ScDiVa: Masked Discrete Diffusion for Joint Modeling of Single-Cell Identity and Expression

Single-cell RNA-seq profiles are high-dimensional, sparse, and unordered, causing autoregressive generation to impose an artificial ordering bias and suffer from error accumulation. To address this, we propose scDiVa, a masked discrete diffusion foundation model that aligns generation with the dropout-like corruption process by defining a continuous-time forward masking mechanism in token space. ScDiVa features a bidirectional denoiser that jointly models discrete gene identities and continuous values, utilizing entropy-normalized serialization and a latent anchor token to maximize information efficiency and preserve global cell identity. The model is trained via depth-invariant time sampling and a dual denoising objective to simulate varying sparsity levels while ensuring precise recovery of both identity and magnitude. Pre-trained on 59 million cells, scDiVa achieves strong transfer performance across major benchmarks, including batch integration, cell type annotation, and perturbation response prediction. These results suggest that masked discrete diffusion serves as a biologically coherent and effective alternative to autoregression.

$λ$-GRPO: Unifying the GRPO Frameworks with Learnable Token Preferences

Reinforcement Learning with Human Feedback (RLHF) has been the dominant approach for improving the reasoning capabilities of Large Language Models (LLMs). Recently, Reinforcement Learning with Verifiable Rewards (RLVR) has simplified this paradigm by replacing the reward and value models with rule-based verifiers. A prominent example is Group Relative Policy Optimization (GRPO). However, GRPO inherently suffers from a length bias, since the same advantage is uniformly assigned to all tokens of a response. As a result, longer responses distribute the reward over more tokens and thus contribute disproportionately to gradient updates. Several variants, such as DAPO and Dr. GRPO, modify the token-level aggregation of the loss, yet these methods remain heuristic and offer limited interpretability regarding their implicit token preferences. In this work, we explore the possibility of allowing the model to learn its own token preference during optimization. We unify existing frameworks under a single formulation and introduce a learnable parameter $\lambda$ that adaptively controls token-level weighting. We use $\lambda$-GRPO to denote our method, and we find that $\lambda$-GRPO achieves consistent improvements over vanilla GRPO and DAPO on multiple mathematical reasoning benchmarks. On Qwen2.5 models with 1.5B, 3B, and 7B parameters, $\lambda$-GRPO improves average accuracy by $+1.9\%$, $+1.0\%$, and $+1.7\%$ compared to GRPO, respectively. Importantly, these gains come without any modifications to the training data or additional computational cost, highlighting the effectiveness and practicality of learning token preferences.