arXiv subjects

Rahul G. Krishnan

Publications and source records attributed to Rahul G. Krishnan.

At least 55 records · Page 3Linked to original sources

arXiv2024

A Geometric Explanation of the Likelihood OOD Detection Paradox

Likelihood-based deep generative models (DGMs) commonly exhibit a puzzling behaviour: when trained on a relatively complex dataset, they assign higher likelihood values to out-of-distribution (OOD) data from simpler sources. Adding to the mystery, OOD samples are never generated by these DGMs despite having higher likelihoods. This two-pronged paradox has yet to be conclusively explained, making likelihood-based OOD detection unreliable. Our primary observation is that high-likelihood regions will not be generated if they contain minimal probability mass. We demonstrate how this seeming contradiction of large densities yet low probability mass can occur around data confined to low-dimensional manifolds. We also show that this scenario can be identified through local intrinsic dimension (LID) estimation, and propose a method for OOD detection which pairs the likelihoods and LID estimates obtained from a pre-trained DGM. Our method can be applied to normalizing flows and score-based diffusion models, and obtains results which match or surpass state-of-the-art OOD detection benchmarks using the same DGM backbones. Our code is available at https://github.com/layer6ai-labs/dgm_ood_detection.

cs.LG↗

arXiv2024

InterpreTabNet: Distilling Predictive Signals from Tabular Data by Salient Feature Interpretation

Tabular data are omnipresent in various sectors of industries. Neural networks for tabular data such as TabNet have been proposed to make predictions while leveraging the attention mechanism for interpretability. However, the inferred attention masks are often dense, making it challenging to come up with rationales about the predictive signal. To remedy this, we propose InterpreTabNet, a variant of the TabNet model that models the attention mechanism as a latent variable sampled from a Gumbel-Softmax distribution. This enables us to regularize the model to learn distinct concepts in the attention masks via a KL Divergence regularizer. It prevents overlapping feature selection by promoting sparsity which maximizes the model's efficacy and improves interpretability to determine the important features when predicting the outcome. To assist in the interpretation of feature interdependencies from our model, we employ a large language model (GPT-4) and use prompt engineering to map from the learned feature mask onto natural language text describing the learned signal. Through comprehensive experiments on real-world datasets, we demonstrate that InterpreTabNet outperforms previous methods for interpreting tabular data while attaining competitive accuracy.

cs.LG↗

arXiv2024

Order-based Structure Learning with Normalizing Flows

Estimating the causal structure of observational data is a challenging combinatorial search problem that scales super-exponentially with graph size. Existing methods use continuous relaxations to make this problem computationally tractable but often restrict the data-generating process to additive noise models (ANMs) through explicit or implicit assumptions. We present Order-based Structure Learning with Normalizing Flows (OSLow), a framework that relaxes these assumptions using autoregressive normalizing flows. We leverage the insight that searching over topological orderings is a natural way to enforce acyclicity in structure discovery and propose a novel, differentiable permutation learning method to find such orderings. Through extensive experiments on synthetic and real-world data, we demonstrate that OSLow outperforms prior baselines and improves performance on the observational Sachs and SynTReN datasets as measured by structural hamming distance and structural intervention distance, highlighting the importance of relaxing the ANM assumption made by existing methods.

cs.LG↗

arXiv2024

Measurement Scheduling for ICU Patients with Offline Reinforcement Learning

Scheduling laboratory tests for ICU patients presents a significant challenge. Studies show that 20-40% of lab tests ordered in the ICU are redundant and could be eliminated without compromising patient safety. Prior work has leveraged offline reinforcement learning (Offline-RL) to find optimal policies for ordering lab tests based on patient information. However, new ICU patient datasets have since been released, and various advancements have been made in Offline-RL methods. In this study, we first introduce a preprocessing pipeline for the newly-released MIMIC-IV dataset geared toward time-series tasks. We then explore the efficacy of state-of-the-art Offline-RL methods in identifying better policies for ICU patient lab test scheduling. Besides assessing methodological performance, we also discuss the overall suitability and practicality of using Offline-RL frameworks for scheduling laboratory tests in ICU settings.

cs.LG↗

arXiv2024

MultiResFormer: Transformer with Adaptive Multi-Resolution Modeling for General Time Series Forecasting

