An important task at the onset of a laparoscopic cholecystectomy (LC) operation is the inspection of gallbladder (GB) to evaluate the thickness of its wall, presence of inflammation and extent of fat. Difficulty in visualization of the GB wall vessels may be due to the previous factors, potentially as a result of chronic inflammation or other diseases. In this paper we propose a multiple-instance learning (MIL) technique for assessment of the GB wall vascularity via computer-vision analysis of images from LC operations. The bags correspond to a labeled (low vs. high) vascularity dataset of 181 GB images, from 53 operations. The instances correspond to unlabeled patches extracted from these images. Each patch is represented by a vector with color, texture and statistical features. We compare various state-of-the-art MIL and single-instance learning approaches, as well as a proposed MIL technique based on variational Bayesian inference. The methods were compared for two experimental tasks: image-based and video-based (i.e. patient-based) classification. The proposed approach presents the best performance with accuracy 92.1% and 90.3% for the first and second task, respectively. A significant advantage of the proposed technique is that it does not require the time-consuming task of manual labelling the instances.
We propose a Deep learning-based weak label learning method for analyzing whole slide images (WSIs) of Hematoxylin and Eosin (H&E) stained tumor tissue not requiring pixel-level or tile-level annotations using Self-supervised pre-training and heterogeneity-aware deep Multiple Instance LEarning (DeepSMILE). We apply DeepSMILE to the task of Homologous recombination deficiency (HRD) and microsatellite instability (MSI) prediction. We utilize contrastive self-supervised learning to pre-train a feature extractor on histopathology tiles of cancer tissue. Additionally, we use variability-aware deep multiple instance learning to learn the tile feature aggregation function while modeling tumor heterogeneity. For MSI prediction in a tumor-annotated and color normalized subset of TCGA-CRC (n=360 patients), contrastive self-supervised learning improves the tile supervision baseline from 0.77 to 0.87 AUROC, on par with our proposed DeepSMILE method. On TCGA-BC (n=1041 patients) without any manual annotations, DeepSMILE improves HRD classification performance from 0.77 to 0.81 AUROC compared to tile supervision with either a self-supervised or ImageNet pre-trained feature extractor. Our proposed methods reach the baseline performance using only 40% of the labeled data on both datasets. These improvements suggest we can use standard self-supervised learning techniques combined with multiple instance learning in the histopathology domain to improve genomic label classification performance with fewer labeled data.
Whole body magnetic resonance imaging (WB-MRI) is the recommended modality for diagnosis of multiple myeloma (MM). WB-MRI is used to detect sites of disease across the entire skeletal system, but it requires significant expertise and is time-consuming to report due to the great number of images. To aid radiological reading, we propose an auxiliary task-based multiple instance learning approach (ATMIL) for MM classification with the ability to localize sites of disease. This approach is appealing as it only requires patient-level annotations where an attention mechanism is used to identify local regions with active disease. We borrow ideas from multi-task learning and define an auxiliary task with adaptive reweighting to support and improve learning efficiency in the presence of data scarcity. We validate our approach on both synthetic and real multi-center clinical data. We show that the MIL attention module provides a mechanism to localize bone regions while the adaptive reweighting of the auxiliary task considerably improves the performance.
In the present study, we propose a novel case-based similar image retrieval (SIR) method for hematoxylin and eosin (H&E)-stained histopathological images of malignant lymphoma. When a whole slide image (WSI) is used as an input query, it is desirable to be able to retrieve similar cases by focusing on image patches in pathologically important regions such as tumor cells. To address this problem, we employ attention-based multiple instance learning, which enables us to focus on tumor-specific regions when the similarity between cases is computed. Moreover, we employ contrastive distance metric learning to incorporate immunohistochemical (IHC) staining patterns as useful supervised information for defining appropriate similarity between heterogeneous malignant lymphoma cases. In the experiment with 249 malignant lymphoma patients, we confirmed that the proposed method exhibited higher evaluation measures than the baseline case-based SIR methods. Furthermore, the subjective evaluation by pathologists revealed that our similarity measure using IHC staining patterns is appropriate for representing the similarity of H&E-stained tissue images for malignant lymphoma.
