arXiv subjects

Kayhan Batmanghelich

Publications and source records attributed to Kayhan Batmanghelich.

54 records · Page 3Linked to original sources

arXiv2020

Context Matters: Graph-based Self-supervised Representation Learning for Medical Images

Supervised learning method requires a large volume of annotated datasets. Collecting such datasets is time-consuming and expensive. Until now, very few annotated COVID-19 imaging datasets are available. Although self-supervised learning enables us to bootstrap the training by exploiting unlabeled data, the generic self-supervised methods for natural images do not sufficiently incorporate the context. For medical images, a desirable method should be sensitive enough to detect deviation from normal-appearing tissue of each anatomical region; here, anatomy is the context. We introduce a novel approach with two levels of self-supervised representation learning objectives: one on the regional anatomical level and another on the patient-level. We use graph neural networks to incorporate the relationship between different anatomical regions. The structure of the graph is informed by anatomical correspondences between each patient and an anatomical atlas. In addition, the graph representation has the advantage of handling any arbitrarily sized image in full resolution. Experiments on large-scale Computer Tomography (CT) datasets of lung images show that our approach compares favorably to baseline methods that do not account for the context. We use the learnt embedding to quantify the clinical progression of COVID-19 and show that our method generalizes well to COVID-19 patients from different hospitals. Qualitative results suggest that our model can identify clinically relevant regions in the images.

eess.IV↗

arXiv2020

Semi-Supervised Hierarchical Drug Embedding in Hyperbolic Space

Learning accurate drug representation is essential for tasks such as computational drug repositioning and prediction of drug side-effects. A drug hierarchy is a valuable source that encodes human knowledge of drug relations in a tree-like structure where drugs that act on the same organs, treat the same disease, or bind to the same biological target are grouped together. However, its utility in learning drug representations has not yet been explored, and currently described drug representations cannot place novel molecules in a drug hierarchy. Here, we develop a semi-supervised drug embedding that incorporates two sources of information: (1) underlying chemical grammar that is inferred from molecular structures of drugs and drug-like molecules (unsupervised), and (2) hierarchical relations that are encoded in an expert-crafted hierarchy of approved drugs (supervised). We use the Variational Auto-Encoder (VAE) framework to encode the chemical structures of molecules and use the knowledge-based drug-drug similarity to induce the clustering of drugs in hyperbolic space. The hyperbolic space is amenable for encoding hierarchical concepts. Both quantitative and qualitative results support that the learned drug embedding can accurately reproduce the chemical structure and induce the hierarchical relations among drugs. Furthermore, our approach can infer the pharmacological properties of novel molecules by retrieving similar drugs from the embedding space. We demonstrate that the learned drug embedding can be used to find new uses for existing drugs and to discover side-effects. We show that it significantly outperforms baselines in both tasks.

cs.LG↗

arXiv2020

Weakly Supervised Disentanglement by Pairwise Similarities

Recently, researches related to unsupervised disentanglement learning with deep generative models have gained substantial popularity. However, without introducing supervision, there is no guarantee that the factors of interest can be successfully recovered. Motivated by a real-world problem, we propose a setting where the user introduces weak supervision by providing similarities between instances based on a factor to be disentangled. The similarity is provided as either a binary (yes/no) or a real-valued label describing whether a pair of instances are similar or not. We propose a new method for weakly supervised disentanglement of latent variables within the framework of Variational Autoencoder. Experimental results demonstrate that utilizing weak supervision improves the performance of the disentanglement method substantially.

cs.LG↗

arXiv2020

Explanation by Progressive Exaggeration

As machine learning methods see greater adoption and implementation in high stakes applications such as medical image diagnosis, the need for model interpretability and explanation has become more critical. Classical approaches that assess feature importance (e.g. saliency maps) do not explain how and why a particular region of an image is relevant to the prediction. We propose a method that explains the outcome of a classification black-box by gradually exaggerating the semantic effect of a given class. Given a query input to a classifier, our method produces a progressive set of plausible variations of that query, which gradually changes the posterior probability from its original class to its negation. These counter-factually generated samples preserve features unrelated to the classification decision, such that a user can employ our method as a "tuning knob" to traverse a data manifold while crossing the decision boundary. Our method is model agnostic and only requires the output value and gradient of the predictor with respect to its input.

