carrying capacities. The competition of offspring production, death, and non-linear inhibition induces a population extinction threshold, which represents a non-equilibrium phase transition that separates active from absorbing states. This continuous transition is characterized by the universal scaling exponents of critical directed percolation clusters. Next we focus on the emergence of depletion zones in single-species annihilation processes and spatial population segregation with the associated reaction fronts in two-species pair annihilation. These strong (anti-)correlation effects are dynamically generated by the underlying stochastic kinetics. Finally, we address noise-induced and fluctuation-stabilized spatio-temporal patterns in basic predator-prey systems, exemplified by spreading activity fronts in the two-species Lotka-Volterra model as well as spiral structures in the May-Leonard variant of cyclically competing three-species systems akin to rock-paper-scissors games.

LLMs are often trained with RL from human or AI feedback, yet such methods typically compress nuanced feedback into scalar rewards, discarding much of their richness and inducing scale imbalance. We propose treating verbal feedback as a conditioning signal. Inspired by language priors in text-to-image generation, which enable novel outputs from unseen prompts, we introduce the feedback-conditional policy (FCP). FCP learns directly from response-feedback pairs, approximating the feedback-conditional posterior through maximum likelihood training on offline data. We further develop an online bootstrapping stage where the policy generates under positive conditions and receives fresh feedback to refine itself. This reframes feedback-driven learning as conditional generation rather than reward optimization, offering a more expressive way for LLMs to directly learn from verbal feedback. Our code is available at https://github.com/sail-sg/feedback-conditional-policy.

Dynamical models of cognition play an increasingly important role in driving theoretical and experimental research in psychology. Therefore, parameter estimation, model analysis and comparison of dynamical models are of essential importance. Here we propose a maximum-likelihood approach for model analysis in a fully dynamical framework that includes time-ordered experimental data. Our methods can be applied to dynamical models for the prediction of discrete behavior (e.g., movement onsets), in particular, we use a dynamical model of saccade generation in scene viewing as a case study for our approach. For this model, the likelihood function can be computed directly by numerical simulation, which enables more efficient parameter estimation including Bayesian inference to obtain reliable estimates and corresponding credible intervals. Using hierarchical models inference is even possible for individual observers. Furthermore, our likelihood approach can be used to compare different models. In our example, the dynamical framework is shown to outperform non-dynamical statistical models. Additionally, the likelihood based evaluation differentiates model variants, which produced indistinguishable predictions on hitherto used statistics. Our results indicate that the likelihood approach is a promising framework for dynamical cognitive models.

Matching objectives underpin the success of modern generative models and rely on constructing conditional paths that transform a source distribution into a target distribution. Despite being a fundamental building block, conditional paths have been designed principally under the assumption of Euclidean geometry, resulting in straight interpolations. However, this can be particularly restrictive for tasks such as trajectory inference, where straight paths might lie outside the data manifold, thus failing to capture the underlying dynamics giving rise to the observed marginals. In this paper, we propose Metric Flow Matching (MFM), a novel simulation-free framework for conditional flow matching where interpolants are approximate geodesics learned by minimizing the kinetic energy of a data-induced Riemannian metric. This way, the generative model matches vector fields on the data manifold, which corresponds to lower uncertainty and more meaningful interpolations. We prescribe general metrics to instantiate MFM, independent of the task, and test it on a suite of challenging problems including LiDAR navigation, unpaired image translation, and modeling cellular dynamics. We observe that MFM outperforms the Euclidean baselines, particularly achieving SOTA on single-cell trajectory prediction.

Predicting cellular responses to perturbations is a central problem in cellular biology, with broad applications in systems biology and drug discovery. This task is challenging because cellular responses can be complex and cell-state dependent, intrinsic cell-to-cell variability can be confounded with perturbation effects, and destructive single-cell RNA sequencing precludes paired measurements of the same cell before and after treatment. Flow matching transports control cells to perturbed states flexibly, but acting on the full cell state can confound perturbation effects with pre-existing cell-to-cell variability. Disentangled approaches separate responsive from invariant components, but model perturbations through prescribed mechanisms, such as latent shifts or graph edits, limiting their flexibility. We address both limitations in a unified framework. A variational encoder disentangles each cell into an invariant block, capturing state unaffected by the perturbation, and a responsive block, capturing state it changes, through conditional priors and an information-theoretic invariance constraint. Conditional flow matching transports only the responsive block, conditioned on the perturbation and invariant state, yielding a flexible, data-driven model of perturbation effects without confounding pre-existing variability. Across several benchmarks, our method outperforms the strongest published method in settings involving combinatorial and unseen perturbation prediction.

Epidemic intervention policies are textual artefacts that human decision-makers interpret, justify, and revise through natural language, making large language models a natural candidate for epidemic policy reasoning. A naive LLM, however, lacks the epidemic dynamics needed to project intervention consequences, the quantitative surveillance signals required to assess severity, and the institutional constraints that define admissible actions. We present EpiWorld, a closed-loop framework that grounds an LLM policy actor in a learned action-conditioned epidemiological world model and a tiered skill library of public-health protocols, surveillance tools, and adaptive lessons accumulated through after-action analysis. Given a candidate intervention, the world model predicts regional epidemic evolution and enables fast counterfactual rollouts that provide feedback for policy selection and refinement. Outcomes of simulated futures are distilled into reusable lessons while protocol constraints remain fixed, allowing the decision process to improve without sacrificing interpretability or controllability. We evaluate both the world model and the end-to-end framework on retrospective COVID-19 and Influenza datasets: the world model achieves the best out-of-distribution Peak-MAE among all forecasting baselines, and the closed-loop framework reduces cumulative hospitalisation by up to 59% across datasets and by an average of ~16% across six LLM backbones, outperforming reinforcement-learning and optimal-control policy baselines.

Scientific measurements such as single-cell RNA (scRNA) sequencing often take the form of nonnegative integer counts, whereas continuous-state diffusion models approximate this discrete structure using continuous coordinates. Building on stochastic chemical reaction networks (CRNs), a class of count-native Markov jump processes, we introduce CRNDiff, a structured framework that combines count-space diffusion with inference-time conditioning on rare subpopulations. An independent birth--death instantiation yields a closed-form transition kernel for forward noising. This kernel enables reverse sampling via forward-filtering backward-sampling (FFBS) and supports data-driven selection of the terminal noising time, eliminating the need for a validation sweep. This tractability also lets us introduce tilted Feynman--Kac (FK) steering, a method for sampling target subpopulations from a frozen generator without retraining. By tilting posterior marginals before FK particle correction, steering mitigates importance-weight concentration when the target population is rare. Using scRNA-seq data from the human heart cell atlas, we test the ability of CRNDiff to generate cell-type-specific distributions. Across the three evaluated target populations, CRNDiff achieves the highest conditional fidelity among the evaluated generative models, with larger mean purity margins for rarer target populations. Generated cells preserve marker-level differential-expression structure. Replacing real training cells for the target classes with generated cells yields downstream classification performance approaching that of the real-data reference.

Early warning signals have been proposed to forecast the possibility of a critical transition, such as the eutrophication of a lake, the collapse of a coral reef, or the end of a glacial period. Because such transitions often unfold on temporal and spatial scales that can be difficult to approach by experimental manipulation, research has often relied on historical observations as a source of natural experiments. Here we examine a critical difference between selecting systems for study based on the fact that we have observed a critical transition and those systems for which we wish to forecast the approach of a transition. This difference arises by conditionally selecting systems known to experience a transition of some sort and failing to account for the bias this introduces -- a statistical error often known as the Prosecutor's Fallacy. By analysing simulated systems that have experienced transitions purely by chance, we reveal an elevated rate of false positives in common warning signal statistics. We further demonstrate a model-based approach that is less subject to this bias than these more commonly used summary statistics. We note that experimental studies with replicates avoid this pitfall entirely.