Temporal language grounding (TLG) is a fundamental and challenging problem for vision and language understanding. Existing methods mainly focus on fully supervised setting with temporal boundary labels for training, which, however, suffers expensive cost of annotation. In this work, we are dedicated to weakly supervised TLG, where multiple description sentences are given to an untrimmed video without temporal boundary labels. In this task, it is critical to learn a strong cross-modal semantic alignment between sentence semantics and visual content. To this end, we introduce a novel weakly supervised temporal adjacent network (WSTAN) for temporal language grounding. Specifically, WSTAN learns cross-modal semantic alignment by exploiting temporal adjacent network in a multiple instance learning (MIL) paradigm, with a whole description paragraph as input. Moreover, we integrate a complementary branch into the framework, which explicitly refines the predictions with pseudo supervision from the MIL stage. An additional self-discriminating loss is devised on both the MIL branch and the complementary branch, aiming to enhance semantic discrimination by self-supervising. Extensive experiments are conducted on three widely used benchmark datasets, \emph{i.e.}, ActivityNet-Captions, Charades-STA, and DiDeMo, and the results demonstrate the effectiveness of our approach.
This document summarizes different visual explanations methods such as CAM, Grad-CAM, Localization using Multiple Instance Learning - Saliency-based methods, Saliency-driven Class-Impressions, Muting pixels in input image - Adversarial methods and Activation visualization, Convolution filter visualization - Feature-based methods. We have also shown the results produced by different methods and a comparison between CAM, GradCAM, and Guided Backpropagation.
Multiple instance learning (MIL) is a powerful tool to solve the weakly supervised classification in whole slide image (WSI) based pathology diagnosis. However, the current MIL methods are usually based on independent and identical distribution hypothesis, thus neglect the correlation among different instances. To address this problem, we proposed a new framework, called correlated MIL, and provided a proof for convergence. Based on this framework, we devised a Transformer based MIL (TransMIL), which explored both morphological and spatial information. The proposed TransMIL can effectively deal with unbalanced/balanced and binary/multiple classification with great visualization and interpretability. We conducted various experiments for three different computational pathology problems and achieved better performance and faster convergence compared with state-of-the-art methods. The test AUC for the binary tumor classification can be up to 93.09% over CAMELYON16 dataset. And the AUC over the cancer subtypes classification can be up to 96.03% and 98.82% over TCGA-NSCLC dataset and TCGA-RCC dataset, respectively. Implementation is available at: https://github.com/szc19990412/TransMIL.
Pancreatic ductal adenocarcinoma (PDAC) is the third most common cause of cancer death in the United States. Predicting tumors like PDACs (including both classification and segmentation) from medical images by deep learning is becoming a growing trend, but usually a large number of annotated data are required for training, which is very labor-intensive and time-consuming. In this paper, we consider a partially supervised setting, where cheap image-level annotations are provided for all the training data, and the costly per-voxel annotations are only available for a subset of them. We propose an Inductive Attention Guidance Network (IAG-Net) to jointly learn a global image-level classifier for normal/PDAC classification and a local voxel-level classifier for semi-supervised PDAC segmentation. We instantiate both the global and the local classifiers by multiple instance learning (MIL), where the attention guidance, indicating roughly where the PDAC regions are, is the key to bridging them: For global MIL based normal/PDAC classification, attention serves as a weight for each instance (voxel) during MIL pooling, which eliminates the distraction from the background; For local MIL based semi-supervised PDAC segmentation, the attention guidance is inductive, which not only provides bag-level pseudo-labels to training data without per-voxel annotations for MIL training, but also acts as a proxy of an instance-level classifier. Experimental results show that our IAG-Net boosts PDAC segmentation accuracy by more than 5% compared with the state-of-the-arts.
