Smoothing the Landscape: Causal Structure Learning via Diffusion Denoising Objectives

Understanding causal dependencies in observational data is critical for informing decision-making. These relationships are often modeled as Bayesian Networks (BNs) and Directed Acyclic Graphs (DAGs). Existing methods, such as NOTEARS and DAG-GNN, often face issues with scalability and stability in high-dimensional data, especially when there is a feature-sample imbalance. Here, we show that the denoising score matching objective of diffusion models could smooth the gradients for faster, more stable convergence. We also propose an adaptive k-hop acyclicity constraint that improves runtime over existing solutions that require matrix inversion. We name this framework Denoising Diffusion Causal Discovery (DDCD). Unlike generative diffusion models, DDCD utilizes the reverse denoising process to infer a parameterized causal structure rather than to generate data. We demonstrate the competitive performance of DDCDs on synthetic benchmarking data. We also show that our methods are practically useful by conducting qualitative analyses on two real-world examples. Code is available at this url: https://github.com/haozhu233/ddcd.

MEDFORD in a Box: Improvements and Future Directions for a Metadata Description Language

Scientific research metadata is vital to ensure the validity, reusability, and cost-effectiveness of research efforts. The MEDFORD metadata language was previously introduced to simplify the process of writing and maintaining metadata for non-programmers. However, barriers to entry and usability remain, including limited automatic validation, difficulty of data transport, and user unfamiliarity with text file editing. To address these issues, we introduce MEDFORD-in-a-Box (MIAB), a documentation ecosystem to facilitate researcher adoption and earlier metadata capture. MIAB contains many improvements, including an updated MEDFORD parser with expanded validation routines and BagIt export capability. MIAB also includes an improved VS Code extension that supports these changes through a visual IDE. By simplifying metadata generation, this new tool supports the creation of correct, consistent, and reusable metadata, ultimately improving research reproducibility.