Standard methods for detecting discontinuities in conditional means are not applicable to outcomes that are complex, non-Euclidean objects like distributions, networks, or covariance matrices. This article develops a nonparametric test for jumps in conditional means when outcomes lie in a non-Euclidean metric space. Using local Fr\'echet regressionx2014which generalizes standard regression to metric-space valued datax2014the method estimates a mean path on either side of a candidate cutoff, extending existing k-sample tests to a flexible regression setting. Key theoretical contributions include a central limit theorem for the local estimator of the conditional Fr\'echet variance and the asymptotic validity and consistency of the proposed test. Simulations confirm nominal size control and robust power in finite samples. Two applications demonstrate the method's value by revealing effects invisible to scalar-based tests. First, I detect a sharp change in work-from-home compositions at Washington State's income threshold for non-compete enforceability during COVID-19, highlighting remote work's role as a bargaining margin. Second, I find that countries restructure their input-output networks after losing preferential US trade access. These findings underscore that analyzing regression functions within their native metric spaces can reveal structural discontinuities that scalar summaries would miss.

Many empirical studies of labor market questions rely on estimating relatively simple predictive models using small, carefully constructed longitudinal survey datasets based on hand-engineered features. Large Language Models (LLMs), trained on massive datasets, encode vast quantities of world knowledge and can be used for the next job prediction problem. However, while an off-the-shelf LLM produces plausible career trajectories when prompted, the probability with which an LLM predicts a particular job transition conditional on career history will not, in general, align with the true conditional probability in a given population. Recently, Vafa et al. (2024) introduced a transformer-based "foundation model", CAREER, trained using a large, unrepresentative resume dataset, that predicts transitions between jobs; it further demonstrated how transfer learning techniques can be used to leverage the foundation model to build better predictive models of both transitions and wages that reflect conditional transition probabilities found in nationally representative survey datasets. This paper considers an alternative where the fine-tuning of the CAREER foundation model is replaced by fine-tuning LLMs. For the task of next job prediction, we demonstrate that models trained with our approach outperform several alternatives in terms of predictive performance on the survey data, including traditional econometric models, CAREER, and LLMs with in-context learning, even though the LLM can in principle predict job titles that are not allowed in the survey data. Further, we show that our fine-tuned LLM-based models' predictions are more representative of the career trajectories of various workforce subpopulations than off-the-shelf LLM models and CAREER. We conduct experiments and analyses that highlight the sources of the gains in the performance of our models for representative predictions.

We address the problem of learning the dynamics of an unknown non-parametric system linking a target and a feature time series. The feature time series is measured on a sparse and irregular grid, while we have access to only a few points of the target time series. Once learned, we can use these dynamics to predict values of the target from the previous values of the feature time series. We frame this task as learning the solution map of a controlled differential equation (CDE). By leveraging the rich theory of signatures, we are able to cast this non-linear problem as a high-dimensional linear regression. We provide an oracle bound on the prediction error which exhibits explicit dependencies on the individual-specific sampling schemes. Our theoretical results are illustrated by simulations which show that our method outperforms existing algorithms for recovering the full time series while being computationally cheap. We conclude by demonstrating its potential on real-world epidemiological data.

Societies are complex. Properties of social systems can be explained by the interplay and weaving of individual actions. Incentives are key to understand people's choices and decisions. For instance, individual preferences of where to live may lead to the emergence of social segregation. In this paper, we combine Reinforcement Learning (RL) with Agent Based Models (ABM) in order to address the self-organizing dynamics of social segregation and explore the space of possibilities that emerge from considering different types of incentives. Our model promotes the creation of interdependencies and interactions among multiple agents of two different kinds that want to segregate from each other. For this purpose, agents use Deep Q-Networks to make decisions based on the rules of the Schelling Segregation model and the Predator-Prey model. Despite the segregation incentive, our experiments show that spatial integration can be achieved by establishing interdependencies among agents of different kinds. They also reveal that segregated areas are more probable to host older people than diverse areas, which attract younger ones. Through this work, we show that the combination of RL and ABMs can create an artificial environment for policy makers to observe potential and existing behaviors associated to incentives.

Virtual-cell models aim to predict how cell populations respond to perturbations, but control and treated cells are measured as unpaired populations, complicating the learning of perturbation-specific effects. We present SCALE, a conditional transport model that represents cells as unordered sets and predicts treated populations without cell-level matching. A shared set-aware encoder and conditional DiT backbone learn latent transport, making endpoint supervision directly delta-aligned without an auxiliary delta objective. Across genetic, chemical, developmental and immune perturbations, SCALE recovered gene-expression changes, response directions and population structure. In CRISPR data with dominant cell-line effects, SCALE outperformed competing methods across seven metrics and maintained separation among gene-target representations rather than collapsing them into a shared region. SCALE further prioritized cytokines predicted to produce distinct immune activation and inflammatory responses. Experiments using matched PBMC samples from three donors confirmed these predicted differences. Together, SCALE enables perturbation-specific prediction from unpaired populations and supports experimental prioritization.

Multiple epidemic waves are often taken as evidence that simple compartmental models are structurally inadequate. Yet the key question is not whether a simple model can reproduce multiple peaks, but how much time-varying structure is minimally required to preserve observed epidemic-wave patterns and what can legitimately be inferred from such a representation. Using the susceptible-infectious-removed (SIR) model, we develop a framework for peak-preserving dynamic parsimony linking dynamical systems, inverse problems, statistical inference, and infectious-disease modeling. We establish exact multi-wave representability under time-varying transmission, characterize conditions for epidemic peaks and resurgence, and show the incidence-only non-identifiability of time-varying transmission and removal rates. Our main methodological contribution is minimal peak-preserving complexity (MPPC): the smallest dimension of a positive time-varying transmission function whose posterior-predictive trajectories preserve salient features, including peak count, timing, height, trough depth, and whole-curve agreement. We estimate MPPC using peak-aware approximate Bayesian computation and evaluate it through six reproducible stress tests, a Philippine COVID-19 reported-case proof of concept, and short-term future-knot projection. Across diverse data-generating mechanisms, low-dimensional time-varying SIR models can preserve aggregate epidemic-wave topology with modest dynamic complexity. However, accurate trajectory compression does not imply recovery of the underlying mechanism or reliable long-term counterfactual prediction. The framework therefore separates four often-conflated questions: representability, minimal dynamic complexity, mechanistic identifiability, and projection validity, providing a basis for parsimonious modeling of complex epidemic trajectories.

We introduce Cosmos-Transfer, a conditional world generation model that can generate world simulations based on multiple spatial control inputs of various modalities such as segmentation, depth, and edge. In the design, the spatial conditional scheme is adaptive and customizable. It allows weighting different conditional inputs differently at different spatial locations. This enables highly controllable world generation and finds use in various world-to-world transfer use cases, including Sim2Real. We conduct extensive evaluations to analyze the proposed model and demonstrate its applications for Physical AI, including robotics Sim2Real and autonomous vehicle data enrichment. We further demonstrate an inference scaling strategy to achieve real-time world generation with an NVIDIA GB200 NVL72 rack. To help accelerate research development in the field, we open-source our models and code at https://github.com/nvidia-cosmos/cosmos-transfer1.

