Shih-Cheng Huang

Rui Yan, Liangqiong Qu, Qingyue Wei et al.

The collection and curation of large-scale medical datasets from multiple institutions is essential for training accurate deep learning models, but privacy concerns often hinder data sharing. Federated learning (FL) is a promising solution that enables privacy-preserving collaborative learning among different institutions, but it generally suffers from performance deterioration due to heterogeneous data distributions and a lack of quality labeled data. In this paper, we present a robust and label-efficient self-supervised FL framework for medical image analysis. Our method introduces a novel Transformer-based self-supervised pre-training paradigm that pre-trains models directly on decentralized target task datasets using masked image modeling, to facilitate more robust representation learning on heterogeneous data and effective knowledge transfer to downstream models. Extensive empirical results on simulated and real-world medical imaging non-IID federated datasets show that masked image modeling with Transformers significantly improves the robustness of models against various degrees of data heterogeneity. Notably, under severe data heterogeneity, our method, without relying on any additional pre-training data, achieves an improvement of 5.06%, 1.53% and 4.58% in test accuracy on retinal, dermatology and chest X-ray classification compared to the supervised baseline with ImageNet pre-training. In addition, we show that our federated self-supervised pre-training methods yield models that generalize better to out-of-distribution data and perform more effectively when fine-tuning with limited labeled data, compared to existing FL algorithms. The code is available at https://github.com/rui-yan/SSL-FL.

Kathryn Wantlin, Chenwei Wu, Shih-Cheng Huang et al. · stanford

Medical data poses a daunting challenge for AI algorithms: it exists in many different modalities, experiences frequent distribution shifts, and suffers from a scarcity of examples and labels. Recent advances, including transformers and self-supervised learning, promise a more universal approach that can be applied flexibly across these diverse conditions. To measure and drive progress in this direction, we present BenchMD: a benchmark that tests how well unified, modality-agnostic methods, including architectures and training techniques (e.g. self-supervised learning, ImageNet pretraining),perform on a diverse array of clinically-relevant medical tasks. BenchMD combines 19 publicly available datasets for 7 medical modalities, including 1D sensor data, 2D images, and 3D volumetric scans. Our benchmark reflects real-world data constraints by evaluating methods across a range of dataset sizes, including challenging few-shot settings that incentivize the use of pretraining. Finally, we evaluate performance on out-of-distribution data collected at different hospitals than the training data, representing naturally-occurring distribution shifts that frequently degrade the performance of medical AI models. Our baseline results demonstrate that no unified learning technique achieves strong performance across all modalities, leaving ample room for improvement on the benchmark. Code is released at https://github.com/rajpurkarlab/BenchMD.

Yuhui Zhang, Jeff Z. HaoChen, Shih-Cheng Huang et al. · stanford

Recent multi-modal contrastive learning models have demonstrated the ability to learn an embedding space suitable for building strong vision classifiers, by leveraging the rich information in large-scale image-caption datasets. Our work highlights a distinct advantage of this multi-modal embedding space: the ability to diagnose vision classifiers through natural language. The traditional process of diagnosing model behaviors in deployment settings involves labor-intensive data acquisition and annotation. Our proposed method can discover high-error data slices, identify influential attributes and further rectify undesirable model behaviors, without requiring any visual data. Through a combination of theoretical explanation and empirical verification, we present conditions under which classifiers trained on embeddings from one modality can be equivalently applied to embeddings from another modality. On a range of image datasets with known error slices, we demonstrate that our method can effectively identify the error slices and influential attributes, and can further use language to rectify failure modes of the classifier.

Yuhui Zhang, Shih-Cheng Huang, Zhengping Zhou et al. · stanford

Given the prevalence of 3D medical imaging technologies such as MRI and CT that are widely used in diagnosing and treating diverse diseases, 3D segmentation is one of the fundamental tasks of medical image analysis. Recently, Transformer-based models have started to achieve state-of-the-art performances across many vision tasks, through pre-training on large-scale natural image benchmark datasets. While works on medical image analysis have also begun to explore Transformer-based models, there is currently no optimal strategy to effectively leverage pre-trained Transformers, primarily due to the difference in dimensionality between 2D natural images and 3D medical images. Existing solutions either split 3D images into 2D slices and predict each slice independently, thereby losing crucial depth-wise information, or modify the Transformer architecture to support 3D inputs without leveraging pre-trained weights. In this work, we use a simple yet effective weight inflation strategy to adapt pre-trained Transformers from 2D to 3D, retaining the benefit of both transfer learning and depth information. We further investigate the effectiveness of transfer from different pre-training sources and objectives. Our approach achieves state-of-the-art performances across a broad range of 3D medical image datasets, and can become a standard strategy easily utilized by all work on Transformer-based models for 3D medical images, to maximize performance.

