Zizhen Deng

Zizhen Deng, Jiaru Zhang, Rui Ding et al.

Supervised Causal Learning (SCL) has shown promise in causal discovery by framing it as a supervised learning problem. However, it suffers from significant out-of-distribution generalization challenges. We reveal three limitations of previous SCL practices: a significant performance gap between synthetic benchmarks and real-world data, fragility to distribution shifts, and failure in compositional generalization, collectively questioning its real-world applicability. To address this, we propose Test-Time Training for Supervised Causal Learning (TTT-SCL), a novel framework that dynamically generates training sets explicitly aligned with any specific test instance. We demonstrate the correlation between TTT-SCL and score-based methods, and design an efficient module for generating training sets based on the classic scoring function. Experiments on synthetic benchmarks, pseudo-real and real-world datasets demonstrate that TTT-SCL significantly outperforms existing SCL and traditional causal discovery methods.

Zizhen Deng, Xiaolong Zheng, Hu Tian et al.

Causal learning has garnered significant attention in recent years because it reveals the essential relationships that underpin phenomena and delineates the mechanisms by which the world evolves. Nevertheless, traditional causal learning methods face numerous challenges and limitations, including high-dimensional, unstructured variables, combinatorial optimization problems, unobserved confounders, selection biases, and estimation inaccuracies. Deep causal learning, which leverages deep neural networks, offers innovative insights and solutions for addressing these challenges. Although numerous deep learning-based methods for causal discovery and inference have been proposed, there remains a dearth of reviews examining the underlying mechanisms by which deep learning can enhance causal learning. In this article, we comprehensively review how deep learning can contribute to causal learning by tackling traditional challenges across three key dimensions: representation, discovery, and inference. We emphasize that deep causal learning is pivotal for advancing the theoretical frontiers and broadening the practical applications of causal science. We conclude by summarizing open issues and outlining potential directions for future research.

Wei Wu, Can Liao, Zizhen Deng et al.

The Platonic Representation Hypothesis suggests a universal, modality-independent reality representation behind different data modalities. Inspired by this, we view each neuron as a system and detect its multi-segment activity data under various peripheral conditions. We assume there's a time-invariant representation for the same neuron, reflecting its intrinsic properties like molecular profiles, location, and morphology. The goal of obtaining these intrinsic neuronal representations has two criteria: (I) segments from the same neuron should have more similar representations than those from different neurons; (II) the representations must generalize well to out-of-domain data. To meet these, we propose the NeurPIR (Neuron Platonic Intrinsic Representation) framework. It uses contrastive learning, with segments from the same neuron as positive pairs and those from different neurons as negative pairs. In implementation, we use VICReg, which focuses on positive pairs and separates dissimilar samples via regularization. We tested our method on Izhikevich model-simulated neuronal population dynamics data. The results accurately identified neuron types based on preset hyperparameters. We also applied it to two real-world neuron dynamics datasets with neuron type annotations from spatial transcriptomics and neuron locations. Our model's learned representations accurately predicted neuron types and locations and were robust on out-of-domain data (from unseen animals). This shows the potential of our approach for understanding neuronal systems and future neuroscience research.

Wei Wu, Zizhen Deng, Chi Zhang et al.

Addressing the unavoidable bias inherent in supervised aging clocks, we introduce Sundial, a novel framework that models molecular dynamics through a diffusion field, capturing both the population-level aging process and the individual-level relative aging order. Sundial enables unbiasedestimation of biological age and the forecast of aging roadmap. Fasteraging individuals from Sundial exhibit a higher disease risk compared to those identified from supervised aging clocks. This framework opens new avenues for exploring key topics, including age- and sex-specific aging dynamics and faster yet healthy aging paths.

Jiaru Zhang, Rui Ding, Qiang Fu et al.

Causal discovery is a structured prediction task that aims to predict causal relations among variables based on their data samples. Supervised Causal Learning (SCL) is an emerging paradigm in this field. Existing Deep Neural Network (DNN)-based methods commonly adopt the "Node-Edge approach", in which the model first computes an embedding vector for each variable-node, then uses these variable-wise representations to concurrently and independently predict for each directed causal-edge. In this paper, we first show that this architecture has some systematic bias that cannot be mitigated regardless of model size and data size. We then propose SiCL, a DNN-based SCL method that predicts a skeleton matrix together with a v-tensor (a third-order tensor representing the v-structures). According to the Markov Equivalence Class (MEC) theory, both the skeleton and the v-structures are identifiable causal structures under the canonical MEC setting, so predictions about skeleton and v-structures do not suffer from the identifiability limit in causal discovery, thus SiCL can avoid the systematic bias in Node-Edge architecture, and enable consistent estimators for causal discovery. Moreover, SiCL is also equipped with a specially designed pairwise encoder module with a unidirectional attention layer to model both internal and external relationships of pairs of nodes. Experimental results on both synthetic and real-world benchmarks show that SiCL significantly outperforms other DNN-based SCL approaches.