Linear-LLM-SCM: Benchmarking LLMs for Coefficient Elicitation in Linear-Gaussian Causal Models

Large language models (LLMs) have shown potential in identifying qualitative causal relations, but their ability to perform quantitative causal reasoning -- estimating effect sizes that parametrize functional relationships -- remains underexplored in continuous domains. We introduce Linear-LLM-SCM, a plug-and-play benchmarking framework for evaluating LLMs on linear Gaussian structural causal model (SCM) parametrization when the DAG is given. The framework decomposes a DAG into local parent-child sets and prompts an LLM to produce a regression-style structural equation per node, which is aggregated and compared against available ground-truth parameters. Our experiments show several challenges in such benchmarking tasks, namely, strong stochasticity in the results in some of the models and susceptibility to DAG misspecification via spurious edges in the continuous domains. Across models, we observe substantial variability in coefficient estimates for some settings and sensitivity to structural and semantic perturbations, highlighting current limitations of LLMs as quantitative causal parameterizers. We also open-sourced the benchmarking framework so that researchers can utilize their DAGs and any off-the-shelf LLMs plug-and-play for evaluation in their domains effortlessly.

IMAGIC-500: IMputation benchmark on A Generative Imaginary Country (500k samples)

Missing data imputation in tabular datasets remains a pivotal challenge in data science and machine learning, particularly within socioeconomic research. However, real-world socioeconomic datasets are typically subject to strict data protection protocols, which often prohibit public sharing, even for synthetic derivatives. This severely limits the reproducibility and accessibility of benchmark studies in such settings. Further, there are very few publicly available synthetic datasets. Thus, there is limited availability of benchmarks for systematic evaluation of imputation methods on socioeconomic datasets, whether real or synthetic. In this study, we utilize the World Bank's publicly available synthetic dataset, Synthetic Data for an Imaginary Country, which closely mimics a real World Bank household survey while being fully public, enabling broad access for methodological research. With this as a starting point, we derived the IMAGIC-500 dataset: we select a subset of 500k individuals across approximately 100k households with 19 socioeconomic features, designed to reflect the hierarchical structure of real-world household surveys. This paper introduces a comprehensive missing data imputation benchmark on IMAGIC-500 under various missing mechanisms (MCAR, MAR, MNAR) and missingness ratios (10\%, 20\%, 30\%, 40\%, 50\%). Our evaluation considers the imputation accuracy for continuous and categorical variables, computational efficiency, and impact on downstream predictive tasks, such as estimating educational attainment at the individual level. The results highlight the strengths and weaknesses of statistical, traditional machine learning, and deep learning imputation techniques, including recent diffusion-based methods. The IMAGIC-500 dataset and benchmark aim to facilitate the development of robust imputation algorithms and foster reproducible social science research.

Rethinking Cancer Gene Identification through Graph Anomaly Analysis

Graph neural networks (GNNs) have shown promise in integrating protein-protein interaction (PPI) networks for identifying cancer genes in recent studies. However, due to the insufficient modeling of the biological information in PPI networks, more faithfully depiction of complex protein interaction patterns for cancer genes within the graph structure remains largely unexplored. This study takes a pioneering step toward bridging biological anomalies in protein interactions caused by cancer genes to statistical graph anomaly. We find a unique graph anomaly exhibited by cancer genes, namely weight heterogeneity, which manifests as significantly higher variance in edge weights of cancer gene nodes within the graph. Additionally, from the spectral perspective, we demonstrate that the weight heterogeneity could lead to the "flattening out" of spectral energy, with a concentration towards the extremes of the spectrum. Building on these insights, we propose the HIerarchical-Perspective Graph Neural Network (HIPGNN) that not only determines spectral energy distribution variations on the spectral perspective, but also perceives detailed protein interaction context on the spatial perspective. Extensive experiments are conducted on two reprocessed datasets STRINGdb and CPDB, and the experimental results demonstrate the superiority of HIPGNN.