Scaling Recurrence-aware Foundation Models for Clinical Records via Next-Visit Prediction

While large-scale pretraining has revolutionized language modeling, its potential remains underexplored in healthcare with structured electronic health records (EHRs). We present RAVEN, a novel generative pretraining strategy for sequential EHR data based on Recurrence-Aware next-Visit EveNt prediction. Leveraging a dataset of over one million unique individuals, our model learns to autoregressively generate tokenized clinical events for the next visit conditioned on patient history. We introduce regularization on predicting repeated events and highlight a key pitfall in EHR-based foundation model evaluations: repeated event tokens can inflate performance metrics when new onsets are not distinguished from subsequent occurrences. Furthermore, we empirically investigate the scaling behaviors in a data-constrained, compute-saturated regime, showing that simply increasing model size is suboptimal without commensurate increases in data volume. We evaluate our model via zero-shot prediction for forecasting the incidence of a diverse set of diseases, where it rivals fully fine-tuned representation-based Transformer models and outperforms widely used simulation-based next-token approaches. Finally, without additional parameter updates, we show that RAVEN can generalize to an external patient cohort under lossy clinical code mappings and feature coverage gaps.

3D Foundation AI Model for Generalizable Disease Detection in Head Computed Tomography

Head computed tomography (CT) imaging is a widely-used imaging modality with multitudes of medical indications, particularly in assessing pathology of the brain, skull, and cerebrovascular system. It is commonly the first-line imaging in neurologic emergencies given its rapidity of image acquisition, safety, cost, and ubiquity. Deep learning models may facilitate detection of a wide range of diseases. However, the scarcity of high-quality labels and annotations, particularly among less common conditions, significantly hinders the development of powerful models. To address this challenge, we introduce FM-CT: a Foundation Model for Head CT for generalizable disease detection, trained using self-supervised learning. Our approach pre-trains a deep learning model on a large, diverse dataset of 361,663 non-contrast 3D head CT scans without the need for manual annotations, enabling the model to learn robust, generalizable features. To investigate the potential of self-supervised learning in head CT, we employed both discrimination with self-distillation and masked image modeling, and we construct our model in 3D rather than at the slice level (2D) to exploit the structure of head CT scans more comprehensively and efficiently. The model's downstream classification performance is evaluated using internal and three external datasets, encompassing both in-distribution (ID) and out-of-distribution (OOD) data. Our results demonstrate that the self-supervised foundation model significantly improves performance on downstream diagnostic tasks compared to models trained from scratch and previous 3D CT foundation models on scarce annotated datasets. This work highlights the effectiveness of self-supervised learning in medical imaging and sets a new benchmark for head CT image analysis in 3D, enabling broader use of artificial intelligence for head CT-based diagnosis.

A Monte Carlo Framework for Calibrated Uncertainty Estimation in Sequence Prediction

Probabilistic prediction of sequences from images and other high-dimensional data is a key challenge, particularly in risk-sensitive applications. In these settings, it is often desirable to quantify the uncertainty associated with the prediction (instead of just determining the most likely sequence, as in language modeling). In this paper, we propose a Monte Carlo framework to estimate probabilities and confidence intervals associated with the distribution of a discrete sequence. Our framework uses a Monte Carlo simulator, implemented as an autoregressively trained neural network, to sample sequences conditioned on an image input. We then use these samples to estimate the probabilities and confidence intervals. Experiments on synthetic and real data show that the framework produces accurate discriminative predictions, but can suffer from miscalibration. In order to address this shortcoming, we propose a time-dependent regularization method, which is shown to produce calibrated predictions.

Making Self-supervised Learning Robust to Spurious Correlation via Learning-speed Aware Sampling

Self-supervised learning (SSL) has emerged as a powerful technique for learning rich representations from unlabeled data. The data representations are able to capture many underlying attributes of data, and be useful in downstream prediction tasks. In real-world settings, spurious correlations between some attributes (e.g. race, gender and age) and labels for downstream tasks often exist, e.g. cancer is usually more prevalent among elderly patients. In this paper, we investigate SSL in the presence of spurious correlations and show that the SSL training loss can be minimized by capturing only a subset of the conspicuous features relevant to those sensitive attributes, despite the presence of other important predictive features for the downstream tasks. To address this issue, we investigate the learning dynamics of SSL and observe that the learning is slower for samples that conflict with such correlations (e.g. elder patients without cancer). Motivated by these findings, we propose a learning-speed aware SSL (LA-SSL) approach, in which we sample each training data with a probability that is inversely related to its learning speed. We evaluate LA-SSL on three datasets that exhibit spurious correlations between different attributes, demonstrating that it improves the robustness of pretrained representations on downstream classification tasks.

Multiple Instance Learning via Iterative Self-Paced Supervised Contrastive Learning

Learning representations for individual instances when only bag-level labels are available is a fundamental challenge in multiple instance learning (MIL). Recent works have shown promising results using contrastive self-supervised learning (CSSL), which learns to push apart representations corresponding to two different randomly-selected instances. Unfortunately, in real-world applications such as medical image classification, there is often class imbalance, so randomly-selected instances mostly belong to the same majority class, which precludes CSSL from learning inter-class differences. To address this issue, we propose a novel framework, Iterative Self-paced Supervised Contrastive Learning for MIL Representations (ItS2CLR), which improves the learned representation by exploiting instance-level pseudo labels derived from the bag-level labels. The framework employs a novel self-paced sampling strategy to ensure the accuracy of pseudo labels. We evaluate ItS2CLR on three medical datasets, showing that it improves the quality of instance-level pseudo labels and representations, and outperforms existing MIL methods in terms of both bag and instance level accuracy.