cs.LG↗

arXiv2019

Learning Depth from Monocular Videos Using Synthetic Data: A Temporally-Consistent Domain Adaptation Approach

Majority of state-of-the-art monocular depth estimation methods are supervised learning approaches. The success of such approaches heavily depends on the high-quality depth labels which are expensive to obtain. Some recent methods try to learn depth networks by leveraging unsupervised cues from monocular videos which are easier to acquire but less reliable. In this paper, we propose to resolve this dilemma by transferring knowledge from synthetic videos with easily obtainable ground-truth depth labels. Due to the stylish difference between synthetic and real images, we propose a temporally-consistent domain adaptation (TCDA) approach that simultaneously explores labels in the synthetic domain and temporal constraints in the videos to improve style transfer and depth prediction. Furthermore, we make use of the ground-truth optical flow and pose information in the synthetic data to learn moving mask and pose prediction networks. The learned moving masks can filter out moving regions that produces erroneous temporal constraints and the estimated poses provide better initializations for estimating temporal constraints. Experimental results demonstrate the effectiveness of our method and comparable performance against state-of-the-art.

cs.CV↗

arXiv2019

Twin Auxiliary Classifiers GAN

Conditional generative models enjoy remarkable progress over the past few years. One of the popular conditional models is Auxiliary Classifier GAN (AC-GAN), which generates highly discriminative images by extending the loss function of GAN with an auxiliary classifier. However, the diversity of the generated samples by AC-GAN tends to decrease as the number of classes increases, hence limiting its power on large-scale data. In this paper, we identify the source of the low diversity issue theoretically and propose a practical solution to solve the problem. We show that the auxiliary classifier in AC-GAN imposes perfect separability, which is disadvantageous when the supports of the class distributions have significant overlap. To address the issue, we propose Twin Auxiliary Classifiers Generative Adversarial Net (TAC-GAN) that further benefits from a new player that interacts with other players (the generator and the discriminator) in GAN. Theoretically, we demonstrate that TAC-GAN can effectively minimize the divergence between the generated and real-data distributions. Extensive experimental results show that our TAC-GAN can successfully replicate the true data distributions on simulated data, and significantly improves the diversity of class-conditional image generation on real datasets.

cs.LG↗

arXiv2019

Robust Ordinal VAE: Employing Noisy Pairwise Comparisons for Disentanglement

Recent work by Locatello et al. (2018) has shown that an inductive bias is required to disentangle factors of interest in Variational Autoencoder (VAE). Motivated by a real-world problem, we propose a setting where such bias is introduced by providing pairwise ordinal comparisons between instances, based on the desired factor to be disentangled. For example, a doctor compares pairs of patients based on the level of severity of their illnesses, and the desired factor is a quantitive level of the disease severity. In a real-world application, the pairwise comparisons are usually noisy. Our method, Robust Ordinal VAE (ROVAE), incorporates the noisy pairwise ordinal comparisons in the disentanglement task. We introduce non-negative random variables in ROVAE, such that it can automatically determine whether each pairwise ordinal comparison is trustworthy and ignore the noisy comparisons. Experimental results demonstrate that ROVAE outperforms existing methods and is more robust to noisy pairwise comparisons in both benchmark datasets and a real-world application.

cs.LG↗

arXiv2019

Generative-Discriminative Complementary Learning

Majority of state-of-the-art deep learning methods are discriminative approaches, which model the conditional distribution of labels given inputs features. The success of such approaches heavily depends on high-quality labeled instances, which are not easy to obtain, especially as the number of candidate classes increases. In this paper, we study the complementary learning problem. Unlike ordinary labels, complementary labels are easy to obtain because an annotator only needs to provide a yes/no answer to a randomly chosen candidate class for each instance. We propose a generative-discriminative complementary learning method that estimates the ordinary labels by modeling both the conditional (discriminative) and instance (generative) distributions. Our method, we call Complementary Conditional GAN (CCGAN), improves the accuracy of predicting ordinary labels and can generate high-quality instances in spite of weak supervision. In addition to the extensive empirical studies, we also theoretically show that our model can retrieve the true conditional distribution from the complementarily-labeled data.

cs.LG↗

arXiv2019

Uncertainty-Driven Semantic Segmentation through Human-Machine Collaborative Learning