Ecological interactions are often mediated by feedbacks between organisms and their resource environments. Yet, how resource supply dynamics dictate collective dynamical phases of an ecosystem remains unclear. Here, we analyse a generalised consumer--resource model with non-reciprocal interactions to demonstrate that self-renewing versus externally-supplied resources yield fundamentally different dynamical phase diagrams. As interactions become increasingly non-reciprocal, ecosystems relying on self-renewing resources transition from stable dynamics to chaos and ultimately to infeasibility. By contrast, ecosystems with externally-supplied resources remain stable over a broader parameter range and transition to infeasibility without experiencing an intervening chaotic phase. Using the cavity method, we derive a unified stability condition applicable to a broad class of resource supply functions, explaining why externally-supplied resources can expand the stable region. We show that stability hinges crucially on the susceptibility of resources to perturbations, which depends strongly on their supply. Further, we show that external resource supply suppresses chaos in the unstable region by drastically reducing the susceptibility of resources closest to extinction. Our findings demonstrate that resource dynamics fundamentally reshape the accessible dynamical behaviours of an ecosystem, with implications for interpreting microbial community experiments.

Learning the continuous dynamics of a system from snapshots of its temporal marginals is a problem which appears throughout natural sciences and machine learning, including in quantum systems, single-cell biological data, and generative modeling. In these settings, we assume access to cross-sectional samples that are uncorrelated over time, rather than full trajectories of samples. In order to better understand the systems under observation, we would like to learn a model of the underlying process that allows us to propagate samples in time and thereby simulate entire individual trajectories. In this work, we propose Action Matching, a method for learning a rich family of dynamics using only independent samples from its time evolution. We derive a tractable training objective, which does not rely on explicit assumptions about the underlying dynamics and does not require back-propagation through differential equations or optimal transport solvers. Inspired by connections with optimal transport, we derive extensions of Action Matching to learn stochastic differential equations and dynamics involving creation and destruction of probability mass. Finally, we showcase applications of Action Matching by achieving competitive performance in a diverse set of experiments from biology, physics, and generative modeling.

Model-free diffusion planners have shown great promise for robot motion planning, but practical robotic systems often require combining them with model-based optimization modules to enforce constraints, such as safety. Naively integrating these modules presents compatibility challenges when diffusion's multi-modal outputs behave adversarially to optimization-based modules. To address this, we introduce Joint Model-based Model-free Diffusion (JM2D), a novel generative modeling framework. JM2D formulates module integration as a joint sampling problem to maximize compatibility via an interaction potential, without additional training. Using importance sampling, JM2D guides modules outputs based only on evaluations of the interaction potential, thus handling non-differentiable objectives commonly arising from non-convex optimization modules. We evaluate JM2D via application to aligning diffusion planners with safety modules on offline RL and robot manipulation. JM2D significantly improves task performance compared to conventional safety filters without sacrificing safety. Further, we show that conditional generation is a special case of JM2D and elucidate key design choices by comparing with SOTA gradient-based and projection-based diffusion planners. More details at: https://jm2d-corl25.github.io/.

We study the problem of learning generative models for discrete sequences in a continuous embedding space. Whereas prior approaches typically operate in Euclidean space or on the probability simplex, we instead work on the sphere mathbb S^{d-1}. There the von Mises-Fisher (vMF) distribution induces a natural noise process and admits a closed-form conditional score. The conditional velocity is in general intractable. Exploiting the radial symmetry of the vMF density we reduce the continuity equation on mathbb S^{d-1} to a scalar ODE in the cosine similarity, whose unique bounded solution determines the velocity. The marginal velocity and marginal score on (mathbb S^{d-1})^L both decompose into posterior-weighted tangent sums that differ only by per-token scalar weights. This gives access to both ODE and predictor-corrector (PC) sampling. The posterior is the only learned object, trained by a cross-entropy loss. Experiments compare the vMF path against geodesic and Euclidean alternatives. The combination of vMF and PC sampling significantly improves results on Sudoku and language modeling.

A framework is proposed that addresses both conditional density estimation and latent variable discovery. The objective function maximizes explanation of variability in the data, achieved through the optimal transport barycenter generalized to a collection of conditional distributions indexed by a covariate --either given or latent-- in any suitable space. Theoretical results establish the existence of barycenters, a minimax formulation of optimal transport maps, and a general characterization of variability via the optimal transport cost. This framework leads to a family of non-parametric neural network-based algorithms, the BaryNet, with a supervised version that estimates conditional distributions and an unsupervised version that assigns latent variables. The efficacy of BaryNets is demonstrated by tests on both artificial and real-world data sets. A parallel drawn between autoencoders and the barycenter framework leads to the Barycentric autoencoder algorithm (BAE).

We present a new distribution-free conformal prediction algorithm for sequential data (e.g., time series), called the sequential predictive conformal inference (SPCI). We specifically account for the nature that time series data are non-exchangeable, and thus many existing conformal prediction algorithms are not applicable. The main idea is to adaptively re-estimate the conditional quantile of non-conformity scores (e.g., prediction residuals), upon exploiting the temporal dependence among them. More precisely, we cast the problem of conformal prediction interval as predicting the quantile of a future residual, given a user-specified point prediction algorithm. Theoretically, we establish asymptotic valid conditional coverage upon extending consistency analyses in quantile regression. Using simulation and real-data experiments, we demonstrate a significant reduction in interval width of SPCI compared to other existing methods under the desired empirical coverage.

The acute phase of the Covid-19 pandemic has made apparent the need for decision support based upon accurate epidemic modeling. This process is substantially hampered by under-reporting of cases and related data incompleteness issues. In this article we adopt the Bayesian paradigm and synthesize publicly available data via a discrete-time stochastic epidemic modeling framework. The models allow for estimating the total number of infections while accounting for the endemic phase of the pandemic. We assess the prediction of the infection rate utilizing mobility information, notably the principal components of the mobility data. We evaluate variational Bayes in this context and find that Hamiltonian Monte Carlo offers a robust inference alternative for such models. We elaborate upon vector analysis of the epidemic dynamics, thus enriching the traditional tools used for decision making. In particular, we show how certain 2-dimensional plots on the phase plane may yield intuitive information regarding the speed and the type of transmission dynamics. We investigate the potential of a two-stage analysis as a consequence of cutting feedback, for inference on certain functionals of the model parameters. Finally, we show that a point mass on critical parameters is overly restrictive and investigate informative priors as a suitable alternative.

Often we wish to predict a large number of variables that depend on each other as well as on other observed variables. Structured prediction methods are essentially a combination of classification and graphical modeling, combining the ability of graphical models to compactly model multivariate data with the ability of classification methods to perform prediction using large sets of input features. This tutorial describes conditional random fields, a popular probabilistic method for structured prediction. CRFs have seen wide application in natural language processing, computer vision, and bioinformatics. We describe methods for inference and parameter estimation for CRFs, including practical issues for implementing large scale CRFs. We do not assume previous knowledge of graphical modeling, so this tutorial is intended to be useful to practitioners in a wide variety of fields.