Interpretable Prediction of Lung Squamous Cell Carcinoma Recurrence With Self-supervised Learning

Lung squamous cell carcinoma (LSCC) has a high recurrence and metastasis rate. Factors influencing recurrence and metastasis are currently unknown and there are no distinct histopathological or morphological features indicating the risks of recurrence and metastasis in LSCC. Our study focuses on the recurrence prediction of LSCC based on H&E-stained histopathological whole-slide images (WSI). Due to the small size of LSCC cohorts in terms of patients with available recurrence information, standard end-to-end learning with various convolutional neural networks for this task tends to overfit. Also, the predictions made by these models are hard to interpret. Histopathology WSIs are typically very large and are therefore processed as a set of smaller tiles. In this work, we propose a novel conditional self-supervised learning (SSL) method to learn representations of WSI at the tile level first, and leverage clustering algorithms to identify the tiles with similar histopathological representations. The resulting representations and clusters from self-supervision are used as features of a survival model for recurrence prediction at the patient level. Using two publicly available datasets from TCGA and CPTAC, we show that our LSCC recurrence prediction survival model outperforms both LSCC pathological stage-based approach and machine learning baselines such as multiple instance learning. The proposed method also enables us to explain the recurrence histopathological risk factors via the derived clusters. This can help pathologists derive new hypotheses regarding morphological features associated with LSCC recurrence.

Deep Probability Estimation

Reliable probability estimation is of crucial importance in many real-world applications where there is inherent uncertainty, such as weather forecasting, medical prognosis, or collision avoidance in autonomous vehicles. Probability-estimation models are trained on observed outcomes (e.g. whether it has rained or not, or whether a patient has died or not), because the ground-truth probabilities of the events of interest are typically unknown. The problem is therefore analogous to binary classification, with the important difference that the objective is to estimate probabilities rather than predicting the specific outcome. The goal of this work is to investigate probability estimation from high-dimensional data using deep neural networks. There exist several methods to improve the probabilities generated by these models but they mostly focus on classification problems where the probabilities are related to model uncertainty. In the case of problems with inherent uncertainty, it is challenging to evaluate performance without access to ground-truth probabilities. To address this, we build a synthetic dataset to study and compare different computable metrics. We evaluate existing methods on the synthetic data as well as on three real-world probability estimation tasks, all of which involve inherent uncertainty: precipitation forecasting from radar images, predicting cancer patient survival from histopathology images, and predicting car crashes from dashcam videos. Finally, we also propose a new method for probability estimation using neural networks, which modifies the training process to promote output probabilities that are consistent with empirical probabilities computed from the data. The method outperforms existing approaches on most metrics on the simulated as well as real-world data.

Adaptive Early-Learning Correction for Segmentation from Noisy Annotations

Deep learning in the presence of noisy annotations has been studied extensively in classification, but much less in segmentation tasks. In this work, we study the learning dynamics of deep segmentation networks trained on inaccurately-annotated data. We discover a phenomenon that has been previously reported in the context of classification: the networks tend to first fit the clean pixel-level labels during an "early-learning" phase, before eventually memorizing the false annotations. However, in contrast to classification, memorization in segmentation does not arise simultaneously for all semantic categories. Inspired by these findings, we propose a new method for segmentation from noisy annotations with two key elements. First, we detect the beginning of the memorization phase separately for each category during training. This allows us to adaptively correct the noisy annotations in order to exploit early learning. Second, we incorporate a regularization term that enforces consistency across scales to boost robustness against annotation noise. Our method outperforms standard approaches on a medical-imaging segmentation task where noises are synthesized to mimic human annotation errors. It also provides robustness to realistic noisy annotations present in weakly-supervised semantic segmentation, achieving state-of-the-art results on PASCAL VOC 2012.

Graph Neural Network on Electronic Health Records for Predicting Alzheimer's Disease

The cause of Alzheimer's disease (AD) is poorly understood, so forecasting AD remains a hard task in population health. Failure of clinical trials for AD treatments indicates that AD should be intervened at the earlier, pre-symptomatic stages. Developing an explainable method for predicting AD is critical for providing better treatment targets, better clinical trial recruitment, and better clinical care for the AD patients. In this paper, we present a novel approach for disease (AD) prediction based on Electronic Health Records (EHR) and graph neural network. Our method improves the performance on sparse data which is common in EHR, and obtains state-of-art results in predicting AD 12 to 24 months in advance on real-world EHR data, compared to other baseline results. Our approach also provides an insight into the structural relationship among different diagnosis, Lab values, and procedures from EHR as per graph structures learned by our model.

Baidu Apollo EM Motion Planner

In this manuscript, we introduce a real-time motion planning system based on the Baidu Apollo (open source) autonomous driving platform. The developed system aims to address the industrial level-4 motion planning problem while considering safety, comfort and scalability. The system covers multilane and single-lane autonomous driving in a hierarchical manner: (1) The top layer of the system is a multilane strategy that handles lane-change scenarios by comparing lane-level trajectories computed in parallel. (2) Inside the lane-level trajectory generator, it iteratively solves path and speed optimization based on a Frenet frame. (3) For path and speed optimization, a combination of dynamic programming and spline-based quadratic programming is proposed to construct a scalable and easy-to-tune framework to handle traffic rules, obstacle decisions and smoothness simultaneously. The planner is scalable to both highway and lower-speed city driving scenarios. We also demonstrate the algorithm through scenario illustrations and on-road test results. The system described in this manuscript has been deployed to dozens of Baidu Apollo autonomous driving vehicles since Apollo v1.5 was announced in September 2017. As of May 16th, 2018, the system has been tested under 3,380 hours and approximately 68,000 kilometers (42,253 miles) of closed-loop autonomous driving under various urban scenarios. The algorithm described in this manuscript is available at https://github.com/ApolloAuto/apollo/tree/master/modules/planning.