Synthetic medical time-series generation can alleviate data scarcity and support the development of reliable clinical prediction models. However, existing methods mainly focus on matching the overall distribution and temporal dynamics of real data, which does not necessarily ensure strong downstream utility on imbalanced medical datasets. Clinically informative patterns often occur at heterogeneous temporal scales, while rare minority-class characteristics can be obscured by dominant population patterns. To address these challenges, we propose MedFlow, a class-aware multi-scale flow matching framework for medical time-series synthesis. MedFlow employs a vector-quantized multi-scale tokenizer to represent medical sequences at complementary temporal resolutions, capturing both coarse clinical trends and fine-grained dynamics. We further introduce Token Marginal Guidance, which incorporates class-conditional token statistics directly into the flow matching process to steer generation toward class-specific regions of the learned tokens. This mechanism strengthens minority-class patterns, while preserving the global and tail distributions of real data. Experiments on four public datasets covering electronic health records, EEG, and ECG signals demonstrate that MedFlow consistently outperforms recent state-of-the-art diffusion-based baselines across downstream prediction tasks. On average, it improves AUPRC by 5.8%, reduces Context-FID by 88.6%, and achieves 3.8× higher sampling throughput.
Continuous physiological time series underpin modern clinical monitoring, yet many of the most informative signals are invasive, expensive, or simply unavailable for a given patient. Conditional generation offers a remedy: an absent signal can be synthesized from co-recorded signals and routine clinical variables. Existing generators, however, are built around a single conditioning modality and degrade when forced to handle the heterogeneous, irregularly missing mix of time-variant signals and static covariates seen in practice. We propose ReCoGen (Represent Conditions, then Generate), a two-stage framework that decouples multimodal condition representation from target generation. Stage I trains one masked autoencoder per modality, distilling each time-variant condition into a compact and missingness-tolerant token sequence. Stage II trains a flow-matching generator that fuses these tokens with static conditions to synthesize the target signal. Across three physiological benchmarks, including continuous glucose monitoring on AI-READI and arterial blood pressure generation on MIMIC-III and MIMIC-IV, ReCoGen attains the best downstream utility on all sixteen (dataset, task, metric) settings, surpassing six representative conditional generators; on thirteen of them its utility also reaches or exceeds the utility measured on the real signal, a reference we read as an approximate anchor rather than a ceiling. Ablations trace the gains to the conditioning path: learnable cross-attention over the frozen per-modality encoders, and a dual token-plus-AdaLN route for the static conditions. ReCoGen thus turns routinely collected signals into informative surrogates for invasive or unavailable ones, a step toward less invasive, lower-cost continuous clinical monitoring.
Unifying multimodal understanding and generation is a compelling frontier that is beginning to emerge in the medical field. However, the limited existing unified medical models typically treat understanding and generation as disjoint objectives, lacking a meaningful functional synergy. In this work, we identify and address a critical question in unified medical modeling: what form of understanding truly benefits generation. We present SynerMedGen, a unified framework built on the proposed principle of generation-aligned understanding, which synergizes understanding objectives with generation tasks via task alignment. SynerMedGen introduces three generation-aligned understanding tasks and a two-stage training strategy that transfers generation-beneficial representations learned during understanding training to medical image synthesis. Remarkably, even with understanding training alone, our SynerMedGen achieves strong zero-shot performance across 22 medical image synthesis tasks and demonstrates robust generalization to unseen datasets. When combined with generation training, SynerMedGen consistently outperforms state-of-the-art specialized medical image synthesis models as well as recent unified medical models. We also release a large-scale dataset named SynerMed consisting of 1M paired synthesis samples and 2M generation-derived understanding instances to support further research on understanding-generation synergy. Our project can be accessed at https://github.com/piooip/SynerMedGen.
Vector quantization (VQ) with autoregressive (AR) token modeling is a widely adopted and highly competitive paradigm for time-series generation. However, such models are fundamentally limited by exposure bias: during inference, errors can accumulate across sequential predictions, leading to pronounced quality degradation in long-horizon generation. To address this, we propose SDFlow (Similarity-Driven Flow Matching), a non-autoregressive framework that operates entirely in the frozen VQ latent space and enables parallel sequence generation via flow matching. We tackle three key challenges in making this transition: (1) eliminating exposure bias by replacing step-wise token prediction with a global transport map; (2) mitigating the high-dimensionality of VQ token spaces via a low-rank manifold decomposition with a learned anchor prior over the latent manifold; and (3) incorporating discrete supervision into continuous transport dynamics by introducing a categorical posterior over codebook indices within a variational flow-matching formulation. Extensive experiments show that SDFlow achieves state-of-the-art performance, improving Discriminative Score and substantially reducing Context-FID, particularly for challenging long-sequence generation. Moreover, SDFlow provides significant inference speedups over autoregressive baselines, offering both high fidelity and computational efficiency. Code is available at https://anonymous.4open.science/r/SDFlow-D6F3/