We propose a novel framework to classify large-scale time series data with long duration. Long time seriesclassification (L-TSC) is a challenging problem because the dataoften contains a large amount of irrelevant information to theclassification target. The irrelevant period degrades the classifica-tion performance while the relevance is unknown to the system.This paper proposes an uncertainty-aware multiple instancelearning (MIL) framework to identify the most relevant periodautomatically. The predictive uncertainty enables designing anattention mechanism that forces the MIL model to learn from thepossibly discriminant period. Moreover, the predicted uncertaintyyields a principled estimator to identify whether a prediction istrustworthy or not. We further incorporate another modality toaccommodate unreliable predictions by training a separate modelbased on its availability and conduct uncertainty aware fusion toproduce the final prediction. Systematic evaluation is conductedon the Automatic Identification System (AIS) data, which is col-lected to identify and track real-world vessels. Empirical resultsdemonstrate that the proposed method can effectively detect thetypes of vessels based on the trajectory and the uncertainty-awarefusion with other available data modality (Synthetic-ApertureRadar or SAR imagery is used in our experiments) can furtherimprove the detection accuracy.
Multiple instance learning (MIL) is a key algorithm for classification of whole slide images (WSI). Histology WSIs can have billions of pixels, which create enormous computational and annotation challenges. Typically, such images are divided into a set of patches (a bag of instances), where only bag-level class labels are provided. Deep learning based MIL methods calculate instance features using convolutional neural network (CNN). Our proposed approach is also deep learning based, with the following two contributions: Firstly, we propose to explicitly account for dependencies between instances during training by embedding self-attention Transformer blocks to capture dependencies between instances. For example, a tumor grade may depend on the presence of several particular patterns at different locations in WSI, which requires to account for dependencies between patches. Secondly, we propose an instance-wise loss function based on instance pseudo-labels. We compare the proposed algorithm to multiple baseline methods, evaluate it on the PANDA challenge dataset, the largest publicly available WSI dataset with over 11K images, and demonstrate state-of-the-art results.
Strongly supervised learning requires detailed knowledge of truth labels at instance levels, and in many machine learning applications this is a major drawback. Multiple instance learning (MIL) is a popular weakly supervised learning method where truth labels are not available at instance level, but only at bag-of-instances level. However, sometimes the nature of the problem requires a more complex description, where a nested architecture of bag-of-bags at different levels can capture underlying relationships, like similar instances grouped together. Predicting the latent labels of instances or inner-bags might be as important as predicting the final bag-of-bags label but is lost in a straightforward nested setting. We propose a Nested Multiple Instance with Attention (NMIA) model architecture combining the concept of nesting with attention mechanisms. We show that NMIA performs as conventional MIL in simple scenarios and can grasp a complex scenario providing insights to the latent labels at different levels.
In pathology, whole-slide images (WSI) based survival prediction has attracted increasing interest. However, given the large size of WSIs and the lack of pathologist annotations, extracting the prognostic information from WSIs remains a challenging task. Previous studies have used multiple instance learning approaches to combine the information from multiple randomly sampled patches, but different visual patterns may contribute differently to prognosis prediction. In this study, we developed a multi-head attention approach to focus on various parts of a tumor slide, for more comprehensive information extraction from WSIs. We evaluated our approach on four cancer types from The Cancer Genome Atlas database. Our model achieved an average c-index of 0.640, outperforming two existing state-of-the-art approaches for WSI-based survival prediction, which have an average c-index of 0.603 and 0.619 on these datasets. Visualization of our attention maps reveals each attention head focuses synergistically on different morphological patterns.
Weakly supervised object detection (WSOD) is a challenging task that requires simultaneously learn object classifiers and estimate object locations under the supervision of image category labels. A major line of WSOD methods roots in multiple instance learning which regards images as bags of instances and selects positive instances from each bag to learn the detector. However, a grand challenge emerges when the detector inclines to converge to discriminative parts of objects rather than the whole objects. In this paper, under the hypothesis that optimal solutions are included in local minima, we propose a discovery-and-selection approach fused with multiple instance learning (DS-MIL), which finds rich local minima and select optimal solution from multiple local minima. To implement DS-MIL, an attention module is proposed so that more context information can be captured by feature maps and more valuable proposals can be collected during training. With proposal candidates, a selection module is proposed to select informative instances for object detector. Experimental results on commonly used benchmarks show that our proposed DS-MIL approach can consistently improve the baselines, reporting state-of-the-art performance.