Transformer-based models have greatly pushed the boundaries of time series forecasting recently. Existing methods typically encode time series data into $\textit{patches}$ using one or a fixed set of patch lengths. This, however, could result in a lack of ability to capture the variety of intricate temporal dependencies present in real-world multi-periodic time series. In this paper, we propose MultiResFormer, which dynamically models temporal variations by adaptively choosing optimal patch lengths. Concretely, at the beginning of each layer, time series data is encoded into several parallel branches, each using a detected periodicity, before going through the transformer encoder block. We conduct extensive evaluations on long- and short-term forecasting datasets comparing MultiResFormer with state-of-the-art baselines. MultiResFormer outperforms patch-based Transformer baselines on long-term forecasting tasks and also consistently outperforms CNN baselines by a large margin, while using much fewer parameters than these baselines.

cs.LG↗

arXiv2023

Structured Neural Networks for Density Estimation and Causal Inference

Injecting structure into neural networks enables learning functions that satisfy invariances with respect to subsets of inputs. For instance, when learning generative models using neural networks, it is advantageous to encode the conditional independence structure of observed variables, often in the form of Bayesian networks. We propose the Structured Neural Network (StrNN), which injects structure through masking pathways in a neural network. The masks are designed via a novel relationship we explore between neural network architectures and binary matrix factorization, to ensure that the desired independencies are respected. We devise and study practical algorithms for this otherwise NP-hard design problem based on novel objectives that control the model architecture. We demonstrate the utility of StrNN in three applications: (1) binary and Gaussian density estimation with StrNN, (2) real-valued density estimation with Structured Autoregressive Flows (StrAFs) and Structured Continuous Normalizing Flows (StrCNF), and (3) interventional and counterfactual analysis with StrAFs for causal inference. Our work opens up new avenues for learning neural networks that enable data-efficient generative modeling and the use of normalizing flows for causal effect estimation.

cs.LG↗

arXiv2023

Clinical Camel: An Open Expert-Level Medical Language Model with Dialogue-Based Knowledge Encoding

We present Clinical Camel, an open large language model (LLM) explicitly tailored for clinical research. Fine-tuned from LLaMA-2 using QLoRA, Clinical Camel achieves state-of-the-art performance across medical benchmarks among openly available medical LLMs. Leveraging efficient single-GPU training, Clinical Camel surpasses GPT-3.5 in five-shot evaluations on all assessed benchmarks, including 64.3% on the USMLE Sample Exam (compared to 58.5% for GPT-3.5), 77.9% on PubMedQA (compared to 60.2%), 60.7% on MedQA (compared to 53.6%), and 54.2% on MedMCQA (compared to 51.0%). In addition to these benchmarks, Clinical Camel demonstrates its broader capabilities, such as synthesizing plausible clinical notes. This work introduces dialogue-based knowledge encoding, a novel method to synthesize conversational data from dense medical texts. While benchmark results are encouraging, extensive and rigorous human evaluation across diverse clinical scenarios is imperative to ascertain safety before implementation. By openly sharing Clinical Camel, we hope to foster transparent and collaborative research, working towards the safe integration of LLMs within the healthcare domain. Significant challenges concerning reliability, bias, and the potential for outdated knowledge persist. Nonetheless, the transparency provided by an open approach reinforces the scientific rigor essential for future clinical applications.

cs.CL↗

arXiv2023

DuETT: Dual Event Time Transformer for Electronic Health Records

Electronic health records (EHRs) recorded in hospital settings typically contain a wide range of numeric time series data that is characterized by high sparsity and irregular observations. Effective modelling for such data must exploit its time series nature, the semantic relationship between different types of observations, and information in the sparsity structure of the data. Self-supervised Transformers have shown outstanding performance in a variety of structured tasks in NLP and computer vision. But multivariate time series data contains structured relationships over two dimensions: time and recorded event type, and straightforward applications of Transformers to time series data do not leverage this distinct structure. The quadratic scaling of self-attention layers can also significantly limit the input sequence length without appropriate input engineering. We introduce the DuETT architecture, an extension of Transformers designed to attend over both time and event type dimensions, yielding robust representations from EHR data. DuETT uses an aggregated input where sparse time series are transformed into a regular sequence with fixed length; this lowers the computational complexity relative to previous EHR Transformer models and, more importantly, enables the use of larger and deeper neural networks. When trained with self-supervised prediction tasks, that provide rich and informative signals for model pre-training, our model outperforms state-of-the-art deep learning models on multiple downstream tasks from the MIMIC-IV and PhysioNet-2012 EHR datasets.