Deep learning-based approaches achieve state-of-the-art performance in the majority of image segmentation benchmarks. However, training of such models requires a sizable amount of manual annotations. In order to reduce this effort, we propose a method based on conditional Generative Adversarial Network (cGAN), which addresses segmentation in a semi-supervised setup and in a human-in-the-loop fashion. More specifically, we use the discriminator to identify unreliable slices for which expert annotation is required and use the generator in the GAN to synthesize segmentations on unlabeled data for which the model is confident. The quantitative results on a conventional standard benchmark show that our method is comparable with the state-of-the-art fully supervised methods in slice-level evaluation requiring far less annotated data.

eess.IV↗

arXiv2019

Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset.

cs.CV↗

arXiv2019

Robust Angular Local Descriptor Learning

In recent years, the learned local descriptors have outperformed handcrafted ones by a large margin, due to the powerful deep convolutional neural network architectures such as L2-Net [1] and triplet based metric learning [2]. However, there are two problems in the current methods, which hinders the overall performance. Firstly, the widely-used margin loss is sensitive to incorrect correspondences, which are prevalent in the existing local descriptor learning datasets. Second, the L2 distance ignores the fact that the feature vectors have been normalized to unit norm. To tackle these two problems and further boost the performance, we propose a robust angular loss which 1) uses cosine similarity instead of L2 distance to compare descriptors and 2) relies on a robust loss function that gives smaller penalty to triplets with negative relative similarity. The resulting descriptor shows robustness on different datasets, reaching the state-of-the-art result on Brown dataset , as well as demonstrating excellent generalization ability on the Hpatches dataset and a Wide Baseline Stereo dataset.

cs.CV↗

arXiv2018

Geometry-Consistent Generative Adversarial Networks for One-Sided Unsupervised Domain Mapping

Unsupervised domain mapping aims to learn a function to translate domain X to Y by a function GXY in the absence of paired examples. Finding the optimal GXY without paired data is an ill-posed problem, so appropriate constraints are required to obtain reasonable solutions. One of the most prominent constraints is cycle consistency, which enforces the translated image by GXY to be translated back to the input image by an inverse mapping GYX. While cycle consistency requires the simultaneous training of GXY and GY X, recent studies have shown that one-sided domain mapping can be achieved by preserving pairwise distances between images. Although cycle consistency and distance preservation successfully constrain the solution space, they overlook the special properties that simple geometric transformations do not change the semantic structure of images. Based on this special property, we develop a geometry-consistent generative adversarial network (GcGAN), which enables one-sided unsupervised domain mapping. GcGAN takes the original image and its counterpart image transformed by a predefined geometric transformation as inputs and generates two images in the new domain coupled with the corresponding geometry-consistency constraint. The geometry-consistency constraint reduces the space of possible solutions while keep the correct solutions in the search space. Quantitative and qualitative comparisons with the baseline (GAN alone) and the state-of-the-art methods including CycleGAN and DistanceGAN demonstrate the effectiveness of our method.

cs.CV↗

arXiv2018

Deep Diffeomorphic Normalizing Flows

The Normalizing Flow (NF) models a general probability density by estimating an invertible transformation applied on samples drawn from a known distribution. We introduce a new type of NF, called Deep Diffeomorphic Normalizing Flow (DDNF). A diffeomorphic flow is an invertible function where both the function and its inverse are smooth. We construct the flow using an ordinary differential equation (ODE) governed by a time-varying smooth vector field. We use a neural network to parametrize the smooth vector field and a recursive neural network (RNN) for approximating the solution of the ODE. Each cell in the RNN is a residual network implementing one Euler integration step. The architecture of our flow enables efficient likelihood evaluation, straightforward flow inversion, and results in highly flexible density estimation. An end-to-end trained DDNF achieves competitive results with state-of-the-art methods on a suite of density estimation and variational inference tasks. Finally, our method brings concepts from Riemannian geometry that, we believe, can open a new research direction for neural density estimation.

stat.ML↗

arXiv2018

Transfer Learning with Label Noise

Transfer learning aims to improve learning in target domain by borrowing knowledge from a related but different source domain. To reduce the distribution shift between source and target domains, recent methods have focused on exploring invariant representations that have similar distributions across domains. However, when learning this invariant knowledge, existing methods assume that the labels in source domain are uncontaminated, while in reality, we often have access to source data with noisy labels. In this paper, we first show how label noise adversely affect the learning of invariant representations and the correcting of label shift in various transfer learning scenarios. To reduce the adverse effects, we propose a novel Denoising Conditional Invariant Component (DCIC) framework, which provably ensures (1) extracting invariant representations given examples with noisy labels in source domain and unlabeled examples in target domain; (2) estimating the label distribution in target domain with no bias. Experimental results on both synthetic and real-world data verify the effectiveness of the proposed method.