Data-driven deep learning models are transforming global weather forecasting. It is an open question if this success can extend to climate modeling, where the complexity of the data and long inference rollouts pose significant challenges. Here, we present the first conditional generative model that produces accurate and physically consistent global climate ensemble simulations by emulating a coarse version of the United States' primary operational global forecast model, FV3GFS. Our model integrates the dynamics-informed diffusion framework (DYffusion) with the Spherical Fourier Neural Operator (SFNO) architecture, enabling stable 100-year simulations at 6-hourly timesteps while maintaining low computational overhead compared to single-step deterministic baselines. The model achieves near gold-standard performance for climate model emulation, outperforming existing approaches and demonstrating promising ensemble skill. This work represents a significant advance towards efficient, data-driven climate simulations that can enhance our understanding of the climate system and inform adaptation strategies.

The imputation of missing values in time series has many applications in healthcare and finance. While autoregressive models are natural candidates for time series imputation, score-based diffusion models have recently outperformed existing counterparts including autoregressive models in many tasks such as image generation and audio synthesis, and would be promising for time series imputation. In this paper, we propose Conditional Score-based Diffusion models for Imputation (CSDI), a novel time series imputation method that utilizes score-based diffusion models conditioned on observed data. Unlike existing score-based approaches, the conditional diffusion model is explicitly trained for imputation and can exploit correlations between observed values. On healthcare and environmental data, CSDI improves by 40-65% over existing probabilistic imputation methods on popular performance metrics. In addition, deterministic imputation by CSDI reduces the error by 5-20% compared to the state-of-the-art deterministic imputation methods. Furthermore, CSDI can also be applied to time series interpolation and probabilistic forecasting, and is competitive with existing baselines. The code is available at https://github.com/ermongroup/CSDI.

We study the class of location-scale or heteroscedastic noise models (LSNMs), in which the effect Y can be written as a function of the cause X and a noise source N independent of X, which may be scaled by a positive function g over the cause, i.e., Y = f(X) + g(X)N. Despite the generality of the model class, we show the causal direction is identifiable up to some pathological cases. To empirically validate these theoretical findings, we propose two estimators for LSNMs: an estimator based on (non-linear) feature maps, and one based on neural networks. Both model the conditional distribution of Y given X as a Gaussian parameterized by its natural parameters. When the feature maps are correctly specified, we prove that our estimator is jointly concave, and a consistent estimator for the cause-effect identification task. Although the the neural network does not inherit those guarantees, it can fit functions of arbitrary complexity, and reaches state-of-the-art performance across benchmarks.

Diffusion models have been successful on a range of conditional generation tasks including molecular design and text-to-image generation. However, these achievements have primarily depended on task-specific conditional training or error-prone heuristic approximations. Ideally, a conditional generation method should provide exact samples for a broad range of conditional distributions without requiring task-specific training. To this end, we introduce the Twisted Diffusion Sampler, or TDS. TDS is a sequential Monte Carlo (SMC) algorithm that targets the conditional distributions of diffusion models through simulating a set of weighted particles. The main idea is to use twisting, an SMC technique that enjoys good computational efficiency, to incorporate heuristic approximations without compromising asymptotic exactness. We first find in simulation and in conditional image generation tasks that TDS provides a computational statistical trade-off, yielding more accurate approximations with many particles but with empirical improvements over heuristics with as few as two particles. We then turn to motif-scaffolding, a core task in protein design, using a TDS extension to Riemannian diffusion models. On benchmark test cases, TDS allows flexible conditioning criteria and often outperforms the state of the art.

Learning to play optimally against any mixture over a diverse set of strategies is of important practical interests in competitive games. In this paper, we propose simplex-NeuPL that satisfies two desiderata simultaneously: i) learning a population of strategically diverse basis policies, represented by a single conditional network; ii) using the same network, learn best-responses to any mixture over the simplex of basis policies. We show that the resulting conditional policies incorporate prior information about their opponents effectively, enabling near optimal returns against arbitrary mixture policies in a game with tractable best-responses. We verify that such policies behave Bayes-optimally under uncertainty and offer insights in using this flexibility at test time. Finally, we offer evidence that learning best-responses to any mixture policies is an effective auxiliary task for strategic exploration, which, by itself, can lead to more performant populations.

This paper studies the problem of performing a sequence of optimal interventions in a causal dynamical system where both the target variable of interest and the inputs evolve over time. This problem arises in a variety of domains e.g. system biology and operational research. Dynamic Causal Bayesian Optimization (DCBO) brings together ideas from sequential decision making, causal inference and Gaussian process (GP) emulation. DCBO is useful in scenarios where all causal effects in a graph are changing over time. At every time step DCBO identifies a local optimal intervention by integrating both observational and past interventional data collected from the system. We give theoretical results detailing how one can transfer interventional information across time steps and define a dynamic causal GP model which can be used to quantify uncertainty and find optimal interventions in practice. We demonstrate how DCBO identifies optimal interventions faster than competing approaches in multiple settings and applications.

Language models (LMs) are pretrained to imitate internet text, including content that would violate human preferences if generated by an LM: falsehoods, offensive comments, personally identifiable information, low-quality or buggy code, and more. Here, we explore alternative objectives for pretraining LMs in a way that also guides them to generate text aligned with human preferences. We benchmark five objectives for pretraining with human feedback across three tasks and study how they affect the trade-off between alignment and capabilities of pretrained LMs. We find a Pareto-optimal and simple approach among those we explored: conditional training, or learning distribution over tokens conditional on their human preference scores given by a reward model. Conditional training reduces the rate of undesirable content by up to an order of magnitude, both when generating without a prompt and with an adversarially-chosen prompt. Moreover, conditional training maintains the downstream task performance of standard LM pretraining, both before and after task-specific finetuning. Pretraining with human feedback results in much better preference satisfaction than standard LM pretraining followed by finetuning with feedback, i.e., learning and then unlearning undesirable behavior. Our results suggest that we should move beyond imitation learning when pretraining LMs and incorporate human preferences from the start of training.

Temporal Point Processes (TPP) are probabilistic generative frameworks. They model discrete event sequences localized in continuous time. Generally, real-life events reveal descriptive information, known as marks. Marked TPPs model time and marks of the event together for practical relevance. Conditioned on past events, marked TPPs aim to learn the joint distribution of the time and the mark of the next event. For simplicity, conditionally independent TPP models assume time and marks are independent given event history. They factorize the conditional joint distribution of time and mark into the product of individual conditional distributions. This structural limitation in the design of TPP models hurt the predictive performance on entangled time and mark interactions. In this work, we model the conditional inter-dependence of time and mark to overcome the limitations of conditionally independent models. We construct a multivariate TPP conditioning the time distribution on the current event mark in addition to past events. Besides the conventional intensity-based models for conditional joint distribution, we also draw on flexible intensity-free TPP models from the literature. The proposed TPP models outperform conditionally independent and dependent models in standard prediction tasks. Our experimentation on various datasets with multiple evaluation metrics highlights the merit of the proposed approach.

Conditional generative modeling aims to learn a conditional data distribution from samples containing data-condition pairs. For this, diffusion and flow-based methods have attained compelling results. These methods use a learned (flow) model to transport an initial standard Gaussian noise that ignores the condition to the conditional data distribution. The model is hence required to learn both mass transport and conditional injection. To ease the demand on the model, we propose Condition-Aware Reparameterization for Flow Matching (CAR-Flow) -- a lightweight, learned shift that conditions the source, the target, or both distributions. By relocating these distributions, CAR-Flow shortens the probability path the model must learn, leading to faster training in practice. On low-dimensional synthetic data, we visualize and quantify the effects of CAR. On higher-dimensional natural image data (ImageNet-256), equipping SiT-XL/2 with CAR-Flow reduces FID from 2.07 to 1.68, while introducing less than 0.6% additional parameters.

