Model transparency is a prerequisite in many domains and an increasingly popular area in machine learning research. In the medical domain, for instance, unveiling the mechanisms behind a disease often has higher priority than the diagnostic itself since it might dictate or guide potential treatments and research directions. One of the most popular approaches to explain model global predictions is the permutation importance where the performance on permuted data is benchmarked against the baseline. However, this method and other related approaches will undervalue the importance of a feature in the presence of covariates since these cover part of its provided information. To address this issue, we propose Covered Information Disentanglement (CID), a method that considers all feature information overlap to correct the values provided by permutation importance. We further show how to compute CID efficiently when coupled with Markov random fields. We demonstrate its efficacy in adjusting permutation importance first on a controlled toy dataset and discuss its effect on real-world medical data.
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Language carries implicit human biases, functioning both as a reflection and a perpetuation of stereotypes that people carry with them. Recently, ML-based NLP methods such as word embeddings have been shown to learn such language biases with striking accuracy. This capability of word embeddings has been successfully exploited as a tool to quantify and study human biases. However, previous studies only consider a predefined set of biased concepts to attest (e.g., whether gender is more or less associated with particular jobs), or just discover biased words without helping to understand their meaning at the conceptual level. As such, these approaches can be either unable to find biased concepts that have not been defined in advance, or the biases they find are difficult to interpret and study. This could make existing approaches unsuitable to discover and interpret biases in online communities, as such communities may carry different biases than those in mainstream culture. This paper improves upon, extends, and evaluates our previous data-driven method to automatically discover and help interpret biased concepts encoded in word embeddings. We apply this approach to study the biased concepts present in the language used in online communities and experimentally show the validity and stability of our method
Causal discovery for purely observational, categorical data is a long-standing challenging problem. Unlike continuous data, the vast majority of existing methods for categorical data focus on inferring the Markov equivalence class only, which leaves the direction of some causal relationships undetermined. This paper proposes an identifiable ordinal causal discovery method that exploits the ordinal information contained in many real-world applications to uniquely identify the causal structure. The proposed method is applicable beyond ordinal data via data discretization. Through real-world and synthetic experiments, we demonstrate that the proposed ordinal causal discovery method combined with simple score-and-search algorithms has favorable and robust performance compared to state-of-the-art alternative methods in both ordinal categorical and non-categorical data. An accompanied R package OCD is freely available at //web.stat.tamu.edu/~yni/files/OCD_0.1.0.tar.gz.
In the last decade, convolutional neural networks (ConvNets) have been a major focus of research in medical image analysis. However, the performances of ConvNets may be limited by a lack of explicit consideration of the long-range spatial relationships in an image. Recently Vision Transformer architectures have been proposed to address the shortcomings of ConvNets and have produced state-of-the-art performances in many medical imaging applications. Transformers may be a strong candidate for image registration because their unlimited receptive field enables a more precise comprehension of the spatial correspondence between moving and fixed images. Here, we present TransMorph, a hybrid Transformer-ConvNet model for volumetric medical image registration. This paper also presents diffeomorphic and Bayesian variants of TransMorph: the diffeomorphic variants ensure the topology-preserving deformations, and the Bayesian variant produces a well-calibrated registration uncertainty estimate. We extensively validated the proposed models using 3D medical images from three applications: inter-patient and atlas-to-patient brain MRI registration and phantom-to-CT registration. The proposed models are evaluated in comparison to a variety of existing registration methods and Transformer architectures. Qualitative and quantitative results demonstrate that the proposed Transformer-based model leads to a substantial performance improvement over the baseline methods, confirming the effectiveness of Transformers for medical image registration.
Approaches based on Functional Causal Models (FCMs) have been proposed to determine causal direction between two variables, by properly restricting model classes; however, their performance is sensitive to the model assumptions, which makes it difficult for practitioners to use. In this paper, we provide a novel dynamical-system view of FCMs and propose a new framework for identifying causal direction in the bivariate case. We first show the connection between FCMs and optimal transport, and then study optimal transport under the constraints of FCMs. Furthermore, by exploiting the dynamical interpretation of optimal transport under the FCM constraints, we determine the corresponding underlying dynamical process of the static cause-effect pair data under the least action principle. It provides a new dimension for describing static causal discovery tasks, while enjoying more freedom for modeling the quantitative causal influences. In particular, we show that Additive Noise Models (ANMs) correspond to volume-preserving pressureless flows. Consequently, based on their velocity field divergence, we introduce a criterion to determine causal direction. With this criterion, we propose a novel optimal transport-based algorithm for ANMs which is robust to the choice of models and extend it to post-noninear models. Our method demonstrated state-of-the-art results on both synthetic and causal discovery benchmark datasets.
