In-context Vectors: Making In Context Learning More Effective and Controllable Through Latent Space Steering

Large language models (LLMs) demonstrate emergent in-context learning capabilities, where they adapt to new tasks based on example demonstrations. However, in-context learning has seen limited effectiveness in many settings, is difficult to quantitatively control and takes up context window space. To overcome these limitations, we propose an alternative approach that recasts in-context learning as in-context vectors (ICV). Using ICV has two steps. We first use a forward pass on demonstration examples to create the in-context vector from the latent embedding of the LLM. This vector captures essential information about the intended task. On a new query, instead of adding demonstrations to the prompt, we shift the latent states of the LLM using the ICV. The ICV approach has several benefits: 1) it enables the LLM to more effectively follow the demonstration examples; 2) it's easy to control by adjusting the magnitude of the ICV; 3) it reduces the length of the prompt by removing the in-context demonstrations; 4) ICV is computationally much more efficient than fine-tuning. We demonstrate that ICV achieves better performance compared to standard in-context learning and fine-tuning on diverse tasks including safety, style transfer, role-playing and formatting. Moreover, we show that we can flexibly teach LLM to simultaneously follow different types of instructions by simple vector arithmetics on the corresponding ICVs.

3D TransUNet: Advancing Medical Image Segmentation through Vision Transformers

Medical image segmentation plays a crucial role in advancing healthcare systems for disease diagnosis and treatment planning. The u-shaped architecture, popularly known as U-Net, has proven highly successful for various medical image segmentation tasks. However, U-Net's convolution-based operations inherently limit its ability to model long-range dependencies effectively. To address these limitations, researchers have turned to Transformers, renowned for their global self-attention mechanisms, as alternative architectures. One popular network is our previous TransUNet, which leverages Transformers' self-attention to complement U-Net's localized information with the global context. In this paper, we extend the 2D TransUNet architecture to a 3D network by building upon the state-of-the-art nnU-Net architecture, and fully exploring Transformers' potential in both the encoder and decoder design. We introduce two key components: 1) A Transformer encoder that tokenizes image patches from a convolution neural network (CNN) feature map, enabling the extraction of global contexts, and 2) A Transformer decoder that adaptively refines candidate regions by utilizing cross-attention between candidate proposals and U-Net features. Our investigations reveal that different medical tasks benefit from distinct architectural designs. The Transformer encoder excels in multi-organ segmentation, where the relationship among organs is crucial. On the other hand, the Transformer decoder proves more beneficial for dealing with small and challenging segmented targets such as tumor segmentation. Extensive experiments showcase the significant potential of integrating a Transformer-based encoder and decoder into the u-shaped medical image segmentation architecture. TransUNet outperforms competitors in various medical applications.

Development and external validation of a lung cancer risk estimation tool using gradient-boosting

Lung cancer is a significant cause of mortality worldwide, emphasizing the importance of early detection for improved survival rates. In this study, we propose a machine learning (ML) tool trained on data from the PLCO Cancer Screening Trial and validated on the NLST to estimate the likelihood of lung cancer occurrence within five years. The study utilized two datasets, the PLCO (n=55,161) and NLST (n=48,595), consisting of comprehensive information on risk factors, clinical measurements, and outcomes related to lung cancer. Data preprocessing involved removing patients who were not current or former smokers and those who had died of causes unrelated to lung cancer. Additionally, a focus was placed on mitigating bias caused by censored data. Feature selection, hyper-parameter optimization, and model calibration were performed using XGBoost, an ensemble learning algorithm that combines gradient boosting and decision trees. The ML model was trained on the pre-processed PLCO dataset and tested on the NLST dataset. The model incorporated features such as age, gender, smoking history, medical diagnoses, and family history of lung cancer. The model was well-calibrated (Brier score=0.044). ROC-AUC was 82% on the PLCO dataset and 70% on the NLST dataset. PR-AUC was 29% and 11% respectively. When compared to the USPSTF guidelines for lung cancer screening, our model provided the same recall with a precision of 13.1% vs. 9.3% on the PLCO dataset and 3.2% vs. 3.1% on the NLST dataset. The developed ML tool provides a freely available web application for estimating the likelihood of developing lung cancer within five years. By utilizing risk factors and clinical data, individuals can assess their risk and make informed decisions regarding lung cancer screening. This research contributes to the efforts in early detection and prevention strategies, aiming to reduce lung cancer-related mortality rates.