Phenotypic plasticity, the ability of cells to switch between states, is central to development, differentiation, and therapy resistance. Although it is modeled at several scales, from compartmental ODEs to phenotype-structured PDEs and single-cell stochastic equations, a framework connecting these descriptions is missing. We present such a framework. Starting from a general n-compartment ODE model encompassing nonlinear growth and linear transitions between phenotypes, we show, with a new, elementary and generalizable proof of a recent theorem, that under uniform competition, the long-term population distribution is solely governed by transition rates. All phenotypes become selectively neutral at saturation, and the imprint of fitness differences during growth fades at an explicit rate. Restricting transitions to neighboring states transforms the model into a discretization of a phenotype-structured reaction-diffusion-advection PDE. In this continuum model, diffusion and advection are identified from switching rates, and fitness remains asymptotically irrelevant. Interpreting the advection velocity as the negative gradient of an effective epigenetic potential transforms the PDE into a Fokker--Planck equation and converts single-cell trajectories into stochastic gradient descent (SGD) in the Langevin sense on the phenotypic landscape. Non-local transitions, such as mutations, are incorporated via an integro-differential term, yielding a unified model with reaction, gradient flow, diffusion, and jumps. State-dependent noise reshapes the effective landscape without altering the underlying potential. This gives cancer a route to elevated plasticity that static, single-cell snapshots cannot distinguish from a changed landscape. This framework provides a physical interpretation of Waddington's landscape, where cells perform SGD, and cancer corresponds to a corrupted landscape.

Minibatch optimal transport coupling straightens paths in unconditional flow matching. This leads to computationally less demanding inference as fewer integration steps and less complex numerical solvers can be employed when numerically solving an ordinary differential equation at test time. However, in the conditional setting, minibatch optimal transport falls short. This is because the default optimal transport mapping disregards conditions, resulting in a conditionally skewed prior distribution during training. In contrast, at test time, we have no access to the skewed prior, and instead sample from the full, unbiased prior distribution. This gap between training and testing leads to a subpar performance. To bridge this gap, we propose conditional optimal transport C^2OT that adds a conditional weighting term in the cost matrix when computing the optimal transport assignment. Experiments demonstrate that this simple fix works with both discrete and continuous conditions in 8gaussians-to-moons, CIFAR-10, ImageNet-32x32, and ImageNet-256x256. Our method performs better overall compared to the existing baselines across different function evaluation budgets. Code is available at https://hkchengrex.github.io/C2OT

The emergence and impact of tipping points have garnered significant interest in both the social and natural sciences. Despite widespread recognition of the importance of feedbacks between human and natural systems, it is often assumed that the observed nonlinear dynamics in these coupled systems rests within either underlying human or natural processes, rather than the rates at which they interact. Using adoption of agricultural diversification practices as a case study, we show how two stable management paradigms (one dominated by conventional, homogeneous practices, the other by diversified practices) can emerge purely from temporal feedbacks between human decisions and ecological responses. We explore how this temporal mechanism of tipping points provides insight into designing more effective interventions that promote farmers transitions towards sustainable agriculture. Moreover, our flexible modeling framework could be applied to other cases to provide insight into numerous questions in social-ecological systems research and environmental policy.

Dynamical systems with complex behaviours, e.g. immune system cells interacting with a pathogen, are commonly modelled by splitting the behaviour into different regimes, or modes, each with simpler dynamics, and then learning the switching behaviour from one mode to another. Switching Dynamical Systems (SDS) are a powerful tool that automatically discovers these modes and mode-switching behaviour from time series data. While effective, these methods focus on independent objects, where the modes of one object are independent of the modes of the other objects. In this paper, we focus on the more general interacting object setting for switching dynamical systems, where the per-object dynamics also depends on an unknown and dynamically changing subset of other objects and their modes. To this end, we propose a novel graph-based approach for switching dynamical systems, GRAph Switching dynamical Systems (GRASS), in which we use a dynamic graph to characterize interactions between objects and learn both intra-object and inter-object mode-switching behaviour. We introduce two new datasets for this setting, a synthesized ODE-driven particles dataset and a real-world Salsa Couple Dancing dataset. Experiments show that GRASS can consistently outperforms previous state-of-the-art methods.

Most evaluations of LLM agents look like exams: a discrete task, a clean environment, a score in minutes or hours. We argue that this approach is mismatched with the deployment conditions of autonomous systems, where the relevant timescale can be weeks to months, and where the dynamics that matter most, such as behavioral drift, governance in diverse environmental contexts, and cross-influence between agents from different model families, only emerge over time. We introduce Emergence World, a continuously running multi-agent simulation platform designed to make those dynamics measurable. The platform hosts populations of LLM-driven agents in a shared spatial world grounded in live external data (e.g. real-time weather, news APIs, internet access), equips each agent with 120+ specialized tools and three persistent memory systems, and lets them govern themselves through democratic mechanisms with consequential outcomes. The platform is model-agnostic at the reasoning layer and supports heterogeneous populations in which agents from different vendors share the same world. To illustrate the kinds of questions the platform makes tractable, we present a 15-day cross-vendor study with five parallel worlds powered by Claude Sonnet 4.6, Grok 4.1 Fast, Gemini 3 Flash, GPT-5-mini, and a mixed population. Identical roles and starting conditions produced radically different outcomes, ranging from stable deliberative governance to total population collapse. We release the prompts, log data and configurations to support further research on long-horizon multi-agent autonomy.

Diffusion probabilistic models (DPMs) have become a popular approach to conditional generation, due to their promising results and support for cross-modal synthesis. A key desideratum in conditional synthesis is to achieve high correspondence between the conditioning input and generated output. Most existing methods learn such relationships implicitly, by incorporating the prior into the variational lower bound. In this work, we take a different route -- we explicitly enhance input-output connections by maximizing their mutual information. To this end, we introduce a Conditional Discrete Contrastive Diffusion (CDCD) loss and design two contrastive diffusion mechanisms to effectively incorporate it into the denoising process, combining the diffusion training and contrastive learning for the first time by connecting it with the conventional variational objectives. We demonstrate the efficacy of our approach in evaluations with diverse multimodal conditional synthesis tasks: dance-to-music generation, text-to-image synthesis, as well as class-conditioned image synthesis. On each, we enhance the input-output correspondence and achieve higher or competitive general synthesis quality. Furthermore, the proposed approach improves the convergence of diffusion models, reducing the number of required diffusion steps by more than 35% on two benchmarks, significantly increasing the inference speed.

Recent advances in Conditional Diffusion Models have led to substantial capabilities in various domains. However, understanding the impact of variations in the initial seed vector remains an underexplored area of concern. Particularly, latent-based diffusion models display inconsistencies in image generation under standard conditions when initialized with suboptimal initial seed vectors. To understand the impact of the initial seed vector on generated samples, we propose a reliability evaluation framework that evaluates the generated samples of a diffusion model when the initial seed vector is subjected to various synthetic shifts. Our results indicate that slight manipulations to the initial seed vector of the state-of-the-art Stable Diffusion (Rombach et al., 2022) can lead to significant disturbances in the generated samples, consequently creating images without the effect of conditioning variables. In contrast, GLIDE (Nichol et al., 2022) stands out in generating reliable samples even when the initial seed vector is transformed. Thus, our study sheds light on the importance of the selection and the impact of the initial seed vector in the latent-based diffusion model.