cs.LG↗

arXiv2023

Copula-Based Deep Survival Models for Dependent Censoring

A survival dataset describes a set of instances (e.g. patients) and provides, for each, either the time until an event (e.g. death), or the censoring time (e.g. when lost to follow-up - which is a lower bound on the time until the event). We consider the challenge of survival prediction: learning, from such data, a predictive model that can produce an individual survival distribution for a novel instance. Many contemporary methods of survival prediction implicitly assume that the event and censoring distributions are independent conditional on the instance's covariates - a strong assumption that is difficult to verify (as we observe only one outcome for each instance) and which can induce significant bias when it does not hold. This paper presents a parametric model of survival that extends modern non-linear survival analysis by relaxing the assumption of conditional independence. On synthetic and semi-synthetic data, our approach significantly improves estimates of survival distributions compared to the standard that assumes conditional independence in the data.

cs.LG↗

arXiv2023

Anamnesic Neural Differential Equations with Orthogonal Polynomial Projections

Neural ordinary differential equations (Neural ODEs) are an effective framework for learning dynamical systems from irregularly sampled time series data. These models provide a continuous-time latent representation of the underlying dynamical system where new observations at arbitrary time points can be used to update the latent representation of the dynamical system. Existing parameterizations for the dynamics functions of Neural ODEs limit the ability of the model to retain global information about the time series; specifically, a piece-wise integration of the latent process between observations can result in a loss of memory on the dynamic patterns of previously observed data points. We propose PolyODE, a Neural ODE that models the latent continuous-time process as a projection onto a basis of orthogonal polynomials. This formulation enforces long-range memory and preserves a global representation of the underlying dynamical system. Our construction is backed by favourable theoretical guarantees and in a series of experiments, we demonstrate that it outperforms previous works in the reconstruction of past and future data, and in downstream prediction tasks.

cs.LG↗

arXiv2023

A Learning Based Hypothesis Test for Harmful Covariate Shift

The ability to quickly and accurately identify covariate shift at test time is a critical and often overlooked component of safe machine learning systems deployed in high-risk domains. While methods exist for detecting when predictions should not be made on out-of-distribution test examples, identifying distributional level differences between training and test time can help determine when a model should be removed from the deployment setting and retrained. In this work, we define harmful covariate shift (HCS) as a change in distribution that may weaken the generalization of a predictive model. To detect HCS, we use the discordance between an ensemble of classifiers trained to agree on training data and disagree on test data. We derive a loss function for training this ensemble and show that the disagreement rate and entropy represent powerful discriminative statistics for HCS. Empirically, we demonstrate the ability of our method to detect harmful covariate shift with statistical certainty on a variety of high-dimensional datasets. Across numerous domains and modalities, we show state-of-the-art performance compared to existing methods, particularly when the number of observed test samples is small.

cs.LG↗

arXiv2022

Learning predictive checklists from continuous medical data

Checklists, while being only recently introduced in the medical domain, have become highly popular in daily clinical practice due to their combined effectiveness and great interpretability. Checklists are usually designed by expert clinicians that manually collect and analyze available evidence. However, the increasing quantity of available medical data is calling for a partially automated checklist design. Recent works have taken a step in that direction by learning predictive checklists from categorical data. In this work, we propose to extend this approach to accomodate learning checklists from continuous medical data using mixed-integer programming approach. We show that this extension outperforms a range of explainable machine learning baselines on the prediction of sepsis from intensive care clinical trajectories.

cs.LG↗

arXiv2022

Partial Identification of Treatment Effects with Implicit Generative Models

We consider the problem of partial identification, the estimation of bounds on the treatment effects from observational data. Although studied using discrete treatment variables or in specific causal graphs (e.g., instrumental variables), partial identification has been recently explored using tools from deep generative modeling. We propose a new method for partial identification of average treatment effects(ATEs) in general causal graphs using implicit generative models comprising continuous and discrete random variables. Since ATE with continuous treatment is generally non-regular, we leverage the partial derivatives of response functions to define a regular approximation of ATE, a quantity we call uniform average treatment derivative (UATD). We prove that our algorithm converges to tight bounds on ATE in linear structural causal models (SCMs). For nonlinear SCMs, we empirically show that using UATD leads to tighter and more stable bounds than methods that directly optimize the ATE.