Multimedia event detection is the task of detecting a specific event of interest in an user-generated video on websites. The most fundamental challenge facing this task lies in the enormously varying quality of the video as well as the high-level semantic abstraction of event inherently. In this paper, we decompose the video into several segments and intuitively model the task of complex event detection as a multiple instance learning problem by representing each video as a "bag" of segments in which each segment is referred to as an instance. Instead of treating the instances equally, we associate each instance with a reliability variable to indicate its importance and then select reliable instances for training. To measure the reliability of the varying instances precisely, we propose a visual-semantic guided loss by exploiting low-level feature from visual information together with instance-event similarity based high-level semantic feature. Motivated by curriculum learning, we introduce a negative elastic-net regularization term to start training the classifier with instances of high reliability and gradually taking the instances with relatively low reliability into consideration. An alternative optimization algorithm is developed to solve the proposed challenging non-convex non-smooth problem. Experimental results on standard datasets, i.e., TRECVID MEDTest 2013 and TRECVID MEDTest 2014, demonstrate the effectiveness and superiority of the proposed method to the baseline algorithms.
Weakly supervised object detection (WSOD) has attracted more and more attention since it only uses image-level labels and can save huge annotation costs. Most of the WSOD methods use Multiple Instance Learning (MIL) as their basic framework, which regard it as an instance classification problem. However, these methods based on MIL tends to converge only on the most discriminate regions of different instances, rather than their corresponding complete regions, that is, insufficient integrity. Inspired by the habit of observing things by the human, we propose a new method by comparing the initial proposals and the extension ones to optimize those initial proposals. Specifically, we propose one new strategy for WSOD by involving contrastive proposal extension (CPE), which consists of multiple directional contrastive proposal extensions (D-CPE), and each D-CPE contains encoders based on LSTM network and corresponding decoders. Firstly, the boundary of initial proposals in MIL is extended to different positions according to well-designed sequential order. Then, CPE compares the extended proposal and the initial proposal by extracting the feature semantics of them using the encoders, and calculates the integrity of the initial proposal to optimize the score of the initial proposal. These contrastive contextual semantics will guide the basic WSOD to suppress bad proposals and improve the scores of good ones. In addition, a simple two-stream network is designed as the decoder to constrain the temporal coding of LSTM and improve the performance of WSOD further. Experiments on PASCAL VOC 2007, VOC 2012 and MS-COCO datasets show that our method has achieved the state-of-the-art results.
Citrus juices and fruits are commodities with great economic potential in the international market, but productivity losses caused by mites and other pests are still far from being a good mark. Despite the integrated pest mechanical aspect, only a few works on automatic classification have handled images with orange mite characteristics, which means tiny and noisy regions of interest. On the computational side, attention-based models have gained prominence in deep learning research, and, along with weakly supervised learning algorithms, they have improved tasks performed with some label restrictions. In agronomic research of pests and diseases, these techniques can improve classification performance while pointing out the location of mites and insects without specific labels, reducing deep learning development costs related to generating bounding boxes. In this context, this work proposes an attention-based activation map approach developed to improve the classification of tiny regions called Two-Weighted Activation Mapping, which also produces locations using feature map scores learned from class labels. We apply our method in a two-stage network process called Attention-based Multiple Instance Learning Guided by Saliency Maps. We analyze the proposed approach in two challenging datasets, the Citrus Pest Benchmark, which was captured directly in the field using magnifying glasses, and the Insect Pest, a large pest image benchmark. In addition, we evaluate and compare our models with weakly supervised methods, such as Attention-based Deep MIL and WILDCAT. The results show that our classifier is superior to literature methods that use tiny regions in their classification tasks, surpassing them in all scenarios by at least 16 percentage points. Moreover, our approach infers bounding box locations for salient insects, even training without any location labels.
The cup-to-disc ratio (CDR) is one of the most significant indicator for glaucoma diagnosis. Different from the use of costly fully supervised learning formulation with pixel-wise annotations in the literature, this study investigates the feasibility of accurate CDR measurement in fundus images using only tight bounding box supervision. For this purpose, we develop a two-task network named as CDRNet for accurate CDR measurement, one for weakly supervised image segmentation, and the other for bounding-box regression. The weakly supervised image segmentation task is implemented based on generalized multiple instance learning formulation and smooth maximum approximation, and the bounding-box regression task outputs class-specific bounding box prediction in a single scale at the original image resolution. To get accurate bounding box prediction, a class-specific bounding-box normalizer and an expected intersection-over-union are proposed. In the experiments, the proposed approach was evaluated by a testing set with 1200 images using CDR error and $F_1$ score for CDR measurement and dice coefficient for image segmentation. A grader study was conducted to compare the performance of the proposed approach with those of individual graders. The experimental results indicate that the proposed approach outperforms the state-of-the-art performance obtained from the fully supervised image segmentation (FSIS) approach using pixel-wise annotation for CDR measurement. Its performance is also better than those of individual graders. In addition, the proposed approach gets performance close to the state-of-the-art obtained from FSIS and the performance of individual graders for optic cup and disc segmentation. The codes are available at \url{https://github.com/wangjuan313/CDRNet}.