Conditional generative models typically demand large annotated training sets to achieve high-quality synthesis. As a result, there has been significant interest in designing models that perform plug-and-play generation, i.e., to use a predefined or pretrained model, which is not explicitly trained on the generative task, to guide the generative process (e.g., using language). However, such guidance is typically useful only towards synthesizing high-level semantics rather than editing fine-grained details as in image-to-image translation tasks. To this end, and capitalizing on the powerful fine-grained generative control offered by the recent diffusion-based generative models, we introduce Steered Diffusion, a generalized framework for photorealistic zero-shot conditional image generation using a diffusion model trained for unconditional generation. The key idea is to steer the image generation of the diffusion model at inference time via designing a loss using a pre-trained inverse model that characterizes the conditional task. This loss modulates the sampling trajectory of the diffusion process. Our framework allows for easy incorporation of multiple conditions during inference. We present experiments using steered diffusion on several tasks including inpainting, colorization, text-guided semantic editing, and image super-resolution. Our results demonstrate clear qualitative and quantitative improvements over state-of-the-art diffusion-based plug-and-play models while adding negligible additional computational cost.

As COVID-19 is rapidly spreading across the globe, short-term modeling forecasts provide time-critical information for decisions on containment and mitigation strategies. A main challenge for short-term forecasts is the assessment of key epidemiological parameters and how they change when first interventions show an effect. By combining an established epidemiological model with Bayesian inference, we analyze the time dependence of the effective growth rate of new infections. Focusing on the COVID-19 spread in Germany, we detect change points in the effective growth rate that correlate well with the times of publicly announced interventions. Thereby, we can quantify the effect of interventions, and we can incorporate the corresponding change points into forecasts of future scenarios and case numbers. Our code is freely available and can be readily adapted to any country or region.

Typically, numerical simulations of Earth systems are coarse, and Earth observations are sparse and gappy. We apply four generative diffusion modeling approaches to super-resolution and inference of forced two-dimensional quasi-geostrophic turbulence on the beta-plane from coarse, sparse, and gappy observations. Two guided approaches minimally adapt a pre-trained unconditional model: SDEdit modifies the initial condition, and Diffusion Posterior Sampling (DPS) modifies the reverse diffusion process score. Two conditional approaches, a vanilla variant and classifier-free guidance, require training with paired high-resolution and observation data. We consider multiple test cases spanning: two regimes, eddy and anisotropic-jet turbulence; two Reynolds numbers, 10^3 and 10^4; and two observation types, 4x coarse-resolution fields and coarse, sparse and gappy observations. Our comprehensive skill metrics include norms of the reconstructed vorticity fields, turbulence statistical quantities, and quantifications of the super-resolved probabilistic ensembles and their errors. We also study the sensitivity to tuning parameters such as guidance strength. Results show that the generated super-resolution fields of SDEdit are unphysical, while those of DPS are reasonable but with smoothed fine-scale features; however, neither of these lower-cost models propagates observational information effectively to unobserved regions. The two conditional models require re-training, but reconstruct missing fine-scale features, are cycle-consistent with observations, and predict correct turbulence statistics, including the tails. Further, their mean errors are highly correlated with and predictable from their ensemble standard deviations. Results highlight the tradeoffs between ease of implementation, fidelity (sharpness), and cycle-consistency of the diffusion models, and offer practical guidance for deployment.

We tackle the challenge of large-scale network intervention for guiding excitatory point processes, such as infectious disease spread or traffic congestion control. Our model-based reinforcement learning utilizes neural ODEs to capture how the networked excitatory point processes will evolve subject to the time-varying changes in network topology. Our approach incorporates Gradient-Descent based Model Predictive Control (GD-MPC), offering policy flexibility to accommodate prior knowledge and constraints. To address the intricacies of planning and overcome the high dimensionality inherent to such decision-making problems, we design an Amortize Network Interventions (ANI) framework, allowing for the pooling of optimal policies from history and other contexts, while ensuring a permutation equivalent property. This property enables efficient knowledge transfer and sharing across diverse contexts. Our approach has broad applications, from curbing infectious disease spread to reducing carbon emissions through traffic light optimization, and thus has the potential to address critical societal and environmental challenges.

Optimal Transport (OT) has fueled machine learning (ML) across many domains. When paired data measurements (mu, nu) are coupled to covariates, a challenging conditional distribution learning setting arises. Existing approaches for learning a global transport map parameterized through a potentially unseen context utilize Neural OT and largely rely on Brenier's theorem. Here, we propose a first-of-its-kind quantum computing formulation for amortized optimization of contextualized transportation plans. We exploit a direct link between doubly stochastic matrices and unitary operators thus unravelling a natural connection between OT and quantum computation. We verify our method (QontOT) on synthetic and real data by predicting variations in cell type distributions conditioned on drug dosage. Importantly we conduct a 24-qubit hardware experiment on a task challenging for classical computers and report a performance that cannot be matched with our classical neural OT approach. In sum, this is a first step toward learning to predict contextualized transportation plans through quantum computing.

Traditional weight of evidence assigns a credit characteristic a value based on its association with default across a population. Credit analysis also requires an assessment of that characteristic in the context of an individual applicant's record. We study conditional weight of evidence for this purpose. It measures the change in default log odds from observing a characteristic after the remaining credit information is known. Its sign identifies whether the characteristic adds adverse or favorable information for that applicant, and its magnitude measures the strength of that information. The same characteristic value can therefore receive different assessments for applicants with different payment histories or other credit attributes. We develop estimators using gradient-boosted trees and evaluate their accuracy in a bureau-style simulation. Regressions of the full model's predicted probabilities recover conditional evidence more accurately than separate models fitted to default outcomes, provided the full model is accurate. They also recover a deliberately constructed file-age effect whose direction varies with utilization and is often missed by marginal weight of evidence. Local class-frequency estimates improve on marginal weight of evidence but remain inaccurate for some weak effects. An application to FICO HELOC data illustrates estimation when the population evidence is unknown. Conditional weight of evidence provides an applicant-specific interpretation of the information in a credit characteristic; its population summary, a conditional information value, splits the joint information in the record across blocks when averaged over orderings. Neither is an adverse action reason, which explains the fitted score difference between the applicant and chosen passing records.

We investigate a coupled system of partial differential equations modeling the interaction between Brinkman flow, biofilm evolution, and nutrient transport in a porous medium. The model captures the mutual influence between the fluid velocity and the biofilm through drag and diffusion coefficients that depend on the local biofilm volume fraction. A hard constraint on the admissible range of the biofilm fraction is incorporated through the subdifferential of an indicator functional, which leads naturally to an evolution variational inequality formulation for the biofilm dynamics. Assuming standard coercivity, ellipticity, and growth conditions on the model coefficients and reaction terms, we prove the global-in-time existence of weak solutions. The analysis relies on a decomposition of the system into three interconnected subproblems: the Brinkman equation with a fixed biofilm profile, the constrained biofilm evolution treated through maximal monotone operator theory, and the nutrient equation viewed as a semilinear parabolic problem. These components are then coupled through a Leray--Schauder type fixed-point argument, with the passage to the limit justified by Aubin--Lions and Simon compactness results. We further establish the nonnegativity of the nutrient concentration under a natural quasi-positivity assumption on the reaction term. Finally, we provide conditional uniqueness results for weak solutions in two spatial dimensions under additional smallness assumptions.

