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byAK and the research community

Jan 7

Gene Regulatory Network Inference in the Presence of Dropouts: a Causal View

Gene regulatory network inference (GRNI) is a challenging problem, particularly owing to the presence of zeros in single-cell RNA sequencing data: some are biological zeros representing no gene expression, while some others are technical zeros arising from the sequencing procedure (aka dropouts), which may bias GRNI by distorting the joint distribution of the measured gene expressions. Existing approaches typically handle dropout error via imputation, which may introduce spurious relations as the true joint distribution is generally unidentifiable. To tackle this issue, we introduce a causal graphical model to characterize the dropout mechanism, namely, Causal Dropout Model. We provide a simple yet effective theoretical result: interestingly, the conditional independence (CI) relations in the data with dropouts, after deleting the samples with zero values (regardless if technical or not) for the conditioned variables, are asymptotically identical to the CI relations in the original data without dropouts. This particular test-wise deletion procedure, in which we perform CI tests on the samples without zeros for the conditioned variables, can be seamlessly integrated with existing structure learning approaches including constraint-based and greedy score-based methods, thus giving rise to a principled framework for GRNI in the presence of dropouts. We further show that the causal dropout model can be validated from data, and many existing statistical models to handle dropouts fit into our model as specific parametric instances. Empirical evaluation on synthetic, curated, and real-world experimental transcriptomic data comprehensively demonstrate the efficacy of our method.

  • 6 authors
·
Mar 21, 2024

Verifier-free Test-Time Sampling for Vision Language Action Models

Vision-Language-Action models (VLAs) have demonstrated remarkable performance in robot control. However, they remain fundamentally limited in tasks that require high precision due to their single-inference paradigm. While test-time scaling approaches using external verifiers have shown promise, they require additional training and fail to generalize to unseen conditions. We propose Masking Distribution Guided Selection (MG-Select), a novel test-time scaling framework for VLAs that leverages the model's internal properties without requiring additional training or external modules. Our approach utilizes KL divergence from a reference action token distribution as a confidence metric for selecting the optimal action from multiple candidates. We introduce a reference distribution generated by the same VLA but with randomly masked states and language conditions as inputs, ensuring maximum uncertainty while remaining aligned with the target task distribution. Additionally, we propose a joint training strategy that enables the model to learn both conditional and unconditional distributions by applying dropout to state and language conditions, thereby further improving the quality of the reference distribution. Our experiments demonstrate that MG-Select achieves significant performance improvements, including a 28%/35% improvement in real-world in-distribution/out-of-distribution tasks, along with a 168% relative gain on RoboCasa pick-and-place tasks trained with 30 demonstrations.

kaist-ai KAIST AI
·
Oct 7, 2025 3