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Qicheng Lao

Publications and source records attributed to Qicheng Lao.

35 records · Page 2Linked to original sources
arXiv2024

Curriculum Prompting Foundation Models for Medical Image Segmentation

Adapting large pre-trained foundation models, e.g., SAM, for medical image segmentation remains a significant challenge. A crucial step involves the formulation of a series of specialized prompts that incorporate specific clinical instructions. Past works have been heavily reliant on a singular type of prompt for each instance, necessitating manual input of an ideally correct prompt, which is less efficient. To tackle this issue, we propose to utilize prompts of different granularity, which are sourced from original images to provide a broader scope of clinical insights. However, combining prompts of varying types can pose a challenge due to potential conflicts. In response, we have designed a coarse-to-fine mechanism, referred to as curriculum prompting, that progressively integrates prompts of different types. Through extensive experiments on three public medical datasets across various modalities, we demonstrate the effectiveness of our proposed approach, which not only automates the prompt generation process but also yields superior performance compared to other SAM-based medical image segmentation methods. Code is available at: https://github.com/AnnaZzz-zxq/Curriculum-Prompting.

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arXiv2024

OpenMEDLab: An Open-source Platform for Multi-modality Foundation Models in Medicine

The emerging trend of advancing generalist artificial intelligence, such as GPTv4 and Gemini, has reshaped the landscape of research (academia and industry) in machine learning and many other research areas. However, domain-specific applications of such foundation models (e.g., in medicine) remain untouched or often at their very early stages. It will require an individual set of transfer learning and model adaptation techniques by further expanding and injecting these models with domain knowledge and data. The development of such technologies could be largely accelerated if the bundle of data, algorithms, and pre-trained foundation models were gathered together and open-sourced in an organized manner. In this work, we present OpenMEDLab, an open-source platform for multi-modality foundation models. It encapsulates not only solutions of pioneering attempts in prompting and fine-tuning large language and vision models for frontline clinical and bioinformatic applications but also building domain-specific foundation models with large-scale multi-modal medical data. Importantly, it opens access to a group of pre-trained foundation models for various medical image modalities, clinical text, protein engineering, etc. Inspiring and competitive results are also demonstrated for each collected approach and model in a variety of benchmarks for downstream tasks. We welcome researchers in the field of medical artificial intelligence to continuously contribute cutting-edge methods and models to OpenMEDLab, which can be accessed via https://github.com/openmedlab.

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arXiv2023

FlowX: Towards Explainable Graph Neural Networks via Message Flows

We investigate the explainability of graph neural networks (GNNs) as a step toward elucidating their working mechanisms. While most current methods focus on explaining graph nodes, edges, or features, we argue that, as the inherent functional mechanism of GNNs, message flows are more natural for performing explainability. To this end, we propose a novel method here, known as FlowX, to explain GNNs by identifying important message flows. To quantify the importance of flows, we propose to follow the philosophy of Shapley values from cooperative game theory. To tackle the complexity of computing all coalitions' marginal contributions, we propose a flow sampling scheme to compute Shapley value approximations as initial assessments of further training. We then propose an information-controlled learning algorithm to train flow scores toward diverse explanation targets: necessary or sufficient explanations. Experimental studies on both synthetic and real-world datasets demonstrate that our proposed FlowX and its variants lead to improved explainability of GNNs. The code is available at https://github.com/divelab/DIG.

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arXiv2023

Deblurring Masked Autoencoder is Better Recipe for Ultrasound Image Recognition

Masked autoencoder (MAE) has attracted unprecedented attention and achieves remarkable performance in many vision tasks. It reconstructs random masked image patches (known as proxy task) during pretraining and learns meaningful semantic representations that can be transferred to downstream tasks. However, MAE has not been thoroughly explored in ultrasound imaging. In this work, we investigate the potential of MAE for ultrasound image recognition. Motivated by the unique property of ultrasound imaging in high noise-to-signal ratio, we propose a novel deblurring MAE approach that incorporates deblurring into the proxy task during pretraining. The addition of deblurring facilitates the pretraining to better recover the subtle details presented in the ultrasound images, thus improving the performance of the downstream classification task. Our experimental results demonstrate the effectiveness of our deblurring MAE, achieving state-of-the-art performance in ultrasound image classification. Overall, our work highlights the potential of MAE for ultrasound image recognition and presents a novel approach that incorporates deblurring to further improve its effectiveness.