This paper presents a weakly supervised image segmentation method that adopts tight bounding box annotations. It proposes generalized multiple instance learning (MIL) and smooth maximum approximation to integrate the bounding box tightness prior into the deep neural network in an end-to-end manner. In generalized MIL, positive bags are defined by parallel crossing lines with a set of different angles, and negative bags are defined as individual pixels outside of any bounding boxes. Two variants of smooth maximum approximation, i.e., $\alpha$-softmax function and $\alpha$-quasimax function, are exploited to conquer the numeral instability introduced by maximum function of bag prediction. The proposed approach was evaluated on two pubic medical datasets using Dice coefficient. The results demonstrate that it outperforms the state-of-the-art methods. The codes are available at \url{https://github.com/wangjuan313/wsis-boundingbox}.
Annotating cancerous regions in whole-slide images (WSIs) of pathology samples plays a critical role in clinical diagnosis, biomedical research, and machine learning algorithms development. However, generating exhaustive and accurate annotations is labor-intensive, challenging, and costly. Drawing only coarse and approximate annotations is a much easier task, less costly, and it alleviates pathologists' workload. In this paper, we study the problem of refining these approximate annotations in digital pathology to obtain more accurate ones. Some previous works have explored obtaining machine learning models from these inaccurate annotations, but few of them tackle the refinement problem where the mislabeled regions should be explicitly identified and corrected, and all of them require a -- often very large -- number of training samples. We present a method, named Label Cleaning Multiple Instance Learning (LC-MIL), to refine coarse annotations on a single WSI without the need of external training data. Patches cropped from a WSI with inaccurate labels are processed jointly within a multiple instance learning framework, mitigating their impact on the predictive model and refining the segmentation. Our experiments on a heterogeneous WSI set with breast cancer lymph node metastasis, liver cancer, and colorectal cancer samples show that LC-MIL significantly refines the coarse annotations, outperforming state-of-the-art alternatives, even while learning from a single slide. Moreover, we demonstrate how real annotations drawn by pathologists can be efficiently refined and improved by the proposed approach. All these results demonstrate that LC-MIL is a promising, light-weight tool to provide fine-grained annotations from coarsely annotated pathology sets.
Pulmonary embolism (PE) represents a thrombus ("blood clot"), usually originating from a lower extremity vein, that travels to the blood vessels in the lung, causing vascular obstruction and in some patients, death. This disorder is commonly diagnosed using CT pulmonary angiography (CTPA). Deep learning holds great promise for the computer-aided CTPA diagnosis (CAD) of PE. However, numerous competing methods for a given task in the deep learning literature exist, causing great confusion regarding the development of a CAD PE system. To address this confusion, we present a comprehensive analysis of competing deep learning methods applicable to PE diagnosis using CTPA at the both image and exam levels. At the image level, we compare convolutional neural networks (CNNs) with vision transformers, and contrast self-supervised learning (SSL) with supervised learning, followed by an evaluation of transfer learning compared with training from scratch. At the exam level, we focus on comparing conventional classification (CC) with multiple instance learning (MIL). Our extensive experiments consistently show: (1) transfer learning consistently boosts performance despite differences between natural images and CT scans, (2) transfer learning with SSL surpasses its supervised counterparts; (3) CNNs outperform vision transformers, which otherwise show satisfactory performance; and (4) CC is, surprisingly, superior to MIL. Compared with the state of the art, our optimal approach provides an AUC gain of 0.2\% and 1.05\% for image-level and exam-level, respectively.