Orr Zohar, Shih-Cheng Huang, Kuan-Chieh Wang et al.

Pre-trained multi-modal vision-language models (VLMs) are becoming increasingly popular due to their exceptional performance on downstream vision applications, particularly in the few- and zero-shot settings. However, selecting the best-performing VLM for some downstream applications is non-trivial, as it is dataset and task-dependent. Meanwhile, the exhaustive evaluation of all available VLMs on a novel application is not only time and computationally demanding but also necessitates the collection of a labeled dataset for evaluation. As the number of open-source VLM variants increases, there is a need for an efficient model selection strategy that does not require access to a curated evaluation dataset. This paper proposes a novel task and benchmark for efficiently evaluating VLMs' zero-shot performance on downstream applications without access to the downstream task dataset. Specifically, we introduce a new task LOVM: Language-Only Vision Model Selection, where methods are expected to perform both model selection and performance prediction based solely on a text description of the desired downstream application. We then introduced an extensive LOVM benchmark consisting of ground-truth evaluations of 35 pre-trained VLMs and 23 datasets, where methods are expected to rank the pre-trained VLMs and predict their zero-shot performance.

Alexander Ke, Shih-Cheng Huang, Chloe P O'Connell et al.

Pretraining on large natural image classification datasets such as ImageNet has aided model development on data-scarce 2D medical tasks. 3D medical tasks often have much less data than 2D medical tasks, prompting practitioners to rely on pretrained 2D models to featurize slices. However, these 2D models have been surpassed by 3D models on 3D computer vision benchmarks since they do not natively leverage cross-sectional or temporal information. In this study, we explore whether natural video pretraining for 3D models can enable higher performance on smaller datasets for 3D medical tasks. We demonstrate video pretraining improves the average performance of seven 3D models on two chest CT datasets, regardless of finetuning dataset size, and that video pretraining allows 3D models to outperform 2D baselines. Lastly, we observe that pretraining on the large-scale out-of-domain Kinetics dataset improves performance more than pretraining on a typically-sized in-domain CT dataset. Our results show consistent benefits of video pretraining across a wide array of architectures, tasks, and training dataset sizes, supporting a shift from small-scale in-domain pretraining to large-scale out-of-domain pretraining for 3D medical tasks. Our code is available at: https://github.com/rajpurkarlab/chest-ct-pretraining

Shih-Cheng Huang, Pin-Zu Li, Yu-Chi Hsu et al.

Recently, the development of open-source large language models (LLMs) has advanced rapidly. Nevertheless, due to data constraints, the capabilities of most open-source LLMs are primarily focused on English. To address this issue, we introduce the concept of $\textit{chat vector}$ to equip pre-trained language models with instruction following and human value alignment via simple model arithmetic. The chat vector is derived by subtracting the weights of a pre-trained base model (e.g. LLaMA2) from those of its corresponding chat model (e.g. LLaMA2-chat). By simply adding the chat vector to a continual pre-trained model's weights, we can endow the model with chat capabilities in new languages without the need for further training. Our empirical studies demonstrate the superior efficacy of the chat vector from three different aspects: instruction following, toxicity mitigation, and multi-turn dialogue. Moreover, to showcase the adaptability of our approach, we extend our experiments to encompass various languages, base models, and chat vectors. The results underscore the chat vector's simplicity, effectiveness, and wide applicability, making it a compelling solution for efficiently enabling conversational capabilities in pre-trained language models. Our code is available at https://github.com/aqweteddy/ChatVector.

Shih-Cheng Huang, Zepeng Huo, Ethan Steinberg et al.

Synthesizing information from multiple data sources plays a crucial role in the practice of modern medicine. Current applications of artificial intelligence in medicine often focus on single-modality data due to a lack of publicly available, multimodal medical datasets. To address this limitation, we introduce INSPECT, which contains de-identified longitudinal records from a large cohort of patients at risk for pulmonary embolism (PE), along with ground truth labels for multiple outcomes. INSPECT contains data from 19,402 patients, including CT images, radiology report impression sections, and structured electronic health record (EHR) data (i.e. demographics, diagnoses, procedures, vitals, and medications). Using INSPECT, we develop and release a benchmark for evaluating several baseline modeling approaches on a variety of important PE related tasks. We evaluate image-only, EHR-only, and multimodal fusion models. Trained models and the de-identified dataset are made available for non-commercial use under a data use agreement. To the best of our knowledge, INSPECT is the largest multimodal dataset integrating 3D medical imaging and EHR for reproducible methods evaluation and research.

