Learning to refine domain knowledge for biological network inference

Perturbation experiments allow biologists to discover causal relationships between variables of interest, but the sparsity and high dimensionality of these data pose significant challenges for causal structure learning algorithms. Biological knowledge graphs can bootstrap the inference of causal structures in these situations, but since they compile vastly diverse information, they can bias predictions towards well-studied systems. Alternatively, amortized causal structure learning algorithms encode inductive biases through data simulation and train supervised models to recapitulate these synthetic graphs. However, realistically simulating biology is arguably even harder than understanding a specific system. In this work, we take inspiration from both strategies and propose an amortized algorithm for refining domain knowledge, based on data observations. On real and synthetic datasets, we show that our approach outperforms baselines in recovering ground truth causal graphs and identifying errors in the prior knowledge with limited interventional data.

Causal-Aware Graph Neural Architecture Search under Distribution Shifts

Graph NAS has emerged as a promising approach for autonomously designing GNN architectures by leveraging the correlations between graphs and architectures. Existing methods fail to generalize under distribution shifts that are ubiquitous in real-world graph scenarios, mainly because the graph-architecture correlations they exploit might be spurious and varying across distributions. We propose to handle the distribution shifts in the graph architecture search process by discovering and exploiting the causal relationship between graphs and architectures to search for the optimal architectures that can generalize under distribution shifts. The problem remains unexplored with following challenges: how to discover the causal graph-architecture relationship that has stable predictive abilities across distributions, and how to handle distribution shifts with the discovered causal graph-architecture relationship to search the generalized graph architectures. To address these challenges, we propose Causal-aware Graph Neural Architecture Search (CARNAS), which is able to capture the causal graph-architecture relationship during the architecture search process and discover the generalized graph architecture under distribution shifts. Specifically, we propose Disentangled Causal Subgraph Identification to capture the causal subgraphs that have stable prediction abilities across distributions. Then, we propose Graph Embedding Intervention to intervene on causal subgraphs within the latent space, ensuring that these subgraphs encapsulate essential features for prediction while excluding non-causal elements. Additionally, we propose Invariant Architecture Customization to reinforce the causal invariant nature of the causal subgraphs, which are utilized to tailor generalized graph architectures. Extensive experiments demonstrate that CARNAS achieves advanced out-of-distribution generalization ability.

LLM-Enhanced Causal Discovery in Temporal Domain from Interventional Data

In the field of Artificial Intelligence for Information Technology Operations, causal discovery is pivotal for operation and maintenance of graph construction, facilitating downstream industrial tasks such as root cause analysis. Temporal causal discovery, as an emerging method, aims to identify temporal causal relationships between variables directly from observations by utilizing interventional data. However, existing methods mainly focus on synthetic datasets with heavy reliance on intervention targets and ignore the textual information hidden in real-world systems, failing to conduct causal discovery for real industrial scenarios. To tackle this problem, in this paper we propose to investigate temporal causal discovery in industrial scenarios, which faces two critical challenges: 1) how to discover causal relationships without the interventional targets that are costly to obtain in practice, and 2) how to discover causal relations via leveraging the textual information in systems which can be complex yet abundant in industrial contexts. To address these challenges, we propose the RealTCD framework, which is able to leverage domain knowledge to discover temporal causal relationships without interventional targets. Specifically, we first develop a score-based temporal causal discovery method capable of discovering causal relations for root cause analysis without relying on interventional targets through strategic masking and regularization. Furthermore, by employing Large Language Models (LLMs) to handle texts and integrate domain knowledge, we introduce LLM-guided meta-initialization to extract the meta-knowledge from textual information hidden in systems to boost the quality of discovery. We conduct extensive experiments on simulation and real-world datasets to show the superiority of our proposed RealTCD framework over existing baselines in discovering temporal causal structures.