We present WeakSTIL, an interpretable two-stage weak label deep learning pipeline for scoring the percentage of stromal tumor infiltrating lymphocytes (sTIL%) in H&E-stained whole-slide images (WSIs) of breast cancer tissue. The sTIL% score is a prognostic and predictive biomarker for many solid tumor types. However, due to the high labeling efforts and high intra- and interobserver variability within and between expert annotators, this biomarker is currently not used in routine clinical decision making. WeakSTIL compresses tiles of a WSI using a feature extractor pre-trained with self-supervised learning on unlabeled histopathology data and learns to predict precise sTIL% scores for each tile in the tumor bed by using a multiple instance learning regressor that only requires a weak WSI-level label. By requiring only a weak label, we overcome the large annotation efforts required to train currently existing TIL detection methods. We show that WeakSTIL is at least as good as other TIL detection methods when predicting the WSI-level sTIL% score, reaching a coefficient of determination of $0.45\pm0.15$ when compared to scores generated by an expert pathologist, and an AUC of $0.89\pm0.05$ when treating it as the clinically interesting sTIL-high vs sTIL-low classification task. Additionally, we show that the intermediate tile-level predictions of WeakSTIL are highly interpretable, which suggests that WeakSTIL pays attention to latent features related to the number of TILs and the tissue type. In the future, WeakSTIL may be used to provide consistent and interpretable sTIL% predictions to stratify breast cancer patients into targeted therapy arms.
Radiomics is an active area of research focusing on high throughput feature extraction from medical images with a wide array of applications in clinical practice, such as clinical decision support in oncology. However, noise in low dose computed tomography (CT) scans can impair the accurate extraction of radiomic features. In this article, we investigate the possibility of using deep learning generative models to improve the performance of radiomics from low dose CTs. We used two datasets of low dose CT scans -NSCLC Radiogenomics and LIDC-IDRI - as test datasets for two tasks - pre-treatment survival prediction and lung cancer diagnosis. We used encoder-decoder networks and conditional generative adversarial networks (CGANs) trained in a previous study as generative models to transform low dose CT images into full dose CT images. Radiomic features extracted from the original and improved CT scans were used to build two classifiers - a support vector machine (SVM) and a deep attention based multiple instance learning model - for survival prediction and lung cancer diagnosis respectively. Finally, we compared the performance of the models derived from the original and improved CT scans. Encoder-decoder networks and CGANs improved the area under the curve (AUC) of survival prediction from 0.52 to 0.57 (p-value<0.01). On the other hand, Encoder-decoder network and CGAN can improve the AUC of lung cancer diagnosis from 0.84 to 0.88 and 0.89 respectively (p-value<0.01). Moreover, there are no statistically significant differences in improving AUC by using encoder-decoder network and CGAN (p-value=0.34) when networks trained at 75 and 100 epochs. Generative models can improve the performance of low dose CT-based radiomics in different tasks. Hence, denoising using generative models seems to be a necessary pre-processing step for calculating radiomic features from low dose CTs.
Multiple Instance Learning (MIL) gains popularity in many real-life machine learning applications due to its weakly supervised nature. However, the corresponding effort on explaining MIL lags behind, and it is usually limited to presenting instances of a bag that are crucial for a particular prediction. In this paper, we fill this gap by introducing ProtoMIL, a novel self-explainable MIL method inspired by the case-based reasoning process that operates on visual prototypes. Thanks to incorporating prototypical features into objects description, ProtoMIL unprecedentedly joins the model accuracy and fine-grained interpretability, which we present with the experiments on five recognized MIL datasets.
Intent detection and slot filling are two main tasks in natural language understanding (NLU) for identifying users' needs from their utterances. These two tasks are highly related and often trained jointly. However, most previous works assume that each utterance only corresponds to one intent, ignoring the fact that a user utterance in many cases could include multiple intents. In this paper, we propose a novel Self-Distillation Joint NLU model (SDJN) for multi-intent NLU. First, we formulate multiple intent detection as a weakly supervised problem and approach with multiple instance learning (MIL). Then, we design an auxiliary loop via self-distillation with three orderly arranged decoders: Initial Slot Decoder, MIL Intent Decoder, and Final Slot Decoder. The output of each decoder will serve as auxiliary information for the next decoder. With the auxiliary knowledge provided by the MIL Intent Decoder, we set Final Slot Decoder as the teacher model that imparts knowledge back to Initial Slot Decoder to complete the loop. The auxiliary loop enables intents and slots to guide mutually in-depth and further boost the overall NLU performance. Experimental results on two public multi-intent datasets indicate that our model achieves strong performance compared to others.