Hsuan Su, Pohan Chi, Shih-Cheng Huang et al.

Much literature has shown that prompt-based learning is an efficient method to make use of the large pre-trained language model. Recent works also exhibit the possibility of steering a chatbot's output by plugging in an appropriate prompt. Gradient-based methods are often used to perturb the prompts. However, some language models are not even available to the public. In this work, we first explored the combination of prompting and reinforcement learning (RL) to steer models' generation without accessing any of the models' parameters. Second, to reduce the training effort and enhance the generalizability to the unseen task, we apply multi-task learning to make the model learn to generalize to new tasks better. The experiment results show that our proposed method can successfully control several state-of-the-art (SOTA) dialogue models without accessing their parameters. Furthermore, the model demonstrates the strong ability to quickly adapt to an unseen task in fewer steps than the baseline model.

Madhuri Shanbhogue, Zhe Li, Shanfeng Zhang et al.

We introduce Gemini Embedding 2, a native multimodal embedding model that allows embedding video, audio, image, and text modalities in a unified representation space. We leverage the multimodal capabilities of Gemini to produce embeddings for arbitrary combinations of interleaved inputs across all these modalities that generalize well across a wide variety of tasks. Applying large-scale contrastive learning in a multi-task multi-stage training setup, we achieve state-of-the-art performance on key embedding benchmarks including unimodal, cross-modal, and multimodal retrieval spanning a diverse set of tasks. We show that our embedding model demonstrates strong performance (with a score of 62.9 R@1 on MSCOCO, 68.8 NDCG@10 on Vatex, 69.9 on MTEB multilingual and 84.0 on MTEB Code) across a variety of tasks surpassing the performance of specialized models. These unified capabilities make Gemini Embedding 2 a promising candidate for downstream use cases such as RAG, recommendation and search. Furthermore, its robust zero-shot performance across distinct fields - from astronomy and bioscience to fine arts and the culinary arts - establishes it as a highly reliable, out-of-the-box representation even for specialized domains.

Shih-Cheng Huang, Shih-Heng Wang, Min-Han Shih et al.

Parameter-efficient (PE) methods (like Prompts or Adapters) for adapting pre-trained language models (PLM) to downstream tasks have been popular recently. However, hindrances still prevent these methods from reaching their full potential. For example, two significant challenges are few-shot adaptation and cross-task generalization. To tackle these issues, we propose a general PE priming framework to enhance and explore the few-shot adaptation and generalization ability of PE methods. In this framework, PLMs are primed with PE methods for rapidly adapting to various target tasks. To evaluate the generalization ability of these PE methods, we conduct experiments on a few-shot cross-domain benchmark containing 160 diverse NLP tasks. Our experiment not only reveals the best priming strategy but also verifies that priming facilitates the adaptation to target tasks.

Juan Manuel Zambrano Chaves, Shih-Cheng Huang, Yanbo Xu et al. · microsoft-research

The scaling laws and extraordinary performance of large foundation models motivate the development and utilization of such models in biomedicine. However, despite early promising results on some biomedical benchmarks, there are still major challenges that need to be addressed before these models can be used in real-world clinics. Frontier general-domain models such as GPT-4V still have significant performance gaps in multimodal biomedical applications. More importantly, less-acknowledged pragmatic issues, including accessibility, model cost, and tedious manual evaluation make it hard for clinicians to use state-of-the-art large models directly on private patient data. Here, we explore training open-source small multimodal models (SMMs) to bridge competency gaps for unmet clinical needs in radiology. To maximize data efficiency, we adopt a modular approach by incorporating state-of-the-art pre-trained models for image and text modalities, and focusing on training a lightweight adapter to ground each modality to the text embedding space, as exemplified by LLaVA-Med. For training, we assemble a large dataset of over 697 thousand radiology image-text pairs. For evaluation, we propose CheXprompt, a GPT-4-based metric for factuality evaluation, and demonstrate its parity with expert evaluation. For best practice, we conduct a systematic ablation study on various choices in data engineering and multimodal training. The resulting LlaVA-Rad (7B) model attains state-of-the-art results on standard radiology tasks such as report generation and cross-modal retrieval, even outperforming much larger models such as GPT-4V and Med-PaLM M (84B). The inference of LlaVA-Rad is fast and can be performed on a single V100 GPU in private settings, offering a promising state-of-the-art tool for real-world clinical applications.