cs.LG↗

arXiv2022

HiCu: Leveraging Hierarchy for Curriculum Learning in Automated ICD Coding

There are several opportunities for automation in healthcare that can improve clinician throughput. One such example is assistive tools to document diagnosis codes when clinicians write notes. We study the automation of medical code prediction using curriculum learning, which is a training strategy for machine learning models that gradually increases the hardness of the learning tasks from easy to difficult. One of the challenges in curriculum learning is the design of curricula -- i.e., in the sequential design of tasks that gradually increase in difficulty. We propose Hierarchical Curriculum Learning (HiCu), an algorithm that uses graph structure in the space of outputs to design curricula for multi-label classification. We create curricula for multi-label classification models that predict ICD diagnosis and procedure codes from natural language descriptions of patients. By leveraging the hierarchy of ICD codes, which groups diagnosis codes based on various organ systems in the human body, we find that our proposed curricula improve the generalization of neural network-based predictive models across recurrent, convolutional, and transformer-based architectures. Our code is available at https://github.com/wren93/HiCu-ICD.

cs.LG↗

arXiv2022

Scaling Vision Transformers to Gigapixel Images via Hierarchical Self-Supervised Learning

Vision Transformers (ViTs) and their multi-scale and hierarchical variations have been successful at capturing image representations but their use has been generally studied for low-resolution images (e.g. - 256x256, 384384). For gigapixel whole-slide imaging (WSI) in computational pathology, WSIs can be as large as 150000x150000 pixels at 20X magnification and exhibit a hierarchical structure of visual tokens across varying resolutions: from 16x16 images capture spatial patterns among cells, to 4096x4096 images characterizing interactions within the tissue microenvironment. We introduce a new ViT architecture called the Hierarchical Image Pyramid Transformer (HIPT), which leverages the natural hierarchical structure inherent in WSIs using two levels of self-supervised learning to learn high-resolution image representations. HIPT is pretrained across 33 cancer types using 10,678 gigapixel WSIs, 408,218 4096x4096 images, and 104M 256x256 images. We benchmark HIPT representations on 9 slide-level tasks, and demonstrate that: 1) HIPT with hierarchical pretraining outperforms current state-of-the-art methods for cancer subtyping and survival prediction, 2) self-supervised ViTs are able to model important inductive biases about the hierarchical structure of phenotypes in the tumor microenvironment.

cs.CV↗

arXiv2022

Using Time-Series Privileged Information for Provably Efficient Learning of Prediction Models

We study prediction of future outcomes with supervised models that use privileged information during learning. The privileged information comprises samples of time series observed between the baseline time of prediction and the future outcome; this information is only available at training time which differs from the traditional supervised learning. Our question is when using this privileged data leads to more sample-efficient learning of models that use only baseline data for predictions at test time. We give an algorithm for this setting and prove that when the time series are drawn from a non-stationary Gaussian-linear dynamical system of fixed horizon, learning with privileged information is more efficient than learning without it. On synthetic data, we test the limits of our algorithm and theory, both when our assumptions hold and when they are violated. On three diverse real-world datasets, we show that our approach is generally preferable to classical learning, particularly when data is scarce. Finally, we relate our estimator to a distillation approach both theoretically and empirically.

cs.LG↗

arXiv2022

Hierarchical Optimal Transport for Comparing Histopathology Datasets

Scarcity of labeled histopathology data limits the applicability of deep learning methods to under-profiled cancer types and labels. Transfer learning allows researchers to overcome the limitations of small datasets by pre-training machine learning models on larger datasets similar to the small target dataset. However, similarity between datasets is often determined heuristically. In this paper, we propose a principled notion of distance between histopathology datasets based on a hierarchical generalization of optimal transport distances. Our method does not require any training, is agnostic to model type, and preserves much of the hierarchical structure in histopathology datasets imposed by tiling. We apply our method to H&E stained slides from The Cancer Genome Atlas from six different cancer types. We show that our method outperforms a baseline distance in a cancer-type prediction task. Our results also show that our optimal transport distance predicts difficulty of transferability in a tumor vs.normal prediction setting.

cs.CV↗

arXiv2022

Mixture-of-experts VAEs can disregard variation in surjective multimodal data

Machine learning systems are often deployed in domains that entail data from multiple modalities, for example, phenotypic and genotypic characteristics describe patients in healthcare. Previous works have developed multimodal variational autoencoders (VAEs) that generate several modalities. We consider subjective data, where single datapoints from one modality (such as class labels) describe multiple datapoints from another modality (such as images). We theoretically and empirically demonstrate that multimodal VAEs with a mixture of experts posterior can struggle to capture variability in such surjective data.

cs.LG↗