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arXiv2023

ConES: Concept Embedding Search for Parameter Efficient Tuning Large Vision Language Models

Large pre-trained vision-language models have shown great prominence in transferring pre-acquired knowledge to various domains and downstream tasks with appropriate prompting or tuning. Existing prevalent tuning methods can be generally categorized into three genres: 1) prompt engineering by creating suitable prompt texts, which is time-consuming and requires domain expertise; 2) or simply fine-tuning the whole model, which is extremely inefficient; 3) prompt tuning through parameterized prompt embeddings with the text encoder. Nevertheless, all methods rely on the text encoder for bridging the modality gap between vision and language. In this work, we question the necessity of the cumbersome text encoder for a more lightweight and efficient tuning paradigm as well as more representative prompt embeddings closer to the image representations. To achieve this, we propose a Concept Embedding Search (ConES) approach by optimizing prompt embeddings -- without the need of the text encoder -- to capture the 'concept' of the image modality through a variety of task objectives. By dropping the text encoder, we are able to significantly speed up the learning process, \eg, from about an hour to just ten minutes in our experiments for personalized text-to-image generation without impairing the generation quality. Moreover, our proposed approach is orthogonal to current existing tuning methods since the searched concept embeddings can be further utilized in the next stage of fine-tuning the pre-trained large models for boosting performance. Extensive experiments show that our approach can beat the prompt tuning and textual inversion methods in a variety of downstream tasks including objection detection, instance segmentation, and image generation. Our approach also shows better generalization capability for unseen concepts in specialized domains, such as the medical domain.

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arXiv2023

SAM on Medical Images: A Comprehensive Study on Three Prompt Modes

The Segment Anything Model (SAM) made an eye-catching debut recently and inspired many researchers to explore its potential and limitation in terms of zero-shot generalization capability. As the first promptable foundation model for segmentation tasks, it was trained on a large dataset with an unprecedented number of images and annotations. This large-scale dataset and its promptable nature endow the model with strong zero-shot generalization. Although the SAM has shown competitive performance on several datasets, we still want to investigate its zero-shot generalization on medical images. As we know, the acquisition of medical image annotation usually requires a lot of effort from professional practitioners. Therefore, if there exists a foundation model that can give high-quality mask prediction simply based on a few point prompts, this model will undoubtedly become the game changer for medical image analysis. To evaluate whether SAM has the potential to become the foundation model for medical image segmentation tasks, we collected more than 12 public medical image datasets that cover various organs and modalities. We also explore what kind of prompt can lead to the best zero-shot performance with different modalities. Furthermore, we find that a pattern shows that the perturbation of the box size will significantly change the prediction accuracy. Finally, Extensive experiments show that the predicted mask quality varied a lot among different datasets. And providing proper prompts, such as bounding boxes, to the SAM will significantly increase its performance.

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arXiv2023

Towards General Purpose Medical AI: Continual Learning Medical Foundation Model

Inevitable domain and task discrepancies in real-world scenarios can impair the generalization performance of the pre-trained deep models for medical data. Therefore, we audaciously propose that we should build a general-purpose medical AI system that can be seamlessly adapted to downstream domains/tasks. Since the domain/task adaption procedures usually involve additional labeling work for the target data, designing a data-efficient adaption algorithm is desired to save the cost of transferring the learned knowledge. Our recent work found that vision-language models (VLMs) are efficient learners with extraordinary cross-domain ability. Therefore, in this work, we further explore the possibility of leveraging pre-trained VLMs as medical foundation models for building general-purpose medical AI, where we thoroughly investigate three machine-learning paradigms, i.e., domain/task-specialized learning, joint learning, and continual learning, for training the VLMs and evaluate their generalization performance on cross-domain and cross-task test sets. To alleviate the catastrophic forgetting during sequential training, we employ rehearsal learning and receive a sharp boost in terms of generalization capability. In a nutshell, our empirical evidence suggests that continual learning may be a practical and efficient learning paradigm for the medical foundation model. And we hope researchers can use our empirical evidence as basement to further explore the path toward medical foundation model.