Ren-Wei Liang, Chin-Ting Hsu, Chan-Hung Yu et al.

Ensuring that large language models (LLMs) are both helpful and harmless is a critical challenge, as overly strict constraints can lead to excessive refusals, while permissive models risk generating harmful content. Existing approaches, such as reinforcement learning from human feedback (RLHF) and direct preference optimization (DPO), attempt to balance these trade-offs but suffer from performance conflicts, limited controllability, and poor extendability. To address these issues, we propose Preference Vector, a novel framework inspired by task arithmetic. Instead of optimizing multiple preferences within a single objective, we train separate models on individual preferences, extract behavior shifts as preference vectors, and dynamically merge them at test time. This modular approach enables fine-grained, user-controllable preference adjustments and facilitates seamless integration of new preferences without retraining. Experiments show that our proposed Preference Vector framework improves helpfulness without excessive conservatism, allows smooth control over preference trade-offs, and supports scalable multi-preference alignment.

Yuyin Zhou, Shih-Cheng Huang, Jason Alan Fries et al.

Despite the routine use of electronic health record (EHR) data by radiologists to contextualize clinical history and inform image interpretation, the majority of deep learning architectures for medical imaging are unimodal, i.e., they only learn features from pixel-level information. Recent research revealing how race can be recovered from pixel data alone highlights the potential for serious biases in models which fail to account for demographics and other key patient attributes. Yet the lack of imaging datasets which capture clinical context, inclusive of demographics and longitudinal medical history, has left multimodal medical imaging underexplored. To better assess these challenges, we present RadFusion, a multimodal, benchmark dataset of 1794 patients with corresponding EHR data and high-resolution computed tomography (CT) scans labeled for pulmonary embolism. We evaluate several representative multimodal fusion models and benchmark their fairness properties across protected subgroups, e.g., gender, race/ethnicity, age. Our results suggest that integrating imaging and EHR data can improve classification performance and robustness without introducing large disparities in the true positive rate between population groups.

Anirudh Joshi, Sabri Eyuboglu, Shih-Cheng Huang et al.

FDG PET/CT imaging is a resource intensive examination critical for managing malignant disease and is particularly important for longitudinal assessment during therapy. Approaches to automate longtudinal analysis present many challenges including lack of available longitudinal datasets, managing complex large multimodal imaging examinations, and need for detailed annotations for traditional supervised machine learning. In this work we develop OncoNet, novel machine learning algorithm that assesses treatment response from a 1,954 pairs of sequential FDG PET/CT exams through weak supervision using the standard uptake values (SUVmax) in associated radiology reports. OncoNet demonstrates an AUROC of 0.86 and 0.84 on internal and external institution test sets respectively for determination of change between scans while also showing strong agreement to clinical scoring systems with a kappa score of 0.8. We also curated a dataset of 1,954 paired FDG PET/CT exams designed for response assessment for the broader machine learning in healthcare research community. Automated assessment of radiographic response from FDG PET/CT with OncoNet could provide clinicians with a valuable tool to rapidly and consistently interpret change over time in longitudinal multi-modal imaging exams.

Imon Banerjee, Ananth Reddy Bhimireddy, John L. Burns et al.

Background: In medical imaging, prior studies have demonstrated disparate AI performance by race, yet there is no known correlation for race on medical imaging that would be obvious to the human expert interpreting the images. Methods: Using private and public datasets we evaluate: A) performance quantification of deep learning models to detect race from medical images, including the ability of these models to generalize to external environments and across multiple imaging modalities, B) assessment of possible confounding anatomic and phenotype population features, such as disease distribution and body habitus as predictors of race, and C) investigation into the underlying mechanism by which AI models can recognize race. Findings: Standard deep learning models can be trained to predict race from medical images with high performance across multiple imaging modalities. Our findings hold under external validation conditions, as well as when models are optimized to perform clinically motivated tasks. We demonstrate this detection is not due to trivial proxies or imaging-related surrogate covariates for race, such as underlying disease distribution. Finally, we show that performance persists over all anatomical regions and frequency spectrum of the images suggesting that mitigation efforts will be challenging and demand further study. Interpretation: We emphasize that model ability to predict self-reported race is itself not the issue of importance. However, our findings that AI can trivially predict self-reported race -- even from corrupted, cropped, and noised medical images -- in a setting where clinical experts cannot, creates an enormous risk for all model deployments in medical imaging: if an AI model secretly used its knowledge of self-reported race to misclassify all Black patients, radiologists would not be able to tell using the same data the model has access to.