arXiv subjects

Rahul G. Krishnan

Publications and source records attributed to Rahul G. Krishnan.

62 records · Page 4Linked to original sources

arXiv2022

Self-Supervised Vision Transformers Learn Visual Concepts in Histopathology

Tissue phenotyping is a fundamental task in learning objective characterizations of histopathologic biomarkers within the tumor-immune microenvironment in cancer pathology. However, whole-slide imaging (WSI) is a complex computer vision in which: 1) WSIs have enormous image resolutions with precludes large-scale pixel-level efforts in data curation, and 2) diversity of morphological phenotypes results in inter- and intra-observer variability in tissue labeling. To address these limitations, current efforts have proposed using pretrained image encoders (transfer learning from ImageNet, self-supervised pretraining) in extracting morphological features from pathology, but have not been extensively validated. In this work, we conduct a search for good representations in pathology by training a variety of self-supervised models with validation on a variety of weakly-supervised and patch-level tasks. Our key finding is in discovering that Vision Transformers using DINO-based knowledge distillation are able to learn data-efficient and interpretable features in histology images wherein the different attention heads learn distinct morphological phenotypes. We make evaluation code and pretrained weights publicly-available at: https://github.com/Richarizardd/Self-Supervised-ViT-Path.

cs.CV↗

arXiv2021

Clustering Interval-Censored Time-Series for Disease Phenotyping

Unsupervised learning is often used to uncover clusters in data. However, different kinds of noise may impede the discovery of useful patterns from real-world time-series data. In this work, we focus on mitigating the interference of interval censoring in the task of clustering for disease phenotyping. We develop a deep generative, continuous-time model of time-series data that clusters time-series while correcting for censorship time. We provide conditions under which clusters and the amount of delayed entry may be identified from data under a noiseless model. On synthetic data, we demonstrate accurate, stable, and interpretable results that outperform several benchmarks. On real-world clinical datasets of heart failure and Parkinson's disease patients, we study how interval censoring can adversely affect the task of disease phenotyping. Our model corrects for this source of error and recovers known clinical subtypes.

stat.ML↗

arXiv2021

Neural Pharmacodynamic State Space Modeling

Modeling the time-series of high-dimensional, longitudinal data is important for predicting patient disease progression. However, existing neural network based approaches that learn representations of patient state, while very flexible, are susceptible to overfitting. We propose a deep generative model that makes use of a novel attention-based neural architecture inspired by the physics of how treatments affect disease state. The result is a scalable and accurate model of high-dimensional patient biomarkers as they vary over time. Our proposed model yields significant improvements in generalization and, on real-world clinical data, provides interpretable insights into the dynamics of cancer progression.

cs.LG↗

arXiv2018

Variational Autoencoders for Collaborative Filtering

We extend variational autoencoders (VAEs) to collaborative filtering for implicit feedback. This non-linear probabilistic model enables us to go beyond the limited modeling capacity of linear factor models which still largely dominate collaborative filtering research.We introduce a generative model with multinomial likelihood and use Bayesian inference for parameter estimation. Despite widespread use in language modeling and economics, the multinomial likelihood receives less attention in the recommender systems literature. We introduce a different regularization parameter for the learning objective, which proves to be crucial for achieving competitive performance. Remarkably, there is an efficient way to tune the parameter using annealing. The resulting model and learning algorithm has information-theoretic connections to maximum entropy discrimination and the information bottleneck principle. Empirically, we show that the proposed approach significantly outperforms several state-of-the-art baselines, including two recently-proposed neural network approaches, on several real-world datasets. We also provide extended experiments comparing the multinomial likelihood with other commonly used likelihood functions in the latent factor collaborative filtering literature and show favorable results. Finally, we identify the pros and cons of employing a principled Bayesian inference approach and characterize settings where it provides the most significant improvements.

stat.ML↗

arXiv2017

On the challenges of learning with inference networks on sparse, high-dimensional data

We study parameter estimation in Nonlinear Factor Analysis (NFA) where the generative model is parameterized by a deep neural network. Recent work has focused on learning such models using inference (or recognition) networks; we identify a crucial problem when modeling large, sparse, high-dimensional datasets -- underfitting. We study the extent of underfitting, highlighting that its severity increases with the sparsity of the data. We propose methods to tackle it via iterative optimization inspired by stochastic variational inference \citep{hoffman2013stochastic} and improvements in the sparse data representation used for inference. The proposed techniques drastically improve the ability of these powerful models to fit sparse data, achieving state-of-the-art results on a benchmark text-count dataset and excellent results on the task of top-N recommendation.

stat.ML↗

arXiv2016

Structured Inference Networks for Nonlinear State Space Models

Gaussian state space models have been used for decades as generative models of sequential data. They admit an intuitive probabilistic interpretation, have a simple functional form, and enjoy widespread adoption. We introduce a unified algorithm to efficiently learn a broad class of linear and non-linear state space models, including variants where the emission and transition distributions are modeled by deep neural networks. Our learning algorithm simultaneously learns a compiled inference network and the generative model, leveraging a structured variational approximation parameterized by recurrent neural networks to mimic the posterior distribution. We apply the learning algorithm to both synthetic and real-world datasets, demonstrating its scalability and versatility. We find that using the structured approximation to the posterior results in models with significantly higher held-out likelihood.

stat.ML↗

arXiv2015

Barrier Frank-Wolfe for Marginal Inference

We introduce a globally-convergent algorithm for optimizing the tree-reweighted (TRW) variational objective over the marginal polytope. The algorithm is based on the conditional gradient method (Frank-Wolfe) and moves pseudomarginals within the marginal polytope through repeated maximum a posteriori (MAP) calls. This modular structure enables us to leverage black-box MAP solvers (both exact and approximate) for variational inference, and obtains more accurate results than tree-reweighted algorithms that optimize over the local consistency relaxation. Theoretically, we bound the sub-optimality for the proposed algorithm despite the TRW objective having unbounded gradients at the boundary of the marginal polytope. Empirically, we demonstrate the increased quality of results found by tightening the relaxation over the marginal polytope as well as the spanning tree polytope on synthetic and real-world instances.

stat.ML↗

arXiv2015

Deep Kalman Filters

Kalman Filters are one of the most influential models of time-varying phenomena. They admit an intuitive probabilistic interpretation, have a simple functional form, and enjoy widespread adoption in a variety of disciplines. Motivated by recent variational methods for learning deep generative models, we introduce a unified algorithm to efficiently learn a broad spectrum of Kalman filters. Of particular interest is the use of temporal generative models for counterfactual inference. We investigate the efficacy of such models for counterfactual inference, and to that end we introduce the "Healing MNIST" dataset where long-term structure, noise and actions are applied to sequences of digits. We show the efficacy of our method for modeling this dataset. We further show how our model can be used for counterfactual inference for patients, based on electronic health record data of 8,000 patients over 4.5 years.

stat.ML↗