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arXiv2023

Medical Image Understanding with Pretrained Vision Language Models: A Comprehensive Study

The large-scale pre-trained vision language models (VLM) have shown remarkable domain transfer capability on natural images. However, it remains unknown whether this capability can also apply to the medical image domain. This paper thoroughly studies the knowledge transferability of pre-trained VLMs to the medical domain, where we show that well-designed medical prompts are the key to elicit knowledge from pre-trained VLMs. We demonstrate that by prompting with expressive attributes that are shared between domains, the VLM can carry the knowledge across domains and improve its generalization. This mechanism empowers VLMs to recognize novel objects with fewer or without image samples. Furthermore, to avoid the laborious manual designing process, we develop three approaches for automatic generation of medical prompts, which can inject expert-level medical knowledge and image-specific information into the prompts for fine-grained grounding. We conduct extensive experiments on thirteen different medical datasets across various modalities, showing that our well-designed prompts greatly improve the zero-shot performance compared to the default prompts, and our fine-tuned models surpass the supervised models by a significant margin.

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arXiv2022

Conditional Generation of Medical Images via Disentangled Adversarial Inference

Synthetic medical image generation has a huge potential for improving healthcare through many applications, from data augmentation for training machine learning systems to preserving patient privacy. Conditional Adversarial Generative Networks (cGANs) use a conditioning factor to generate images and have shown great success in recent years. Intuitively, the information in an image can be divided into two parts: 1) content which is presented through the conditioning vector and 2) style which is the undiscovered information missing from the conditioning vector. Current practices in using cGANs for medical image generation, only use a single variable for image generation (i.e., content) and therefore, do not provide much flexibility nor control over the generated image. In this work we propose a methodology to learn from the image itself, disentangled representations of style and content, and use this information to impose control over the generation process. In this framework, style is learned in a fully unsupervised manner, while content is learned through both supervised learning (using the conditioning vector) and unsupervised learning (with the inference mechanism). We undergo two novel regularization steps to ensure content-style disentanglement. First, we minimize the shared information between content and style by introducing a novel application of the gradient reverse layer (GRL); second, we introduce a self-supervised regularization method to further separate information in the content and style variables. We show that in general, two latent variable models achieve better performance and give more control over the generated image. We also show that our proposed model (DRAI) achieves the best disentanglement score and has the best overall performance.

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arXiv2021

Towards Adversarial Robustness via Transductive Learning

There has been emerging interest to use transductive learning for adversarial robustness (Goldwasser et al., NeurIPS 2020; Wu et al., ICML 2020). Compared to traditional "test-time" defenses, these defense mechanisms "dynamically retrain" the model based on test time input via transductive learning; and theoretically, attacking these defenses boils down to bilevel optimization, which seems to raise the difficulty for adaptive attacks. In this paper, we first formalize and analyze modeling aspects of transductive robustness. Then, we propose the principle of attacking model space for solving bilevel attack objectives, and present an instantiation of the principle which breaks previous transductive defenses. These attacks thus point to significant difficulties in the use of transductive learning to improve adversarial robustness. To this end, we present new theoretical and empirical evidence in support of the utility of transductive learning.

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arXiv2020

Hypothesis Disparity Regularized Mutual Information Maximization

We propose a hypothesis disparity regularized mutual information maximization~(HDMI) approach to tackle unsupervised hypothesis transfer -- as an effort towards unifying hypothesis transfer learning (HTL) and unsupervised domain adaptation (UDA) -- where the knowledge from a source domain is transferred solely through hypotheses and adapted to the target domain in an unsupervised manner. In contrast to the prevalent HTL and UDA approaches that typically use a single hypothesis, HDMI employs multiple hypotheses to leverage the underlying distributions of the source and target hypotheses. To better utilize the crucial relationship among different hypotheses -- as opposed to unconstrained optimization of each hypothesis independently -- while adapting to the unlabeled target domain through mutual information maximization, HDMI incorporates a hypothesis disparity regularization that coordinates the target hypotheses jointly learn better target representations while preserving more transferable source knowledge with better-calibrated prediction uncertainty. HDMI achieves state-of-the-art adaptation performance on benchmark datasets for UDA in the context of HTL, without the need to access the source data during the adaptation.

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arXiv2020

Implicit Class-Conditioned Domain Alignment for Unsupervised Domain Adaptation

We present an approach for unsupervised domain adaptation---with a strong focus on practical considerations of within-domain class imbalance and between-domain class distribution shift---from a class-conditioned domain alignment perspective. Current methods for class-conditioned domain alignment aim to explicitly minimize a loss function based on pseudo-label estimations of the target domain. However, these methods suffer from pseudo-label bias in the form of error accumulation. We propose a method that removes the need for explicit optimization of model parameters from pseudo-labels directly. Instead, we present a sampling-based implicit alignment approach, where the sample selection procedure is implicitly guided by the pseudo-labels. Theoretical analysis reveals the existence of a domain-discriminator shortcut in misaligned classes, which is addressed by the proposed implicit alignment approach to facilitate domain-adversarial learning. Empirical results and ablation studies confirm the effectiveness of the proposed approach, especially in the presence of within-domain class imbalance and between-domain class distribution shift.