Consistency-guided Meta-Learning for Bootstrapping Semi-Supervised Medical Image Segmentation

Medical imaging has witnessed remarkable progress but usually requires a large amount of high-quality annotated data which is time-consuming and costly to obtain. To alleviate this burden, semi-supervised learning has garnered attention as a potential solution. In this paper, we present Meta-Learning for Bootstrapping Medical Image Segmentation (MLB-Seg), a novel method for tackling the challenge of semi-supervised medical image segmentation. Specifically, our approach first involves training a segmentation model on a small set of clean labeled images to generate initial labels for unlabeled data. To further optimize this bootstrapping process, we introduce a per-pixel weight mapping system that dynamically assigns weights to both the initialized labels and the model's own predictions. These weights are determined using a meta-process that prioritizes pixels with loss gradient directions closer to those of clean data, which is based on a small set of precisely annotated images. To facilitate the meta-learning process, we additionally introduce a consistency-based Pseudo Label Enhancement (PLE) scheme that improves the quality of the model's own predictions by ensembling predictions from various augmented versions of the same input. In order to improve the quality of the weight maps obtained through multiple augmentations of a single input, we introduce a mean teacher into the PLE scheme. This method helps to reduce noise in the weight maps and stabilize its generation process. Our extensive experimental results on public atrial and prostate segmentation datasets demonstrate that our proposed method achieves state-of-the-art results under semi-supervision. Our code is available at https://github.com/aijinrjinr/MLB-Seg.

Towards Medical Artificial General Intelligence via Knowledge-Enhanced Multimodal Pretraining

Medical artificial general intelligence (MAGI) enables one foundation model to solve different medical tasks, which is very practical in the medical domain. It can significantly reduce the requirement of large amounts of task-specific data by sufficiently sharing medical knowledge among different tasks. However, due to the challenges of designing strongly generalizable models with limited and complex medical data, most existing approaches tend to develop task-specific models. To take a step towards MAGI, we propose a new paradigm called Medical-knOwledge-enhanced mulTimOdal pretRaining (MOTOR). In MOTOR, we combine two kinds of basic medical knowledge, i.e., general and specific knowledge, in a complementary manner to boost the general pretraining process. As a result, the foundation model with comprehensive basic knowledge can learn compact representations from pretraining radiographic data for better cross-modal alignment. MOTOR unifies the understanding and generation, which are two kinds of core intelligence of an AI system, into a single medical foundation model, to flexibly handle more diverse medical tasks. To enable a comprehensive evaluation and facilitate further research, we construct a medical multimodal benchmark including a wide range of downstream tasks, such as chest x-ray report generation and medical visual question answering. Extensive experiments on our benchmark show that MOTOR obtains promising results through simple task-oriented adaptation. The visualization shows that the injected knowledge successfully highlights key information in the medical data, demonstrating the excellent interpretability of MOTOR. Our MOTOR successfully mimics the human practice of fulfilling a "medical student" to accelerate the process of becoming a "specialist". We believe that our work makes a significant stride in realizing MAGI.

Learning Treatment Plan Representations for Content Based Image Retrieval

Objective: Knowledge based planning (KBP) typically involves training an end-to-end deep learning model to predict dose distributions. However, training end-to-end KBP methods may be associated with practical limitations due to the limited size of medical datasets that are often used. To address these limitations, we propose a content based image retrieval (CBIR) method for retrieving dose distributions of previously planned patients based on anatomical similarity. Approach: Our proposed CBIR method trains a representation model that produces latent space embeddings of a patient's anatomical information. The latent space embeddings of new patients are then compared against those of previous patients in a database for image retrieval of dose distributions. Summary metrics (e.g. dose-volume histogram, conformity index, homogeneity index, etc.) are computed and can then be utilized in subsequent automated planning. All source code for this project is available on github. Main Results: The retrieval performance of various CBIR methods is evaluated on a dataset consisting of both publicly available plans and clinical plans from our institution. This study compares various encoding methods, ranging from simple autoencoders to more recent Siamese networks like SimSiam, and the best performance was observed for the multitask Siamese network. Significance: Applying CBIR to inform subsequent treatment planning potentially addresses many limitations associated with end-to-end KBP. Our current results demonstrate that excellent image retrieval performance can be obtained through slight changes to previously developed Siamese networks. We hope to integrate CBIR into automated planning workflow in future works, potentially through methods like the MetaPlanner framework.