We consider the task of learning causal structures from data stored on multiple machines, and propose a novel structure learning method called distributed annealing on regularized likelihood score (DARLS) to solve this problem. We model causal structures by a directed acyclic graph that is parameterized with generalized linear models, so that our method is applicable to various types of data. To obtain a high-scoring causal graph, DARLS simulates an annealing process to search over the space of topological sorts, where the optimal graphical structure compatible with a sort is found by a distributed optimization method. This distributed optimization relies on multiple rounds of communication between local and central machines to estimate the optimal structure. We establish its convergence to a global optimizer of the overall score that is computed on all data across local machines. To the best of our knowledge, DARLS is the first distributed method for learning causal graphs with such theoretical guarantees. Through extensive simulation studies, DARLS has shown competing performance against existing methods on distributed data, and achieved comparable structure learning accuracy and test-data likelihood with competing methods applied to pooled data across all local machines. In a real-world application for modeling protein-DNA binding networks with distributed ChIP-Sequencing data, DARLS also exhibits higher predictive power than other methods, demonstrating a great advantage in estimating causal networks from distributed data.
While self-training has advanced semi-supervised semantic segmentation, it severely suffers from the long-tailed class distribution on real-world semantic segmentation datasets that make the pseudo-labeled data bias toward majority classes. In this paper, we present a simple and yet effective Distribution Alignment and Random Sampling (DARS) method to produce unbiased pseudo labels that match the true class distribution estimated from the labeled data. Besides, we also contribute a progressive data augmentation and labeling strategy to facilitate model training with pseudo-labeled data. Experiments on both Cityscapes and PASCAL VOC 2012 datasets demonstrate the effectiveness of our approach. Albeit simple, our method performs favorably in comparison with state-of-the-art approaches. Code will be available at //github.com/CVMI-Lab/DARS.
Optimal transport distances have found many applications in machine learning for their capacity to compare non-parametric probability distributions. Yet their algorithmic complexity generally prevents their direct use on large scale datasets. Among the possible strategies to alleviate this issue, practitioners can rely on computing estimates of these distances over subsets of data, {\em i.e.} minibatches. While computationally appealing, we highlight in this paper some limits of this strategy, arguing it can lead to undesirable smoothing effects. As an alternative, we suggest that the same minibatch strategy coupled with unbalanced optimal transport can yield more robust behavior. We discuss the associated theoretical properties, such as unbiased estimators, existence of gradients and concentration bounds. Our experimental study shows that in challenging problems associated to domain adaptation, the use of unbalanced optimal transport leads to significantly better results, competing with or surpassing recent baselines.
Recently, image-to-image translation has made significant progress in achieving both multi-label (\ie, translation conditioned on different labels) and multi-style (\ie, generation with diverse styles) tasks. However, due to the unexplored independence and exclusiveness in the labels, existing endeavors are defeated by involving uncontrolled manipulations to the translation results. In this paper, we propose Hierarchical Style Disentanglement (HiSD) to address this issue. Specifically, we organize the labels into a hierarchical tree structure, in which independent tags, exclusive attributes, and disentangled styles are allocated from top to bottom. Correspondingly, a new translation process is designed to adapt the above structure, in which the styles are identified for controllable translations. Both qualitative and quantitative results on the CelebA-HQ dataset verify the ability of the proposed HiSD. We hope our method will serve as a solid baseline and provide fresh insights with the hierarchically organized annotations for future research in image-to-image translation. The code has been released at //github.com/imlixinyang/HiSD.
The information bottleneck (IB) method is a technique for extracting information that is relevant for predicting the target random variable from the source random variable, which is typically implemented by optimizing the IB Lagrangian that balances the compression and prediction terms. However, the IB Lagrangian is hard to optimize, and multiple trials for tuning values of Lagrangian multiplier are required. Moreover, we show that the prediction performance strictly decreases as the compression gets stronger during optimizing the IB Lagrangian. In this paper, we implement the IB method from the perspective of supervised disentangling. Specifically, we introduce Disentangled Information Bottleneck (DisenIB) that is consistent on compressing source maximally without target prediction performance loss (maximum compression). Theoretical and experimental results demonstrate that our method is consistent on maximum compression, and performs well in terms of generalization, robustness to adversarial attack, out-of-distribution detection, and supervised disentangling.
We present new intuitions and theoretical assessments of the emergence of disentangled representation in variational autoencoders. Taking a rate-distortion theory perspective, we show the circumstances under which representations aligned with the underlying generative factors of variation of data emerge when optimising the modified ELBO bound in $\beta$-VAE, as training progresses. From these insights, we propose a modification to the training regime of $\beta$-VAE, that progressively increases the information capacity of the latent code during training. This modification facilitates the robust learning of disentangled representations in $\beta$-VAE, without the previous trade-off in reconstruction accuracy.
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