Explanations of Classifiers Enhance Medical Image Segmentation via End-to-end Pre-training

Medical image segmentation aims to identify and locate abnormal structures in medical images, such as chest radiographs, using deep neural networks. These networks require a large number of annotated images with fine-grained masks for the regions of interest, making pre-training strategies based on classification datasets essential for sample efficiency. Based on a large-scale medical image classification dataset, our work collects explanations from well-trained classifiers to generate pseudo labels of segmentation tasks. Specifically, we offer a case study on chest radiographs and train image classifiers on the CheXpert dataset to identify 14 pathological observations in radiology. We then use Integrated Gradients (IG) method to distill and boost the explanations obtained from the classifiers, generating massive diagnosis-oriented localization labels (DoLL). These DoLL-annotated images are used for pre-training the model before fine-tuning it for downstream segmentation tasks, including COVID-19 infectious areas, lungs, heart, and clavicles. Our method outperforms other baselines, showcasing significant advantages in model performance and training efficiency across various segmentation settings.

Towards Explainable Artificial Intelligence (XAI): A Data Mining Perspective

Given the complexity and lack of transparency in deep neural networks (DNNs), extensive efforts have been made to make these systems more interpretable or explain their behaviors in accessible terms. Unlike most reviews, which focus on algorithmic and model-centric perspectives, this work takes a "data-centric" view, examining how data collection, processing, and analysis contribute to explainable AI (XAI). We categorize existing work into three categories subject to their purposes: interpretations of deep models, referring to feature attributions and reasoning processes that correlate data points with model outputs; influences of training data, examining the impact of training data nuances, such as data valuation and sample anomalies, on decision-making processes; and insights of domain knowledge, discovering latent patterns and fostering new knowledge from data and models to advance social values and scientific discovery. Specifically, we distill XAI methodologies into data mining operations on training and testing data across modalities, such as images, text, and tabular data, as well as on training logs, checkpoints, models and other DNN behavior descriptors. In this way, our study offers a comprehensive, data-centric examination of XAI from a lens of data mining methods and applications.

CUPre: Cross-domain Unsupervised Pre-training for Few-Shot Cell Segmentation

While pre-training on object detection tasks, such as Common Objects in Contexts (COCO) [1], could significantly boost the performance of cell segmentation, it still consumes on massive fine-annotated cell images [2] with bounding boxes, masks, and cell types for every cell in every image, to fine-tune the pre-trained model. To lower the cost of annotation, this work considers the problem of pre-training DNN models for few-shot cell segmentation, where massive unlabeled cell images are available but only a small proportion is annotated. Hereby, we propose Cross-domain Unsupervised Pre-training, namely CUPre, transferring the capability of object detection and instance segmentation for common visual objects (learned from COCO) to the visual domain of cells using unlabeled images. Given a standard COCO pre-trained network with backbone, neck, and head modules, CUPre adopts an alternate multi-task pre-training (AMT2) procedure with two sub-tasks -- in every iteration of pre-training, AMT2 first trains the backbone with cell images from multiple cell datasets via unsupervised momentum contrastive learning (MoCo) [3], and then trains the whole model with vanilla COCO datasets via instance segmentation. After pre-training, CUPre fine-tunes the whole model on the cell segmentation task using a few annotated images. We carry out extensive experiments to evaluate CUPre using LIVECell [2] and BBBC038 [4] datasets in few-shot instance segmentation settings. The experiment shows that CUPre can outperform existing pre-training methods, achieving the highest average precision (AP) for few-shot cell segmentation and detection.