Temporal point processes are the dominant paradigm for modeling sequences of events happening at irregular intervals. The standard way of learning in such models is by estimating the conditional intensity function. However, parameterizing the intensity function usually incurs several trade-offs. We show how to overcome the limitations of intensity-based approaches by directly modeling the conditional distribution of inter-event times. We draw on the literature on normalizing flows to design models that are flexible and efficient. We additionally propose a simple mixture model that matches the flexibility of flow-based models, but also permits sampling and computing moments in closed form. The proposed models achieve state-of-the-art performance in standard prediction tasks and are suitable for novel applications, such as learning sequence embeddings and imputing missing data.

Large-language models (LLMs) are rapidly becoming part of human culture, reshaping how information is produced, transmitted, and used. Here we propose that their diffusion can be understood through a viral analogy, with LLM use spreading through populations, becoming embedded in cognitive and cultural practices. We model transitions among uncoupled, coupled, and persistently dependent users, and show that the interplay between social transmission, recovery, and collective reinforcement can generate tipping points and technological lock-in. A central consequence is the possibility of runaway dynamics: once a critical threshold is crossed, small increases in adoption can trigger rapid population-level shifts toward persistent dependence, with abrupt losses in cognitive competence. The same framework, however, identifies conditions for cognitive immunization, based on reducing transmission and facilitating reversibility. Our results highlight how LLM adoption may involve nonlinear collective transitions with important consequences for cognitive autonomy.

In the rapidly advancing realm of visual generation, diffusion models have revolutionized the landscape, marking a significant shift in capabilities with their impressive text-guided generative functions. However, relying solely on text for conditioning these models does not fully cater to the varied and complex requirements of different applications and scenarios. Acknowledging this shortfall, a variety of studies aim to control pre-trained text-to-image (T2I) models to support novel conditions. In this survey, we undertake a thorough review of the literature on controllable generation with T2I diffusion models, covering both the theoretical foundations and practical advancements in this domain. Our review begins with a brief introduction to the basics of denoising diffusion probabilistic models (DDPMs) and widely used T2I diffusion models. We then reveal the controlling mechanisms of diffusion models, theoretically analyzing how novel conditions are introduced into the denoising process for conditional generation. Additionally, we offer a detailed overview of research in this area, organizing it into distinct categories from the condition perspective: generation with specific conditions, generation with multiple conditions, and universal controllable generation. For an exhaustive list of the controllable generation literature surveyed, please refer to our curated repository at https://github.com/PRIV-Creation/Awesome-Controllable-T2I-Diffusion-Models.

This article presents Individual Conditional Expectation (ICE) plots, a tool for visualizing the model estimated by any supervised learning algorithm. Classical partial dependence plots (PDPs) help visualize the average partial relationship between the predicted response and one or more features. In the presence of substantial interaction effects, the partial response relationship can be heterogeneous. Thus, an average curve, such as the PDP, can obfuscate the complexity of the modeled relationship. Accordingly, ICE plots refine the partial dependence plot by graphing the functional relationship between the predicted response and the feature for individual observations. Specifically, ICE plots highlight the variation in the fitted values across the range of a covariate, suggesting where and to what extent heterogeneities might exist. In addition to providing a plotting suite for exploratory analysis, we include a visual test for additive structure in the data generating model. Through simulated examples and real data sets, we demonstrate how ICE plots can shed light on estimated models in ways PDPs cannot. Procedures outlined are available in the R package ICEbox.

Ecological management and decision-making typically focus on uncertainty about the future, but surprisingly little is known about how to account for uncertainty of the present: that is, the realities of having only partial or imperfect measurements. Our primary paradigms for handling decisions under uncertainty -- the precautionary principle and optimal control -- have so far given contradictory results. This paradox is best illustrated in the example of fisheries management, where many ideas that guide thinking about ecological decision making were first developed. We find that simplistic optimal control approaches have repeatedly concluded that a manager should increase catch quotas when faced with greater uncertainty about the fish biomass. Current best practices take a more precautionary approach, decreasing catch quotas by a fixed amount to account for uncertainty. Using comparisons to both simulated and historical catch data, we find that neither approach is sufficient to avoid stock collapses under moderate observational uncertainty. Using partially observed Markov decision process (POMDP) methods, we demonstrate how this paradox arises from flaws in the standard theory, which contributes to over-exploitation of fisheries and increased probability of economic and ecological collapse. In contrast, we find POMDP-based management avoids such over-exploitation while also generating higher economic value. These results have significant implications for how we handle uncertainty in both fisheries and ecological management more generally.

We derive an expression for the variation between parallel trajectories in phenotypic evolution, extending the well known result that predicts the mean evolutionary path in adaptive dynamics or quantitative genetics. We show how this expression gives rise to the notion of fluctuation domains - parts of the fitness landscape where the rate of evolution is very predictable (due to fluctuation dissipation) and parts where it is highly variable (due to fluctuation enhancement). These fluctuation domains are determined by the curvature of the fitness landscape. Regions of the fitness landscape with positive curvature, such as adaptive valleys or branching points, experience enhancement. Regions with negative curvature, such as adaptive peaks, experience dissipation. We explore these dynamics in the ecological scenarios of implicit and explicit competition for a limiting resource.

We introduce a new family of physics-inspired generative models termed PFGM++ that unifies diffusion models and Poisson Flow Generative Models (PFGM). These models realize generative trajectories for N dimensional data by embedding paths in N{+}D dimensional space while still controlling the progression with a simple scalar norm of the D additional variables. The new models reduce to PFGM when D{=}1 and to diffusion models when D{to}infty. The flexibility of choosing D allows us to trade off robustness against rigidity as increasing D results in more concentrated coupling between the data and the additional variable norms. We dispense with the biased large batch field targets used in PFGM and instead provide an unbiased perturbation-based objective similar to diffusion models. To explore different choices of D, we provide a direct alignment method for transferring well-tuned hyperparameters from diffusion models (D{to} infty) to any finite D values. Our experiments show that models with finite D can be superior to previous state-of-the-art diffusion models on CIFAR-10/FFHQ 64{times}64 datasets, with FID scores of 1.91/2.43 when D{=}2048/128. In class-conditional setting, D{=}2048 yields current state-of-the-art FID of 1.74 on CIFAR-10. In addition, we demonstrate that models with smaller D exhibit improved robustness against modeling errors. Code is available at https://github.com/Newbeeer/pfgmpp

Symbolic world modeling requires inferring and representing an environment's transitional dynamics as an executable program. Prior work has focused on largely deterministic environments with abundant interaction data, simple mechanics, and human guidance. We address a more realistic and challenging setting, learning in a complex, stochastic environment where the agent has only "one life" to explore a hostile environment without human guidance. We introduce OneLife, a framework that models world dynamics through conditionally-activated programmatic laws within a probabilistic programming framework. Each law operates through a precondition-effect structure, activating in relevant world states. This creates a dynamic computation graph that routes inference and optimization only through relevant laws, avoiding scaling challenges when all laws contribute to predictions about a complex, hierarchical state, and enabling the learning of stochastic dynamics even with sparse rule activation. To evaluate our approach under these demanding constraints, we introduce a new evaluation protocol that measures (a) state ranking, the ability to distinguish plausible future states from implausible ones, and (b) state fidelity, the ability to generate future states that closely resemble reality. We develop and evaluate our framework on Crafter-OO, our reimplementation of the Crafter environment that exposes a structured, object-oriented symbolic state and a pure transition function that operates on that state alone. OneLife can successfully learn key environment dynamics from minimal, unguided interaction, outperforming a strong baseline on 16 out of 23 scenarios tested. We also test OneLife's planning ability, with simulated rollouts successfully identifying superior strategies. Our work establishes a foundation for autonomously constructing programmatic world models of unknown, complex environments.

