Fine-grained annotations---e.g. dense image labels, image segmentation and text tagging---are useful in many ML applications but they are labor-intensive to generate. Moreover there are often systematic, structured errors in these fine-grained annotations. For example, a car might be entirely unannotated in the image, or the boundary between a car and street might only be coarsely annotated. Standard ML training on data with such structured errors produces models with biases and poor performance. In this work, we propose a novel framework of Error-Correcting Networks (ECN) to address the challenge of learning in the presence structured error in fine-grained annotations. Given a large noisy dataset with commonly occurring structured errors, and a much smaller dataset with more accurate annotations, ECN is able to substantially improve the prediction of fine-grained annotations compared to standard approaches for training on noisy data. It does so by learning to leverage the structures in the annotations and in the noisy labels. Systematic experiments on image segmentation and text tagging demonstrate the strong performance of ECN in improving training on noisy structured labels.
Accessibility is a major challenge of machine learning (ML). Typical ML models are built by specialists and require specialized hardware/software as well as ML experience to validate. This makes it challenging for non-technical collaborators and endpoint users (e.g. physicians) to easily provide feedback on model development and to gain trust in ML. The accessibility challenge also makes collaboration more difficult and limits the ML researcher's exposure to realistic data and scenarios that occur in the wild. To improve accessibility and facilitate collaboration, we developed an open-source Python package, Gradio, which allows researchers to rapidly generate a visual interface for their ML models. Gradio makes accessing any ML model as easy as sharing a URL. Our development of Gradio is informed by interviews with a number of machine learning researchers who participate in interdisciplinary collaborations. Their feedback identified that Gradio should support a variety of interfaces and frameworks, allow for easy sharing of the interface, allow for input manipulation and interactive inference by the domain expert, as well as allow embedding the interface in iPython notebooks. We developed these features and carried out a case study to understand Gradio's usefulness and usability in the setting of a machine learning collaboration between a researcher and a cardiologist.
Variational autoencoders are powerful algorithms for identifying dominant latent structure in a single dataset. In many applications, however, we are interested in modeling latent structure and variation that are enriched in a target dataset compared to some background---e.g. enriched in patients compared to the general population. Contrastive learning is a principled framework to capture such enriched variation between the target and background, but state-of-the-art contrastive methods are limited to linear models. In this paper, we introduce the contrastive variational autoencoder (cVAE), which combines the benefits of contrastive learning with the power of deep generative models. The cVAE is designed to identify and enhance salient latent features. The cVAE is trained on two related but unpaired datasets, one of which has minimal contribution from the salient latent features. The cVAE explicitly models latent features that are shared between the datasets, as well as those that are enriched in one dataset relative to the other, which allows the algorithm to isolate and enhance the salient latent features. The algorithm is straightforward to implement, has a similar run-time to the standard VAE, and is robust to noise and dataset purity. We conduct experiments across diverse types of data, including gene expression and facial images, showing that the cVAE effectively uncovers latent structure that is salient in a particular analysis.
We introduce the concrete autoencoder, an end-to-end differentiable method for global feature selection, which efficiently identifies a subset of the most informative features and simultaneously learns a neural network to reconstruct the input data from the selected features. Our method is unsupervised, and is based on using a concrete selector layer as the encoder and using a standard neural network as the decoder. During the training phase, the temperature of the concrete selector layer is gradually decreased, which encourages a user-specified number of discrete features to be learned. During test time, the selected features can be used with the decoder network to reconstruct the remaining input features. We evaluate concrete autoencoders on a variety of datasets, where they significantly outperform state-of-the-art methods for feature selection and data reconstruction. In particular, on a large-scale gene expression dataset, the concrete autoencoder selects a small subset of genes whose expression levels can be use to impute the expression levels of the remaining genes. In doing so, it improves on the current widely-used expert-curated L1000 landmark genes, potentially reducing measurement costs by 20%. The concrete autoencoder can be implemented by adding just a few lines of code to a standard autoencoder.
