Gene Regulatory Network Inference in the Presence of Dropouts: a Causal View

Gene regulatory network inference (GRNI) is a challenging problem, particularly owing to the presence of zeros in single-cell RNA sequencing data: some are biological zeros representing no gene expression, while some others are technical zeros arising from the sequencing procedure (aka dropouts), which may bias GRNI by distorting the joint distribution of the measured gene expressions. Existing approaches typically handle dropout error via imputation, which may introduce spurious relations as the true joint distribution is generally unidentifiable. To tackle this issue, we introduce a causal graphical model to characterize the dropout mechanism, namely, Causal Dropout Model. We provide a simple yet effective theoretical result: interestingly, the conditional independence (CI) relations in the data with dropouts, after deleting the samples with zero values (regardless if technical or not) for the conditioned variables, are asymptotically identical to the CI relations in the original data without dropouts. This particular test-wise deletion procedure, in which we perform CI tests on the samples without zeros for the conditioned variables, can be seamlessly integrated with existing structure learning approaches including constraint-based and greedy score-based methods, thus giving rise to a principled framework for GRNI in the presence of dropouts. We further show that the causal dropout model can be validated from data, and many existing statistical models to handle dropouts fit into our model as specific parametric instances. Empirical evaluation on synthetic, curated, and real-world experimental transcriptomic data comprehensively demonstrate the efficacy of our method.

Local Causal Discovery with Linear non-Gaussian Cyclic Models

Local causal discovery is of great practical significance, as there are often situations where the discovery of the global causal structure is unnecessary, and the interest lies solely on a single target variable. Most existing local methods utilize conditional independence relations, providing only a partially directed graph, and assume acyclicity for the ground-truth structure, even though real-world scenarios often involve cycles like feedback mechanisms. In this work, we present a general, unified local causal discovery method with linear non-Gaussian models, whether they are cyclic or acyclic. We extend the application of independent component analysis from the global context to independent subspace analysis, enabling the exact identification of the equivalent local directed structures and causal strengths from the Markov blanket of the target variable. We also propose an alternative regression-based method in the particular acyclic scenarios. Our identifiability results are empirically validated using both synthetic and real-world datasets.

On the Three Demons in Causality in Finance: Time Resolution, Nonstationarity, and Latent Factors

Financial data is generally time series in essence and thus suffers from three fundamental issues: the mismatch in time resolution, the time-varying property of the distribution - nonstationarity, and causal factors that are important but unknown/unobserved. In this paper, we follow a causal perspective to systematically look into these three demons in finance. Specifically, we reexamine these issues in the context of causality, which gives rise to a novel and inspiring understanding of how the issues can be addressed. Following this perspective, we provide systematic solutions to these problems, which hopefully would serve as a foundation for future research in the area.

ML4C: Seeing Causality Through Latent Vicinity

Supervised Causal Learning (SCL) aims to learn causal relations from observational data by accessing previously seen datasets associated with ground truth causal relations. This paper presents a first attempt at addressing a fundamental question: What are the benefits from supervision and how does it benefit? Starting from seeing that SCL is not better than random guessing if the learning target is non-identifiable a priori, we propose a two-phase paradigm for SCL by explicitly considering structure identifiability. Following this paradigm, we tackle the problem of SCL on discrete data and propose ML4C. The core of ML4C is a binary classifier with a novel learning target: it classifies whether an Unshielded Triple (UT) is a v-structure or not. Starting from an input dataset with the corresponding skeleton provided, ML4C orients each UT once it is classified as a v-structure. These v-structures are together used to construct the final output. To address the fundamental question of SCL, we propose a principled method for ML4C featurization: we exploit the vicinity of a given UT (i.e., the neighbors of UT in skeleton), and derive features by considering the conditional dependencies and structural entanglement within the vicinity. We further prove that ML4C is asymptotically perfect. Last but foremost, thorough experiments conducted on benchmark datasets demonstrate that ML4C remarkably outperforms other state-of-the-art algorithms in terms of accuracy, robustness, tolerance and transferability. In summary, ML4C shows promising results on validating the effectiveness of supervision for causal learning.

What do CNN neurons learn: Visualization & Clustering

In recent years convolutional neural networks (CNN) have shown striking progress in various tasks. However, despite the high performance, the training and prediction process remains to be a black box, leaving it a mystery to extract what neurons learn in CNN. In this paper, we address the problem of interpreting a CNN from the aspects of the input image's focus and preference, and the neurons' domination, activation and contribution to a concrete final prediction. Specifically, we use two techniques - visualization and clustering - to tackle the problems above. Visualization means the method of gradient descent on image pixel, and in clustering section two algorithms are proposed to cluster respectively over image categories and network neurons. Experiments and quantitative analyses have demonstrated the effectiveness of the two methods in explaining the question: what do neurons learn.