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arXiv2020

FoCL: Feature-Oriented Continual Learning for Generative Models

In this paper, we propose a general framework in continual learning for generative models: Feature-oriented Continual Learning (FoCL). Unlike previous works that aim to solve the catastrophic forgetting problem by introducing regularization in the parameter space or image space, FoCL imposes regularization in the feature space. We show in our experiments that FoCL has faster adaptation to distributional changes in sequentially arriving tasks, and achieves the state-of-the-art performance for generative models in task incremental learning. We discuss choices of combined regularization spaces towards different use case scenarios for boosted performance, e.g., tasks that have high variability in the background. Finally, we introduce a forgetfulness measure that fairly evaluates the degree to which a model suffers from forgetting. Interestingly, the analysis of our proposed forgetfulness score also implies that FoCL tends to have a mitigated forgetting for future tasks.

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arXiv2020

Continuous Domain Adaptation with Variational Domain-Agnostic Feature Replay

Learning in non-stationary environments is one of the biggest challenges in machine learning. Non-stationarity can be caused by either task drift, i.e., the drift in the conditional distribution of labels given the input data, or the domain drift, i.e., the drift in the marginal distribution of the input data. This paper aims to tackle this challenge in the context of continuous domain adaptation, where the model is required to learn new tasks adapted to new domains in a non-stationary environment while maintaining previously learned knowledge. To deal with both drifts, we propose variational domain-agnostic feature replay, an approach that is composed of three components: an inference module that filters the input data into domain-agnostic representations, a generative module that facilitates knowledge transfer, and a solver module that applies the filtered and transferable knowledge to solve the queries. We address the two fundamental scenarios in continuous domain adaptation, demonstrating the effectiveness of our proposed approach for practical usage.

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arXiv2019

Dual Adversarial Inference for Text-to-Image Synthesis

Synthesizing images from a given text description involves engaging two types of information: the content, which includes information explicitly described in the text (e.g., color, composition, etc.), and the style, which is usually not well described in the text (e.g., location, quantity, size, etc.). However, in previous works, it is typically treated as a process of generating images only from the content, i.e., without considering learning meaningful style representations. In this paper, we aim to learn two variables that are disentangled in the latent space, representing content and style respectively. We achieve this by augmenting current text-to-image synthesis frameworks with a dual adversarial inference mechanism. Through extensive experiments, we show that our model learns, in an unsupervised manner, style representations corresponding to certain meaningful information present in the image that are not well described in the text. The new framework also improves the quality of synthesized images when evaluated on Oxford-102, CUB and COCO datasets.

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arXiv2019

Case-Based Histopathological Malignancy Diagnosis using Convolutional Neural Networks

In practice, histopathological diagnosis of tumor malignancy often requires a human expert to scan through histopathological images at multiple magnification levels, after which a final diagnosis can be accurately determined. However, previous research on such classification tasks using convolutional neural networks primarily determine a diagnosis for a single magnification level. In this paper, we propose a case-based approach using deep residual neural networks for histopathological malignancy diagnosis, where a case is defined as a sequence of images from the patient at all available levels of magnification. Effectively, through mimicking what a human expert would actually do, our approach makes a diagnosis decision based on features learned in combination at multiple magnification levels. Our results show that the case-based approach achieves better performance than the state-of-the-art methods when evaluated on BreaKHis, a histopathological image dataset for breast tumors.

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arXiv2018

Leveraging Disease Progression Learning for Medical Image Recognition

Unlike natural images, medical images often have intrinsic characteristics that can be leveraged for neural network learning. For example, images that belong to different stages of a disease may continuously follow a certain progression pattern. In this paper, we propose a novel method that leverages disease progression learning for medical image recognition. In our method, sequences of images ordered by disease stages are learned by a neural network that consists of a shared vision model for feature extraction and a long short-term memory network for the learning of stage sequences. Auxiliary vision outputs are also included to capture stage features that tend to be discrete along the disease progression. Our proposed method is evaluated on a public diabetic retinopathy dataset, and achieves about 3.3% improvement in disease staging accuracy, compared to the baseline method that does not use disease progression learning.

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