arXiv AI

MOSAIC: Module Discovery via Sparse Additive Identifiable Causal Learning for Scientific Time Series

MOSAIC is a sparse temporal variational autoencoder that merges causal representation learning with support recovery to identify interpretable latent modules in scientific time series. It leverages regime‑conditioned temporal variation to discover latent variables and uses an additive decoder to recover a sparse set of observations linked to each latent, providing module‑level interpretability. The method offers theoretical guarantees for ANOVA main‑effect identifiability under smooth mixing functions and demonstrates empirical success across diverse domains such as RNA dynamics, solar wind, ENSO climate, industrial process control, and synthetic tokamak data.

arXiv AI
Jul 14

CDFM: Towards a General-Purpose Causal Discovery Foundation Model

arXiv:2607. 11508v1 Announce Type: cross Abstract: Causal discovery, the process of recovering underlying causal structures from observational data, is a fundamental pursuit across scientific disciplines.

By Jie Qiao, Ruichu Cai, Zijian Li, Weilin Chen, Pengfei Hua, Boyan Xu, Zhengming Chen, Zhifeng Hao, Peng Cui
arXiv Machine Learning
Oct 8

DSReg: Provably Recovering Individual World Latents without Reconstruction

The paper introduces DSReg, a method that provably recovers individual world latent variables without relying on reconstruction, decoders, or labels. It leverages a Structural Diversity condition—distinct dependency footprints of different latents—to achieve full identifiability up to signed permutation. DSReg can be applied post hoc to any linearly identified representation, preserving dense prediction while improving latent recovery across synthetic and real-world experiments.

By Yujia Zheng, David Klindt, Randall Balestriero, Bernhard Sch\"olkopf
arXiv Machine Learning
Sep 29

I Act Therefore I Am: When Is JEPA's Action-Conditioning Enough to Learn Causal Mechanisms?

The paper studies when joint-embedding predictive architectures (JEPAs) can recover underlying causal states from high‑dimensional observations. It introduces a latent variable model where observations arise from causal states with action‑conditioned dynamics, and proposes an information‑theoretic objective that maximizes conditional likelihood while preserving state entropy. The authors prove identifiability conditions—particularly sufficient action‑induced variation—and instantiate the objective as an action‑modulated Gaussian additive‑noise model (A‑JEPA), demonstrating theoretical and empirical success in synthetic and visual benchmarks.

By Yuhang Liu, Zhuo Huang, Javen Qinfeng Shi
arXiv Machine Learning
4d ago

Complete or Sparse: A Tale of Two Identifiabilities

The paper investigates when supervised learning can recover the true latent variables that generate data, focusing on two causal settings: generative (labels cause latents) and discriminative (latents cause labels). It shows that if the representation space has at least as many dimensions as the latent space, optimal encoders are linear; otherwise, identifiability fails and encoders become nonlinear. Additional constraints—such as non‑negative activations in the generative case or sparsity and spark conditions in the discriminative case—enable recovery of individual latent variables, linking nonlinear ICA, compressed sensing, and neural network interpretability.

By Junze Zhou, David Klindt
arXiv Machine Learning
Aug 3

Nonparametric Partial Disentanglement via Mechanism Sparsity: Sparse Actions, Interventions and Sparse Temporal Dependencies

arXiv:2401. 04890v2 Announce Type: replace-cross Abstract: This work introduces a novel principle for disentanglement we call mechanism sparsity regularization, which applies when the latent factors of interest depend sparsely on observed auxiliary variables and/or past latent factors.

By S\'ebastien Lachapelle, Pau Rodr\'iguez L\'opez, Yash Sharma, Katie Everett, R\'emi Le Priol, Alexandre Lacoste, Simon Lacoste-Julien
arXiv AI
Oct 7

CausalBind: Causal Modeling and Learning for Protein-Molecule Virtual Screening

CausalBind introduces a causal modeling framework for protein‑molecule virtual screening that focuses on sparse cross‑modality interactions rather than dense holistic alignment. By formalizing a V‑structure causal model with Heckman‑style selection, the authors prove that latent interaction concepts are identifiable only under sparsity constraints and propose three implementation variants. Experiments on DUD‑E and LIT‑PCBA benchmarks demonstrate that all variants outperform strong retrieval baselines, especially in early enrichment and out‑of‑distribution generalization.

By Loka Li, Jin Tian, Kun Zhang
arXiv AI
Jul 23

Causal dictionary learning reveals and validates transcription-factor binding features in genomic language models

arXiv:2607. 19618v1 Announce Type: cross Abstract: Genomic language models achieve strong performance across regulatory-genomics tasks, yet what these models internally represent remains opaque, and the field lacks a principled procedure for verifying that an apparent ``concept'' inside a model is real rather than an artifact of sequence composition.

By Sarwan Ali
arXiv Machine Learning
Aug 19

TabCausal: Pretraining Across Causal Environments for Tabular Causal Discovery

TabCausal is a causal discovery foundation model that learns to map datasets directly to causal graphs by pretraining across diverse causal environments. It uses a dynamic task construction strategy to expose the model to varied graph priors, mechanisms, noise models, dimensions, sample sizes, and intervention regimes, improving transferability from observational and mixed‑interventional data. On large synthetic benchmarks and a new protocol‑guided semantic benchmark, TabCausal outperforms many classical baselines and shows robust structure recovery, especially when interventional evidence is available.

By Zi-Rong Li, Si-Yang Liu, Tian-Zuo Wang, Han-Jia Ye