Label-Efficient Self-Supervised Federated Learning for Tackling Data Heterogeneity in Medical Imaging

The curation of large-scale medical datasets from multiple institutions necessary for training deep learning models is challenged by the difficulty in sharing patient data with privacy-preserving. Federated learning (FL), a paradigm that enables privacy-protected collaborative learning among different institutions, is a promising solution to this challenge. However, FL generally suffers from performance deterioration due to heterogeneous data distributions across institutions and the lack of quality labeled data. In this paper, we present a robust and label-efficient self-supervised FL framework for medical image analysis. Specifically, we introduce a novel distributed self-supervised pre-training paradigm into the existing FL pipeline (i.e., pre-training the models directly on the decentralized target task datasets). Built upon the recent success of Vision Transformers, we employ masked image encoding tasks for self-supervised pre-training, to facilitate more effective knowledge transfer to downstream federated models. Extensive empirical results on simulated and real-world medical imaging federated datasets show that self-supervised pre-training largely benefits the robustness of federated 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 with the supervised baseline with ImageNet pre-training. Moreover, we show that our self-supervised FL algorithm generalizes well to out-of-distribution data and learns federated models more effectively in limited label scenarios, surpassing the supervised baseline by 10.36% and the semi-supervised FL method by 8.3% in test accuracy.

CSN: Component-Supervised Network for Few-Shot Classification

The few-shot classification (FSC) task has been a hot research topic in recent years. It aims to address the classification problem with insufficient labeled data on a cross-category basis. Typically, researchers pre-train a feature extractor with base data, then use it to extract the features of novel data and recognize them. Notably, the novel set only has a few annotated samples and has entirely different categories from the base set, which leads to that the pre-trained feature extractor can not adapt to the novel data flawlessly. We dub this problem as Feature-Extractor-Maladaptive (FEM) problem. Starting from the root cause of this problem, this paper presents a new scheme, Component-Supervised Network (CSN), to improve the performance of FSC. We believe that although the categories of base and novel sets are different, the composition of the sample's components is similar. For example, both cat and dog contain leg and head components. Actually, such entity components are intra-class stable. They have fine cross-category versatility and new category generalization. Therefore, we refer to WordNet, a dictionary commonly used in natural language processing, to collect component information of samples and construct a component-based auxiliary task to improve the adaptability of the feature extractor. We conduct experiments on two benchmark datasets (mini-ImageNet and tiered-ImageNet), the improvements of $0.9\%$-$5.8\%$ compared with state-of-the-arts have evaluated the efficiency of our CSN.

Learning to Bootstrap for Combating Label Noise

Deep neural networks are powerful tools for representation learning, but can easily overfit to noisy labels which are prevalent in many real-world scenarios. Generally, noisy supervision could stem from variation among labelers, label corruption by adversaries, etc. To combat such label noises, one popular line of approach is to apply customized weights to the training instances, so that the corrupted examples contribute less to the model learning. However, such learning mechanisms potentially erase important information about the data distribution and therefore yield suboptimal results. To leverage useful information from the corrupted instances, an alternative is the bootstrapping loss, which reconstructs new training targets on-the-fly by incorporating the network's own predictions (i.e., pseudo-labels). In this paper, we propose a more generic learnable loss objective which enables a joint reweighting of instances and labels at once. Specifically, our method dynamically adjusts the per-sample importance weight between the real observed labels and pseudo-labels, where the weights are efficiently determined in a meta process. Compared to the previous instance reweighting methods, our approach concurrently conducts implicit relabeling, and thereby yield substantial improvements with almost no extra cost. Extensive experimental results demonstrated the strengths of our approach over existing methods on multiple natural and medical image benchmark datasets, including CIFAR-10, CIFAR-100, ISIC2019 and Clothing 1M. The code is publicly available at https://github.com/yuyinzhou/L2B.

Image Classification using Graph Neural Network and Multiscale Wavelet Superpixels

Prior studies using graph neural networks (GNNs) for image classification have focused on graphs generated from a regular grid of pixels or similar-sized superpixels. In the latter, a single target number of superpixels is defined for an entire dataset irrespective of differences across images and their intrinsic multiscale structure. On the contrary, this study investigates image classification using graphs generated from an image-specific number of multiscale superpixels. We propose WaveMesh, a new wavelet-based superpixeling algorithm, where the number and sizes of superpixels in an image are systematically computed based on its content. WaveMesh superpixel graphs are structurally different from similar-sized superpixel graphs. We use SplineCNN, a state-of-the-art network for image graph classification, to compare WaveMesh and similar-sized superpixels. Using SplineCNN, we perform extensive experiments on three benchmark datasets under three local-pooling settings: 1) no pooling, 2) GraclusPool, and 3) WavePool, a novel spatially heterogeneous pooling scheme tailored to WaveMesh superpixels. Our experiments demonstrate that SplineCNN learns from multiscale WaveMesh superpixels on-par with similar-sized superpixels. In all WaveMesh experiments, GraclusPool performs poorer than no pooling / WavePool, indicating that poor choice of pooling can result in inferior performance while learning from multiscale superpixels.