Cutting plane methods play a significant role in modern solvers for tackling mixed-integer programming (MIP) problems. Proper selection of cuts would remove infeasible solutions in the early stage, thus largely reducing the computational burden without hurting the solution accuracy. However, the major cut selection approaches heavily rely on heuristics, which strongly depend on the specific problem at hand and thus limit their generalization capability. In this paper, we propose a data-driven and generalizable cut selection approach, named Cut Ranking, in the settings of multiple instance learning. To measure the quality of the candidate cuts, a scoring function, which takes the instance-specific cut features as inputs, is trained and applied in cut ranking and selection. In order to evaluate our method, we conduct extensive experiments on both synthetic datasets and real-world datasets. Compared with commonly used heuristics for cut selection, the learning-based policy has shown to be more effective, and is capable of generalizing over multiple problems with different properties. Cut Ranking has been deployed in an industrial solver for large-scale MIPs. In the online A/B testing of the product planning problems with more than $10^7$ variables and constraints daily, Cut Ranking has achieved the average speedup ratio of 12.42% over the production solver without any accuracy loss of solution.
We introduce WyPR, a Weakly-supervised framework for Point cloud Recognition, requiring only scene-level class tags as supervision. WyPR jointly addresses three core 3D recognition tasks: point-level semantic segmentation, 3D proposal generation, and 3D object detection, coupling their predictions through self and cross-task consistency losses. We show that in conjunction with standard multiple-instance learning objectives, WyPR can detect and segment objects in point cloud data without access to any spatial labels at training time. We demonstrate its efficacy using the ScanNet and S3DIS datasets, outperforming prior state of the art on weakly-supervised segmentation by more than 6% mIoU. In addition, we set up the first benchmark for weakly-supervised 3D object detection on both datasets, where WyPR outperforms standard approaches and establishes strong baselines for future work.
Drug repurposing can accelerate the identification of effective compounds for clinical use against SARS-CoV-2, with the advantage of pre-existing clinical safety data and an established supply chain. RNA viruses such as SARS-CoV-2 manipulate cellular pathways and induce reorganization of subcellular structures to support their life cycle. These morphological changes can be quantified using bioimaging techniques. In this work, we developed DEEMD: a computational pipeline using deep neural network models within a multiple instance learning framework, to identify putative treatments effective against SARS-CoV-2 based on morphological analysis of the publicly available RxRx19a dataset. This dataset consists of fluorescence microscopy images of SARS-CoV-2 non-infected cells and infected cells, with and without drug treatment. DEEMD first extracts discriminative morphological features to generate cell morphological profiles from the non-infected and infected cells. These morphological profiles are then used in a statistical model to estimate the applied treatment efficacy on infected cells based on similarities to non-infected cells. DEEMD is capable of localizing infected cells via weak supervision without any expensive pixel-level annotations. DEEMD identifies known SARS-CoV-2 inhibitors, such as Remdesivir and Aloxistatin, supporting the validity of our approach. DEEMD can be explored for use on other emerging viruses and datasets to rapidly identify candidate antiviral treatments in the future}. Our implementation is available online at https://www.github.com/Sadegh-Saberian/DEEMD
Multiple instance learning (MIL) is the preferred approach for whole slide image classification. However, most MIL approaches do not exploit the interdependencies of tiles extracted from a whole slide image, which could provide valuable cues for classification. This paper presents a novel MIL approach that exploits the spatial relationship of tiles for classifying whole slide images. To do so, a sparse map is built from tiles embeddings, and is then classified by a sparse-input CNN. It obtained state-of-the-art performance over popular MIL approaches on the classification of cancer subtype involving 10000 whole slide images. Our results suggest that the proposed approach might (i) improve the representation learning of instances and (ii) exploit the context of instance embeddings to enhance the classification performance. The code of this work is open-source at {github censored for review}.
Multiple-instance learning is a subset of weakly supervised learning where labels are applied to sets of instances rather than the instances themselves. Under the standard assumption, a set is positive only there is if at least one instance in the set which is positive. This paper introduces a series of multiple-instance learning benchmarks generated from MNIST, Fashion-MNIST, and CIFAR10. These benchmarks test the standard, presence, absence, and complex assumptions and provide a framework for future benchmarks to be distributed. I implement and evaluate several multiple-instance learning techniques against the benchmarks. Further, I evaluate the Noisy-And method with label noise and find mixed results with different datasets. The models are implemented in TensorFlow 2.4.1 and are available on GitHub. The benchmarks are available from PyPi as mil-benchmarks and on GitHub.