In order for machine learning to be deployed and trusted in many applications, it is crucial to be able to reliably explain why the machine learning algorithm makes certain predictions. For example, if an algorithm classifies a given pathology image to be a malignant tumor, then the doctor may need to know which parts of the image led the algorithm to this classification. How to interpret black-box predictors is thus an important and active area of research. A fundamental question is: how much can we trust the interpretation itself? In this paper, we show that interpretation of deep learning predictions is extremely fragile in the following sense: two perceptively indistinguishable inputs with the same predicted label can be assigned very different interpretations. We systematically characterize the fragility of several widely-used feature-importance interpretation methods (saliency maps, relevance propagation, and DeepLIFT) on ImageNet and CIFAR-10. Our experiments show that even small random perturbation can change the feature importance and new systematic perturbations can lead to dramatically different interpretations without changing the label. We extend these results to show that interpretations based on exemplars (e.g. influence functions) are similarly fragile. Our analysis of the geometry of the Hessian matrix gives insight on why fragility could be a fundamental challenge to the current interpretation approaches.
We introduce Contrastive Multivariate Singular Spectrum Analysis, a novel unsupervised method for dimensionality reduction and signal decomposition of time series data. By utilizing an appropriate background dataset, the method transforms a target time series dataset in a way that evinces the sub-signals that are enhanced in the target dataset, as opposed to only those that account for the greatest variance. This shifts the goal from finding signals that explain the most variance to signals that matter the most to the analyst. We demonstrate our method on an illustrative synthetic example, as well as show the utility of our method in the downstream clustering of electrocardiogram signals from the public MHEALTH dataset.
Measuring similarities between unlabeled time series trajectories is an important problem in domains as diverse as medicine, astronomy, finance, and computer vision. It is often unclear what is the appropriate metric to use because of the complex nature of noise in the trajectories (e.g. different sampling rates or outliers). Domain experts typically hand-craft or manually select a specific metric, such as dynamic time warping (DTW), to apply on their data. In this paper, we propose Autowarp, an end-to-end algorithm that optimizes and learns a good metric given unlabeled trajectories. We define a flexible and differentiable family of warping metrics, which encompasses common metrics such as DTW, Euclidean, and edit distance. Autowarp then leverages the representation power of sequence autoencoders to optimize for a member of this warping distance family. The output is a metric which is easy to interpret and can be robustly learned from relatively few trajectories. In systematic experiments across different domains, we show that Autowarp often outperforms hand-crafted trajectory similarity metrics.
We consider the problem of inference in a linear regression model in which the relative ordering of the input features and output labels is not known. Such datasets naturally arise from experiments in which the samples are shuffled or permuted during the protocol. In this work, we propose a framework that treats the unknown permutation as a latent variable. We maximize the likelihood of observations using a stochastic expectation-maximization (EM) approach. We compare this to the dominant approach in the literature, which corresponds to hard EM in our framework. We show on synthetic data that the stochastic EM algorithm we develop has several advantages, including lower parameter error, less sensitivity to the choice of initialization, and significantly better performance on datasets that are only partially shuffled. We conclude by performing two experiments on real datasets that have been partially shuffled, in which we show that the stochastic EM algorithm can recover the weights with modest error.
We present a new technique called contrastive principal component analysis (cPCA) that is designed to discover low-dimensional structure that is unique to a dataset, or enriched in one dataset relative to other data. The technique is a generalization of standard PCA, for the setting where multiple datasets are available -- e.g. a treatment and a control group, or a mixed versus a homogeneous population -- and the goal is to explore patterns that are specific to one of the datasets. We conduct a wide variety of experiments in which cPCA identifies important dataset-specific patterns that are missed by PCA, demonstrating that it is useful for many applications: subgroup discovery, visualizing trends, feature selection, denoising, and data-dependent standardization. We provide geometrical interpretations of cPCA and show that it satisfies desirable theoretical guarantees. We also extend cPCA to nonlinear settings in the form of kernel cPCA. We have released our code as a python package and documentation is on Github.