TiC: Exploring Vision Transformer in Convolution

While models derived from Vision Transformers (ViTs) have been phonemically surging, pre-trained models cannot seamlessly adapt to arbitrary resolution images without altering the architecture and configuration, such as sampling the positional encoding, limiting their flexibility for various vision tasks. For instance, the Segment Anything Model (SAM) based on ViT-Huge requires all input images to be resized to 1024$\times$1024. To overcome this limitation, we propose the Multi-Head Self-Attention Convolution (MSA-Conv) that incorporates Self-Attention within generalized convolutions, including standard, dilated, and depthwise ones. Enabling transformers to handle images of varying sizes without retraining or rescaling, the use of MSA-Conv further reduces computational costs compared to global attention in ViT, which grows costly as image size increases. Later, we present the Vision Transformer in Convolution (TiC) as a proof of concept for image classification with MSA-Conv, where two capacity enhancing strategies, namely Multi-Directional Cyclic Shifted Mechanism and Inter-Pooling Mechanism, have been proposed, through establishing long-distance connections between tokens and enlarging the effective receptive field. Extensive experiments have been carried out to validate the overall effectiveness of TiC. Additionally, ablation studies confirm the performance improvement made by MSA-Conv and the two capacity enhancing strategies separately. Note that our proposal aims at studying an alternative to the global attention used in ViT, while MSA-Conv meets our goal by making TiC comparable to state-of-the-art on ImageNet-1K. Code will be released at https://github.com/zs670980918/MSA-Conv.

MUSCLE: Multi-task Self-supervised Continual Learning to Pre-train Deep Models for X-ray Images of Multiple Body Parts

While self-supervised learning (SSL) algorithms have been widely used to pre-train deep models, few efforts [11] have been done to improve representation learning of X-ray image analysis with SSL pre-trained models. In this work, we study a novel self-supervised pre-training pipeline, namely Multi-task Self-super-vised Continual Learning (MUSCLE), for multiple medical imaging tasks, such as classification and segmentation, using X-ray images collected from multiple body parts, including heads, lungs, and bones. Specifically, MUSCLE aggregates X-rays collected from multiple body parts for MoCo-based representation learning, and adopts a well-designed continual learning (CL) procedure to further pre-train the backbone subject various X-ray analysis tasks jointly. Certain strategies for image pre-processing, learning schedules, and regularization have been used to solve data heterogeneity, overfitting, and catastrophic forgetting problems for multi-task/dataset learning in MUSCLE.We evaluate MUSCLE using 9 real-world X-ray datasets with various tasks, including pneumonia classification, skeletal abnormality classification, lung segmentation, and tuberculosis (TB) detection. Comparisons against other pre-trained models [7] confirm the proof-of-concept that self-supervised multi-task/dataset continual pre-training could boost the performance of X-ray image analysis.

Natural Language based Context Modeling and Reasoning with LLMs: A Tutorial

Large language models (LLMs) have become phenomenally surging, since 2018--two decades after introducing context-awareness into computing systems. Through taking into account the situations of ubiquitous devices, users and the societies, context-aware computing has enabled a wide spectrum of innovative applications, such as assisted living, location-based social network services and so on. To recognize contexts and make decisions for actions accordingly, various artificial intelligence technologies, such as Ontology and OWL, have been adopted as representations for context modeling and reasoning. Recently, with the rise of LLMs and their improved natural language understanding and reasoning capabilities, it has become feasible to model contexts using natural language and perform context reasoning by interacting with LLMs such as ChatGPT and GPT-4. In this tutorial, we demonstrate the use of texts, prompts, and autonomous agents (AutoAgents) that enable LLMs to perform context modeling and reasoning without requiring fine-tuning of the model. We organize and introduce works in the related field, and name this computing paradigm as the LLM-driven Context-aware Computing (LCaC). In the LCaC paradigm, users' requests, sensors reading data, and the command to actuators are supposed to be represented as texts. Given the text of users' request and sensor data, the AutoAgent models the context by prompting and sends to the LLM for context reasoning. LLM generates a plan of actions and responds to the AutoAgent, which later follows the action plan to foster context-awareness. To prove the concepts, we use two showcases--(1) operating a mobile z-arm in an apartment for assisted living, and (2) planning a trip and scheduling the itinerary in a context-aware and personalized manner.