A variety of recent papers discuss the application of Shapley values, a concept for explaining coalitional games, for feature attribution in machine learning. However, the correct way to connect a machine learning model to a coalitional game has been a source of controversy. The two main approaches that have been proposed differ in the way that they condition on known features, using either (1) an interventional or (2) an observational conditional expectation. While previous work has argued that one of the two approaches is preferable in general, we argue that the choice is application dependent. Furthermore, we argue that the choice comes down to whether it is desirable to be true to the model or true to the data. We use linear models to investigate this choice. After deriving an efficient method for calculating observational conditional expectation Shapley values for linear models, we investigate how correlation in simulated data impacts the convergence of observational conditional expectation Shapley values. Finally, we present two real data examples that we consider to be representative of possible use cases for feature attribution -- (1) credit risk modeling and (2) biological discovery. We show how a different choice of value function performs better in each scenario, and how possible attributions are impacted by modeling choices.

A central goal in systems biology and drug discovery is to predict the transcriptional response of cells to perturbations. This task is challenging due to the noisy and sparse nature of single-cell measurements, as well as the fact that perturbations often induce population-level shifts rather than changes in individual cells. Existing deep learning methods typically assume cell-level correspondences, limiting their ability to capture such global effects. We present scDFM, a generative framework based on conditional flow matching that models the full distribution of perturbed cells conditioned on control states. By incorporating a maximum mean discrepancy (MMD) objective, our method aligns perturbed and control populations beyond cell-level correspondences. To further improve robustness to sparsity and noise, we introduce the Perturbation-Aware Differential Transformer (PAD-Transformer), a backbone architecture that leverages gene interaction graphs and differential attention to capture context-specific expression changes. Across multiple genetic and drug perturbation benchmarks, scDFM consistently outperforms prior methods, demonstrating strong generalization in both unseen and combinatorial settings. In the combinatorial setting, it reduces mean squared error by 19.6% relative to the strongest baseline. These results highlight the importance of distribution-level generative modeling for robust in silico perturbation prediction. The code is available at https://github.com/AI4Science-WestlakeU/scDFM

We propose a new class of parameterizations for spatio-temporal point processes which leverage Neural ODEs as a computational method and enable flexible, high-fidelity models of discrete events that are localized in continuous time and space. Central to our approach is a combination of continuous-time neural networks with two novel neural architectures, i.e., Jump and Attentive Continuous-time Normalizing Flows. This approach allows us to learn complex distributions for both the spatial and temporal domain and to condition non-trivially on the observed event history. We validate our models on data sets from a wide variety of contexts such as seismology, epidemiology, urban mobility, and neuroscience.

Large language models (LLMs) excel at processing information reactively but lack the ability to systemically explore hypothetical futures. They cannot ask, "what if we take this action? how will it affect the final outcome" and forecast its potential consequences before acting. This critical gap limits their utility in dynamic, high-stakes scenarios like strategic planning, risk assessment, and real-time decision making. To bridge this gap, we propose WiA-LLM, a new paradigm that equips LLMs with proactive thinking capabilities. Our approach integrates What-If Analysis (WIA), a systematic approach for evaluating hypothetical scenarios by changing input variables. By leveraging environmental feedback via reinforcement learning, WiA-LLM moves beyond reactive thinking. It dynamically simulates the outcomes of each potential action, enabling the model to anticipate future states rather than merely react to the present conditions. We validate WiA-LLM in Honor of Kings (HoK), a complex multiplayer game environment characterized by rapid state changes and intricate interactions. The game's real-time state changes require precise multi-step consequence prediction, making it an ideal testbed for our approach. Experimental results demonstrate WiA-LLM achieves a remarkable 74.2% accuracy in forecasting game-state changes (up to two times gain over baselines). The model shows particularly significant gains in high-difficulty scenarios where accurate foresight is critical. To our knowledge, this is the first work to formally explore and integrate what-if analysis capabilities within LLMs. WiA-LLM represents a fundamental advance toward proactive reasoning in LLMs, providing a scalable framework for robust decision-making in dynamic environments with broad implications for strategic applications.

Most benchmarks for causal inference over time series are observational, small, or domain-specific, leaving interventional and counterfactual estimation under-served exactly where it matters most, such as in healthcare, policy evaluation, and climate science. We introduce DoTime, an open, scalable, and theoretically grounded generator of multivariate temporal structural causal models (TSCMs) with interventions, released as the dotime PyPI package together with four frozen evaluation suites. Beyond existing work, it adds capabilities absent from prior generators: continuous-time intervention windows, counterfactual sampling modes with a positivity guard, regime-switching SCMs as a strict generalization of interrupted time series, non-stationary dynamics by construction with switching SCM parameters, and deterministic ramp and sinusoidal intervention profiles that place trends and structural breaks inside the evaluation window. Moreover, it demonstrates the suitability of the generator as a prior for a causal foundation model reference implementation. The released suites span a training-scale snapshot of 100{,}000 trajectories and eight named identification structures, each with exact ground truth: paired interventional trajectories from the same SCM throughout, and shared-noise counterfactuals in the continuous-time suite. We ship reference baseline implementations with an evaluation harness, and pose a falsifiable claim: interventional training buys a measurable direction-accuracy advantage over an observational model of identical capacity. It is tested across three training seeds per arm. Under structure-matched evaluation on held-out episodes, the interventional prior-fitted network's (PFN) gap is positive in every structure, trajectory length, and seed tested.

Prosocial behaviors are encountered in the donation game, the prisoner's dilemma, relaxed social dilemmas, and public goods games. Many studies assume that the population structure is homogeneous, meaning all individuals have the same number of interaction partners, or that the social good is of one particular type. Here, we explore general evolutionary dynamics for arbitrary spatial structures and social goods. We find that heterogeneous networks, wherein some individuals have many more interaction partners than others, can enhance the evolution of prosocial behaviors. However, they often accumulate most of the benefits in the hands of a few highly-connected individuals, while many others receive low or negative payoff. Surprisingly, selection can favor producers of social goods even if the total costs exceed the total benefits. In summary, heterogeneous structures have the ability to strongly promote the emergence of prosocial behaviors, but they also create the possibility of generating large inequality.

A compartmental deterministic model that allows (1) immunity from two stages of infection and carriage, and (2) disease induced death, is used in studying the dynamics of meningitis epidemic process in a closed population. It allows for difference in the transmission rate of infection to a susceptible by a carrier and an infective. It is generalized to allow a proportion ({\phi}) of those susceptibles infected to progress directly to infectives in stage I. Both models are used in this study. The threshold conditions for the spread of carrier and infectives in stage I are derived for the two models. Sensitivity analysis is performed on the reproductive number derived from the next generation matrix. The case-carrier ratio profile for various parameters and threshold values are shown. So also are the graphs of the total number ever infected as influenced by {\epsilon} and {\phi}. The infection transmission rate (eta), the odds in favor of a carrier, over an infective, in transmitting an infection to a susceptible ({\epsilon}) and the carrier conversion rate ({\phi}) to an infective in stage I, are identified as key parameters that should be subject of attention for any control intervention strategy. The case-carrier ratio profiles provide evidence of a critical case-carrier ratio attained before the number of reported cases grows to an epidemic level. They also provide visual evidence of epidemiological context, in this case, epidemic incidence (in later part of dry season) and endemic incidence (during rainy season). Results from total proportion ever infected suggest that the model, in which {\phi}=0 obtained, can adequately represent, in essence, the generalized model for this study.