Causal Structure Learning

Modeling dynamical systems and unraveling their underlying structural dependencies is central to many domains in the natural sciences. Various physical systems, such as those arising in cell biology, are inherently high-dimensional and stochastic in nature, and admit only partial, noisy state measurements. Our primary motivating setting is single-cell biology, where destructive measurements yield unpaired population snapshots rather than longitudinal trajectories of the same cells. This poses a significant challenge for addressing the problems of modeling the underlying dynamics and inferring the network structure of these systems. Existing methods are typically tailored either for structure learning or modeling dynamics at the population level, but are limited in their ability to address both problems together. In this work, we address both problems simultaneously: we present StructureFlow, a novel and principled simulation-free training approach for jointly learning the structure and stochastic population dynamics of physical systems. We showcase the utility of StructureFlow for the tasks of structure learning from interventions and dynamical (trajectory) inference of conditional population dynamics. We empirically evaluate our approach on high-dimensional synthetic systems, a set of biologically plausible simulated systems, and an experimental single-cell dataset. We show that StructureFlow can learn the structure of underlying systems while simultaneously modeling their conditional population dynamics --- a key step toward model-based mechanistic understanding of systems behavior.

Causal discovery has shifted from data-centric methods to hybrid strategies that integrate semantic knowledge from experts or large language models (LLMs). Such external information is vital for identifying causal structures beyond the Markov Equivalence Class (MEC), which data alone cannot resolve. However, expert availability is often limited, and LLMs frequently misidentify causal directions in specialized domains. To overcome such shortcomings, we propose a tag-based approach that leverages semantically meaningful labels while deriving causal directionality directly from data. Using variable-level tag assignments from available sources (e.g., LLMs), our tags for DAGs method learns from identifiable data structures to extract higher-level causal relations. These are then used to orient undirected edges, enabling causal discovery to move beyond the MEC without reliance on fallible external knowledge.

For two causal structures with the same set of visible variables, one is said to observationally dominate the other if the set of distributions over the visible variables realizable by the first contains the set of distributions over the visible variables realizable by the second. Knowing such dominance relations is useful for adjudicating between these structures given observational data. Here, we consider the problem of determining the partial order of equivalence classes of causal structures with latent variables relative to observational dominance. We provide a complete characterization of the dominance order in the case of three visible variables, and a partial characterization in the case of four visible variables. Our techniques also help to identify which observational equivalence classes have a set of realizable distributions that is characterized by nontrivial inequality constraints, analogous to Bell inequalities and instrumental inequalities. We find evidence that as one increases the number of visible variables, the equivalence classes satisfying nontrivial inequality constraints become ubiquitous. (Because such classes are the ones for which there can be a difference in the distributions that are quantumly and classically realizable, this implies that the potential for quantum-classical gaps is also ubiquitous.) Furthermore, we find evidence that constraint-based causal discovery algorithms that rely solely on conditional independence constraints have a significantly weaker distinguishing power among observational equivalence classes than algorithms that go beyond these (i.e., algorithms that also leverage nested Markov constraints and inequality constraints).

Large language models (LLMs) have developed rapidly, and their reasoning capabilities have become a hot research topic. However, there is still limited exploration of abductive reasoning. The multi-perspective and multi-level of causes is one of the core challenges of abductive reasoning, which cannot be solved well by existing methods. We construct a specialized dataset named DeepAbduction, which is designed for tracing the causes of pollution and disease, addressing the lack of datasets in this field. We propose \textsc{Inverse-Forward Abductive Reasoning} (IFAR) framework for LLMs multi-perspective and multi-level abductive reasoning. IFAR is zero-shot and combines generalized backward reasoning with relation-by-relation forward verification. Experimental results show that IFAR achieves an improvement of approximately 40% in the F1 score compared to other methods under mainstream LLMs, while maintaining a balance between recall and precision. Furthermore, IFAR enhances the performance of non-reasoning LLMs to surpass LLMs which have been trained for reasoning, and remains effective when applied to the latter. Code will be released after the acceptance of our work.

We study the problem of restricting a Markov equivalence class of maximal ancestral graphs (MAGs) to only those MAGs that contain certain edge marks, which we refer to as expert or orientation knowledge. Such a restriction of the Markov equivalence class can be uniquely represented by a restricted essential ancestral graph. Our contributions are several-fold. First, we prove certain properties for the entire Markov equivalence class including a conjecture from Ali et al. (2009). Second, we present several new sound graphical orientation rules for adding orientation knowledge to an essential ancestral graph. We also show that some orientation rules of Zhang (2008b) are not needed for restricting the Markov equivalence class with orientation knowledge. Third, we provide an algorithm for including this orientation knowledge and show that in certain settings the output of our algorithm is a restricted essential ancestral graph. Finally, outside of the specified settings, we provide an algorithm for checking whether a graph is a restricted essential graph and discuss its runtime. This work can be seen as a generalization of Meek (1995) to settings which allow for latent confounding.

The ability to understand causality significantly impacts the competence of large language models (LLMs) in output explanation and counterfactual reasoning, as causality reveals the underlying data distribution. However, the lack of a comprehensive benchmark currently limits the evaluation of LLMs' causal learning capabilities. To fill this gap, this paper develops CausalBN-Bench based on data from the causal research community, enabling comparative evaluations of LLMs against traditional causal learning algorithms. To provide a comprehensive investigation, we offer three tasks of varying difficulties, including correlation, causal skeleton, and causality identification. Evaluations of 19 leading LLMs reveal that, while closed-source LLMs show potential for simple causal relationships, they significantly lag behind traditional algorithms on larger-scale networks ($>50$ nodes). Specifically, LLMs struggle with collider structures but excel at chain structures, especially at long-chain causality analogous to Chain-of-Thought techniques. This supports the current prompt approaches while suggesting directions to enhance LLMs' causal reasoning capability. Furthermore, CausalBN-Bench incorporates background knowledge and training data into prompts to thoroughly unlock LLMs' text-comprehension ability during evaluation, whose findings indicate that, LLM understand causality through semantic associations with distinct entities, rather than directly from contextual information or numerical distributions.