We introduce \textit{OneFlowSBI}, a unified framework for simulation-based inference that learns a single flow-matching generative model over the joint distribution of parameters and observations. Leveraging a query-aware masking distribution during training, the same model supports multiple inference tasks, including posterior sampling, likelihood estimation, and arbitrary conditional distributions, without task-specific retraining. We evaluate \textit{OneFlowSBI} on ten benchmark inference problems and two high-dimensional real-world inverse problems across multiple simulation budgets. \textit{OneFlowSBI} is shown to deliver competitive performance against state-of-the-art generalized inference solvers and specialized posterior estimators, while enabling efficient sampling with few ODE integration steps and remaining robust under noisy and partially observed data.

Free-space trajectory similarity calculation, e.g., DTW, Hausdorff, and Frechet, often incur quadratic time complexity, thus learning-based methods have been proposed to accelerate the computation. The core idea is to train an encoder to transform trajectories into representation vectors and then compute vector similarity to approximate the ground truth. However, existing methods face dual challenges of effectiveness and efficiency: 1) they all utilize Euclidean distance to compute representation similarity, which leads to the severe curse of dimensionality issue -- reducing the distinguishability among representations and significantly affecting the accuracy of subsequent similarity search tasks; 2) most of them are trained in triplets manner and often necessitate additional information which downgrades the efficiency; 3) previous studies, while emphasizing the scalability in terms of efficiency, overlooked the deterioration of effectiveness when the dataset size grows. To cope with these issues, we propose a simple, yet accurate, fast, scalable model that only uses a single-layer vanilla transformer encoder as the feature extractor and employs tailored representation similarity functions to approximate various ground truth similarity measures. Extensive experiments demonstrate our model significantly mitigates the curse of dimensionality issue and outperforms the state-of-the-arts in effectiveness, efficiency, and scalability.

Amortized Bayesian inference trains neural networks to solve stochastic inference problems using model simulations, thereby making it possible to rapidly perform Bayesian inference for any newly observed data. However, current simulation-based amortized inference methods are simulation-hungry and inflexible: They require the specification of a fixed parametric prior, simulator, and inference tasks ahead of time. Here, we present a new amortized inference method -- the Simformer -- which overcomes these limitations. By training a probabilistic diffusion model with transformer architectures, the Simformer outperforms current state-of-the-art amortized inference approaches on benchmark tasks and is substantially more flexible: It can be applied to models with function-valued parameters, it can handle inference scenarios with missing or unstructured data, and it can sample arbitrary conditionals of the joint distribution of parameters and data, including both posterior and likelihood. We showcase the performance and flexibility of the Simformer on simulators from ecology, epidemiology, and neuroscience, and demonstrate that it opens up new possibilities and application domains for amortized Bayesian inference on simulation-based models.