Robust Cross-Modal Knowledge Distillation for Unconstrained Videos

Cross-modal distillation has been widely used to transfer knowledge across different modalities, enriching the representation of the target unimodal one. Recent studies highly relate the temporal synchronization between vision and sound to the semantic consistency for cross-modal distillation. However, such semantic consistency from the synchronization is hard to guarantee in unconstrained videos, due to the irrelevant modality noise and differentiated semantic correlation. To this end, we first propose a \textit{Modality Noise Filter} (MNF) module to erase the irrelevant noise in teacher modality with cross-modal context. After this purification, we then design a \textit{Contrastive Semantic Calibration} (CSC) module to adaptively distill useful knowledge for target modality, by referring to the differentiated sample-wise semantic correlation in a contrastive fashion. Extensive experiments show that our method could bring a performance boost compared with other distillation methods in both visual action recognition and video retrieval task. We also extend to the audio tagging task to prove the generalization of our method. The source code is available at \href{https://github.com/GeWu-Lab/cross-modal-distillation}{https://github.com/GeWu-Lab/cross-modal-distillation}.

Doubly Stochastic Models: Learning with Unbiased Label Noises and Inference Stability

Random label noises (or observational noises) widely exist in practical machine learning settings. While previous studies primarily focus on the affects of label noises to the performance of learning, our work intends to investigate the implicit regularization effects of the label noises, under mini-batch sampling settings of stochastic gradient descent (SGD), with assumptions that label noises are unbiased. Specifically, we analyze the learning dynamics of SGD over the quadratic loss with unbiased label noises, where we model the dynamics of SGD as a stochastic differentiable equation (SDE) with two diffusion terms (namely a Doubly Stochastic Model). While the first diffusion term is caused by mini-batch sampling over the (label-noiseless) loss gradients as many other works on SGD, our model investigates the second noise term of SGD dynamics, which is caused by mini-batch sampling over the label noises, as an implicit regularizer. Our theoretical analysis finds such implicit regularizer would favor some convergence points that could stabilize model outputs against perturbation of parameters (namely inference stability). Though similar phenomenon have been investigated, our work doesn't assume SGD as an Ornstein-Uhlenbeck like process and achieve a more generalizable result with convergence of approximation proved. To validate our analysis, we design two sets of empirical studies to analyze the implicit regularizer of SGD with unbiased random label noises for deep neural networks training and linear regression.

Video4MRI: An Empirical Study on Brain Magnetic Resonance Image Analytics with CNN-based Video Classification Frameworks

To address the problem of medical image recognition, computer vision techniques like convolutional neural networks (CNN) are frequently used. Recently, 3D CNN-based models dominate the field of magnetic resonance image (MRI) analytics. Due to the high similarity between MRI data and videos, we conduct extensive empirical studies on video recognition techniques for MRI classification to answer the questions: (1) can we directly use video recognition models for MRI classification, (2) which model is more appropriate for MRI, (3) are the common tricks like data augmentation in video recognition still useful for MRI classification? Our work suggests that advanced video techniques benefit MRI classification. In this paper, four datasets of Alzheimer's and Parkinson's disease recognition are utilized in experiments, together with three alternative video recognition models and data augmentation techniques that are frequently applied to video tasks. In terms of efficiency, the results reveal that the video framework performs better than 3D-CNN models by 5% - 11% with 50% - 66% less trainable parameters. This report pushes forward the potential fusion of 3D medical imaging and video understanding research.

Towards Long-Term Time-Series Forecasting: Feature, Pattern, and Distribution

Long-term time-series forecasting (LTTF) has become a pressing demand in many applications, such as wind power supply planning. Transformer models have been adopted to deliver high prediction capacity because of the high computational self-attention mechanism. Though one could lower the complexity of Transformers by inducing the sparsity in point-wise self-attentions for LTTF, the limited information utilization prohibits the model from exploring the complex dependencies comprehensively. To this end, we propose an efficient Transformerbased model, named Conformer, which differentiates itself from existing methods for LTTF in three aspects: (i) an encoder-decoder architecture incorporating a linear complexity without sacrificing information utilization is proposed on top of sliding-window attention and Stationary and Instant Recurrent Network (SIRN); (ii) a module derived from the normalizing flow is devised to further improve the information utilization by inferring the outputs with the latent variables in SIRN directly; (iii) the inter-series correlation and temporal dynamics in time-series data are modeled explicitly to fuel the downstream self-attention mechanism. Extensive experiments on seven real-world datasets demonstrate that Conformer outperforms the state-of-the-art methods on LTTF and generates reliable prediction results with uncertainty quantification.