As a challenging task of high-level video understanding, weakly supervised temporal action localization has been attracting increasing attention. With only video annotations, most existing methods seek to handle this task with a localization-by-classification framework, which generally adopts a selector to select snippets of high probabilities of actions or namely the foreground. Nevertheless, the existing foreground selection strategies have a major limitation of only considering the unilateral relation from foreground to actions, which cannot guarantee the foreground-action consistency. In this paper, we present a framework named FAC-Net based on the I3D backbone, on which three branches are appended, named class-wise foreground classification branch, class-agnostic attention branch and multiple instance learning branch. First, our class-wise foreground classification branch regularizes the relation between actions and foreground to maximize the foreground-background separation. Besides, the class-agnostic attention branch and multiple instance learning branch are adopted to regularize the foreground-action consistency and help to learn a meaningful foreground classifier. Within each branch, we introduce a hybrid attention mechanism, which calculates multiple attention scores for each snippet, to focus on both discriminative and less-discriminative snippets to capture the full action boundaries. Experimental results on THUMOS14 and ActivityNet1.3 demonstrate the state-of-the-art performance of our method. Our code is available at https://github.com/LeonHLJ/FAC-Net.
Due to domain shift, a large performance drop is usually observed when a trained crowd counting model is deployed in the wild. While existing domain-adaptive crowd counting methods achieve promising results, they typically regard each crowd image as a whole and reduce domain discrepancies in a holistic manner, thus limiting further improvement of domain adaptation performance. To this end, we propose to untangle \emph{domain-invariant} crowd and \emph{domain-specific} background from crowd images and design a fine-grained domain adaption method for crowd counting. Specifically, to disentangle crowd from background, we propose to learn crowd segmentation from point-level crowd counting annotations in a weakly-supervised manner. Based on the derived segmentation, we design a crowd-aware domain adaptation mechanism consisting of two crowd-aware adaptation modules, i.e., Crowd Region Transfer (CRT) and Crowd Density Alignment (CDA). The CRT module is designed to guide crowd features transfer across domains beyond background distractions. The CDA module dedicates to regularising target-domain crowd density generation by its own crowd density distribution. Our method outperforms previous approaches consistently in the widely-used adaptation scenarios.
Deep learning based analysis of histopathology images shows promise in advancing the understanding of tumor progression, tumor micro-environment, and their underpinning biological processes. So far, these approaches have focused on extracting information associated with annotations. In this work, we ask how much information can be learned from the tissue architecture itself. We present an adversarial learning model to extract feature representations of cancer tissue, without the need for manual annotations. We show that these representations are able to identify a variety of morphological characteristics across three cancer types: Breast, colon, and lung. This is supported by 1) the separation of morphologic characteristics in the latent space; 2) the ability to classify tissue type with logistic regression using latent representations, with an AUC of 0.97 and 85% accuracy, comparable to supervised deep models; 3) the ability to predict the presence of tumor in Whole Slide Images (WSIs) using multiple instance learning (MIL), achieving an AUC of 0.98 and 94% accuracy. Our results show that our model captures distinct phenotypic characteristics of real tissue samples, paving the way for further understanding of tumor progression and tumor micro-environment, and ultimately refining histopathological classification for diagnosis and treatment. The code and pretrained models are available at: https://github.com/AdalbertoCq/Adversarial-learning-of-cancer-tissue-representations
Existing anomaly detection paradigms overwhelmingly focus on training detection models using exclusively normal data or unlabeled data (mostly normal samples). One notorious issue with these approaches is that they are weak in discriminating anomalies from normal samples due to the lack of the knowledge about the anomalies. Here, we study the problem of few-shot anomaly detection, in which we aim at using a few labeled anomaly examples to train sample-efficient discriminative detection models. To address this problem, we introduce a novel weakly-supervised anomaly detection framework to train detection models without assuming the examples illustrating all possible classes of anomaly. Specifically, the proposed approach learns discriminative normality (regularity) by leveraging the labeled anomalies and a prior probability to enforce expressive representations of normality and unbounded deviated representations of abnormality. This is achieved by an end-to-end optimization of anomaly scores with a neural deviation learning, in which the anomaly scores of normal samples are imposed to approximate scalar scores drawn from the prior while that of anomaly examples is enforced to have statistically significant deviations from these sampled scores in the upper tail. Furthermore, our model is optimized to learn fine-grained normality and abnormality by top-K multiple-instance-learning-based feature subspace deviation learning, allowing more generalized representations. Comprehensive experiments on nine real-world image anomaly detection benchmarks show that our model is substantially more sample-efficient and robust, and performs significantly better than state-of-the-art competing methods in both closed-set and open-set settings. Our model can also offer explanation capability as a result of its prior-driven anomaly score learning. Code and datasets are available at: https://git.io/DevNet.