Conditional Generation

Modeling single-cell gene expression across diverse biological and technical conditions is crucial for characterizing cellular states and simulating unseen scenarios. Existing methods often treat genes as independent tokens, overlooking their high-level biological relationships and leading to poor performance. We introduce SAVE, a unified generative framework based on conditional Transformers for multi-condition single-cell modeling. SAVE leverages a coarse-grained representation by grouping semantically related genes into blocks, capturing higher-order dependencies among gene modules. A Flow Matching mechanism and condition-masking strategy further enhance flexible simulation and enable generalization to unseen condition combinations. We evaluate SAVE on a range of benchmarks, including conditional generation, batch effect correction, and perturbation prediction. SAVE consistently outperforms state-of-the-art methods in generation fidelity and extrapolative generalization, especially in low-resource or combinatorially held-out settings. Overall, SAVE offers a scalable and generalizable solution for modeling complex single-cell data, with broad utility in virtual cell synthesis and biological interpretation. Our code is publicly available at https://github.com/fdu-wangfeilab/sc-save

We present TCAM (Track and Caption Any Motion), a generative framework that watches a video and with no text query and no region prompt decides what is moving, describes each motion in open vocabulary, locates it in time, and points to the exact trajectories that carry it. Two mature lines of work make this possible yet leave it unsolved: dense point trackers follow pixels with sub-object precision but emit no language, while video-language models produce fluent descriptions only when handed a query and only from clip-level features that cannot resolve which pixels move. Object-level captioners narrow the gap but still reason over detector boxes or masks, never reaching individual trajectories. TCAM couples tracking and language at point granularity through a Caption-Aware Resampler, where a small set of learnable queries cross-attends to dense point trajectory tokens and distills them into a fixed-length motion context that conditions a language decoder. The decoder generates an entire video's events in a single pass, each with a free-form caption, a start and end time, and a pointer to the trajectories it refers to, for sequential events and several subjects active at once. Training uses only existing segmentation annotations, with no extra event labeling, to supervise caption quality, pointer-mask alignment, and pointer diversity. On over 50K clips, TCAM outperforms dense video captioning baselines and matches dedicated, query-based grounding and point-tracking methods despite using no query, showing that trajectory-conditioned generation is a direct route to motion-driven video understanding.

Recent advances in continuous conditional generative modeling, including Continuous conditional Generative Adversarial Network (CcGAN) and Continuous Conditional Diffusion Model (CCDM), estimate high-dimensional data distributions conditioned on scalar regression labels such as angles, ages, or temperatures. However, fixed-size vicinal training in CcGAN can be sensitive to non-uniform label densities, whereas CCDM relies on computationally expensive iterative sampling. To address these issues, we propose CcGAN-AVAR, an imbalance-aware extension of CcGAN that combines soft/hybrid adaptive vicinity with auxiliary discriminator-guided regularization. The adaptive vicinity constructs a label-dependent local radius according to the available samples around each target condition, and the multi-task discriminator supplies both a regression signal for label consistency and a density-ratio-estimation signal for distribution matching. We further provide a theoretical interpretation characterizing how adaptive vicinal weighting affects the local bias-variance behavior of the discriminator target, how hybrid truncation reduces objective-level cross-condition mixing, and how the density-ratio-based generator penalty approximates a Pearson Chi-square discrepancy up to the estimation error of the density-ratio branch. Extensive experiments on four datasets, including the newly constructed imbalanced RC-49-I, covering resolutions from 64x64 to 256x256 across eleven settings, demonstrate that CcGAN-AVAR obtains strong generation quality and label consistency while preserving the one-step sampling efficiency of GANs, achieving 300x--2000x faster inference than CCDM.

We introduce MolMiner, a fragment-based, geometry-aware, and order-agnostic autoregressive model for molecular design. MolMiner supports high-dimensional conditional control over twelve physicochemical and structural properties from partial specifications, constructs molecules via symmetry-aware fragment attachments, and conditions each generation step on force-field-relaxed three-dimensional geometry of the partial structure. Conditional control emerges without auxiliary property losses. On targeted property windows, conditioning lifts hit rates by up to 5.25x over unconditional generation and 3.5x over the training distribution itself -- overriding the model's intrinsic biases -- at the cost of a small reduction in unconditional distributional fidelity. MolMiner unifies dynamic geometry, symmetry handling, order-agnostic generation, and scalable multi-property conditioning within a single framework.