LLM4GRN: Discovering Causal Gene Regulatory Networks with LLMs -- Evaluation through Synthetic Data Generation

Gene regulatory networks (GRNs) represent the causal relationships between transcription factors (TFs) and target genes in single-cell RNA sequencing (scRNA-seq) data. Understanding these networks is crucial for uncovering disease mechanisms and identifying therapeutic targets. In this work, we investigate the potential of large language models (LLMs) for GRN discovery, leveraging their learned biological knowledge alone or in combination with traditional statistical methods. We develop a task-based evaluation strategy to address the challenge of unavailable ground truth causal graphs. Specifically, we use the GRNs suggested by LLMs to guide causal synthetic data generation and compare the resulting data against the original dataset. Our statistical and biological assessments show that LLMs can support statistical modeling and data synthesis for biological research.

BaBE: Enhancing Fairness via Estimation of Latent Explaining Variables

We consider the problem of unfair discrimination between two groups and propose a pre-processing method to achieve fairness. Corrective methods like statistical parity usually lead to bad accuracy and do not really achieve fairness in situations where there is a correlation between the sensitive attribute S and the legitimate attribute E (explanatory variable) that should determine the decision. To overcome these drawbacks, other notions of fairness have been proposed, in particular, conditional statistical parity and equal opportunity. However, E is often not directly observable in the data, i.e., it is a latent variable. We may observe some other variable Z representing E, but the problem is that Z may also be affected by S, hence Z itself can be biased. To deal with this problem, we propose BaBE (Bayesian Bias Elimination), an approach based on a combination of Bayes inference and the Expectation-Maximization method, to estimate the most likely value of E for a given Z for each group. The decision can then be based directly on the estimated E. We show, by experiments on synthetic and real data sets, that our approach provides a good level of fairness as well as high accuracy.