arXiv:2608. 08430v1 Announce Type: cross Abstract: Virtual cells employ machine learning models to simulate and predict cellular behaviors, serving as a critical computational framework for investigating health and disease.
arXiv:2509. 01916v2 Announce Type: replace Abstract: Causal disentanglement from soft interventions is identifiable under the assumptions of linear interventional faithfulness and availability of both observational and interventional data.
arXiv:2606. 24488v1 Announce Type: cross Abstract: Learning causal models from fragmented biomedical data is challenging because clinical, molecular, and imaging variables are often incomplete or not jointly observed.
arXiv:2606. 08816v1 Announce Type: cross Abstract: Predicting the effect of an unseen gene knockout perturbation on transcriptomic gene expression remains a highly challenging problem for virtual cell models.
arXiv:2605. 07267v2 Announce Type: replace Abstract: Personalized healthcare decisions require reasoning about how physiological and behavioral variables influence an individual patient over time.
arXiv:2606. 06440v1 Announce Type: new Abstract: Data-driven causal relationship identification is pertinent to advancing understanding of complex systems both within and beyond science.
arXiv:2606. 01042v1 Announce Type: cross Abstract: Perturbation experiments are central to understanding cellular mechanisms, but remain costly and sparse, motivating prediction of gene expression responses for unobserved conditions.
arXiv:2606. 18287v1 Announce Type: new Abstract: Multimodal neuroimaging, integrating functional connectivity from fMRI and structural connectivity from DTI, enables non-invasive analysis of brain networks using graph neural networks.
The paper introduces Causal Integrated Gradients (CIG) and Causal Expected Gradients (CEG), which extend integrated gradients by incorporating known causal relationships among input features. By routing the integration path along a causal graph, the methods decompose each feature’s attribution into direct and mediated effects, enabling scalable feature attribution that aligns with true causal influence. Experiments on synthetic data, simulated single‑cell gene expression, and real interferon‑β stimulation data demonstrate that CIG outperforms existing gradient‑based methods in identifying upstream drivers while maintaining computational efficiency.
The paper introduces Cluster-DAGs as a flexible prior knowledge framework to improve causal discovery. It presents two modified constraint‑based algorithms, Cluster‑PC and Cluster‑FCI, tailored for fully and partially observed data. Experiments on simulated data show that these methods outperform baseline algorithms that lack prior knowledge.
CausalArena is a new benchmark designed to evaluate causal discovery methods in the era of foundation models. It unifies synthetic structural causal models (SCMs), semantically grounded SCMs, and formula‑grounded SCMs, while also including real‑world datasets for external validation. Experiments show that performance rankings vary widely across different SCM families and protocols, indicating that strong results on one benchmark do not necessarily transfer to others.
arXiv:2606. 05972v1 Announce Type: new Abstract: Causal graphs provide a high-level language for making mechanisms transparent.
arXiv:2607. 11510v1 Announce Type: new Abstract: Causal discovery from observational tabular data remains fundamentally challenging, primarily due to the heterogeneity of underlying causal mechanisms and the high-dimensional combinatorial search space of Directed Acyclic Graphs (DAGs).