stat.ML↗

arXiv2018

Causal Generative Domain Adaptation Networks

An essential problem in domain adaptation is to understand and make use of distribution changes across domains. For this purpose, we first propose a flexible Generative Domain Adaptation Network (G-DAN) with specific latent variables to capture changes in the generating process of features across domains. By explicitly modeling the changes, one can even generate data in new domains using the generating process with new values for the latent variables in G-DAN. In practice, the process to generate all features together may involve high-dimensional latent variables, requiring dealing with distributions in high dimensions and making it difficult to learn domain changes from few source domains. Interestingly, by further making use of the causal representation of joint distributions, we then decompose the joint distribution into separate modules, each of which involves different low-dimensional latent variables and can be learned separately, leading to a Causal G-DAN (CG-DAN). This improves both statistical and computational efficiency of the learning procedure. Finally, by matching the feature distribution in the target domain, we can recover the target-domain joint distribution and derive the learning machine for the target domain. We demonstrate the efficacy of both G-DAN and CG-DAN in domain generation and cross-domain prediction on both synthetic and real data experiments.

stat.ML↗

arXiv2018

Deep Ordinal Regression Network for Monocular Depth Estimation

Monocular depth estimation, which plays a crucial role in understanding 3D scene geometry, is an ill-posed problem. Recent methods have gained significant improvement by exploring image-level information and hierarchical features from deep convolutional neural networks (DCNNs). These methods model depth estimation as a regression problem and train the regression networks by minimizing mean squared error, which suffers from slow convergence and unsatisfactory local solutions. Besides, existing depth estimation networks employ repeated spatial pooling operations, resulting in undesirable low-resolution feature maps. To obtain high-resolution depth maps, skip-connections or multi-layer deconvolution networks are required, which complicates network training and consumes much more computations. To eliminate or at least largely reduce these problems, we introduce a spacing-increasing discretization (SID) strategy to discretize depth and recast depth network learning as an ordinal regression problem. By training the network using an ordinary regression loss, our method achieves much higher accuracy and \dd{faster convergence in synch}. Furthermore, we adopt a multi-scale network structure which avoids unnecessary spatial pooling and captures multi-scale information in parallel. The method described in this paper achieves state-of-the-art results on four challenging benchmarks, i.e., KITTI [17], ScanNet [9], Make3D [50], and NYU Depth v2 [42], and win the 1st prize in Robust Vision Challenge 2018. Code has been made available at: https://github.com/hufu6371/DORN.

cs.CV↗

arXiv2017

Causal Discovery in the Presence of Measurement Error: Identifiability Conditions

Measurement error in the observed values of the variables can greatly change the output of various causal discovery methods. This problem has received much attention in multiple fields, but it is not clear to what extent the causal model for the measurement-error-free variables can be identified in the presence of measurement error with unknown variance. In this paper, we study precise sufficient identifiability conditions for the measurement-error-free causal model and show what information of the causal model can be recovered from observed data. In particular, we present two different sets of identifiability conditions, based on the second-order statistics and higher-order statistics of the data, respectively. The former was inspired by the relationship between the generating model of the measurement-error-contaminated data and the factor analysis model, and the latter makes use of the identifiability result of the over-complete independent component analysis problem.

stat.ME↗

arXiv2016

Nonparametric Spherical Topic Modeling with Word Embeddings

Traditional topic models do not account for semantic regularities in language. Recent distributional representations of words exhibit semantic consistency over directional metrics such as cosine similarity. However, neither categorical nor Gaussian observational distributions used in existing topic models are appropriate to leverage such correlations. In this paper, we propose to use the von Mises-Fisher distribution to model the density of words over a unit sphere. Such a representation is well-suited for directional data. We use a Hierarchical Dirichlet Process for our base topic model and propose an efficient inference algorithm based on Stochastic Variational Inference. This model enables us to naturally exploit the semantic structures of word embeddings while flexibly discovering the number of topics. Experiments demonstrate that our method outperforms competitive approaches in terms of topic coherence on two different text corpora while offering efficient inference.

cs.CL↗