Intracranial hemorrhage is a life-threatening disease, which requires fast medical intervention. Owing to the duration of data annotation, head CT images are usually available only with slice-level labeling. This paper presents a weakly supervised method of precise hemorrhage localization in axial slices using only position-free labels, which is based on multiple instance learning. An algorithm is introduced that generates hemorrhage likelihood maps and finds the coordinates of bleeding. The Dice coefficient of 58.08 % is achieved on data from a publicly available dataset.
Early diagnosis of lung cancer is a key intervention for the treatment of lung cancer computer aided diagnosis (CAD) can play a crucial role. However, most published CAD methods treat lung cancer diagnosis as a lung nodule classification problem, which does not reflect clinical practice, where clinicians diagnose a patient based on a set of images of nodules, instead of one specific nodule. Besides, the low interpretability of the output provided by these methods presents an important barrier for their adoption. In this article, we treat lung cancer diagnosis as a multiple instance learning (MIL) problem in order to better reflect the diagnosis process in the clinical setting and for the higher interpretability of the output. We chose radiomics as the source of input features and deep attention-based MIL as the classification algorithm.The attention mechanism provides higher interpretability by estimating the importance of each instance in the set for the final diagnosis.In order to improve the model's performance in a small imbalanced dataset, we introduce a new bag simulation method for MIL.The results show that our method can achieve a mean accuracy of 0.807 with a standard error of the mean (SEM) of 0.069, a recall of 0.870 (SEM 0.061), a positive predictive value of 0.928 (SEM 0.078), a negative predictive value of 0.591 (SEM 0.155) and an area under the curve (AUC) of 0.842 (SEM 0.074), outperforming other MIL methods.Additional experiments show that the proposed oversampling strategy significantly improves the model's performance. In addition, our experiments show that our method provides an indication of the importance of each nodule in determining the diagnosis, which combined with the well-defined radiomic features, make the results more interpretable and acceptable for doctors and patients.
Melanoma is an aggressive neoplasm responsible for the majority of deaths from skin cancer. Specifically, spitzoid melanocytic tumors are one of the most challenging melanocytic lesions due to their ambiguous morphological features. The gold standard for its diagnosis and prognosis is the analysis of skin biopsies. In this process, dermatopathologists visualize skin histology slides under a microscope, in a high time-consuming and subjective task. In the last years, computer-aided diagnosis (CAD) systems have emerged as a promising tool that could support pathologists in daily clinical practice. Nevertheless, no automatic CAD systems have yet been proposed for the analysis of spitzoid lesions. Regarding common melanoma, no proposed system allows both the selection of the tumoral region and the prediction of the diagnosis as benign or malignant. Motivated by this, we propose a novel end-to-end weakly-supervised deep learning model, based on inductive transfer learning with an improved convolutional neural network (CNN) to refine the embedding features of the latent space. The framework is composed of a source model in charge of finding the tumor patch-level patterns, and a target model focuses on the specific diagnosis of a biopsy. The latter retrains the backbone of the source model through a multiple instance learning workflow to obtain the biopsy-level scoring. To evaluate the performance of the proposed methods, we perform extensive experiments on a private skin database with spitzoid lesions. Test results reach an accuracy of 0.9231 and 0.80 for the source and the target models, respectively. Besides, the heat map findings are directly in line with the clinicians' medical decision and even highlight, in some cases, patterns of interest that were overlooked by the pathologist due to the huge workload.
Anomaly detection in surveillance videos is a challenging task due to the diversity of anomalous video content and duration. In this paper, we consider video anomaly detection as a regression problem with respect to anomaly scores of video clips under weak supervision. Hence, we propose an anomaly detection framework, called Anomaly Regression Net (AR-Net), which only requires video-level labels in training stage. Further, to learn discriminative features for anomaly detection, we design a dynamic multiple-instance learning loss and a center loss for the proposed AR-Net. The former is used to enlarge the inter-class distance between anomalous and normal instances, while the latter is proposed to reduce the intra-class distance of normal instances. Comprehensive experiments are performed on a challenging benchmark: ShanghaiTech. Our method yields a new state-of-the-art result for video anomaly detection on ShanghaiTech dataset
Multiple instance learning (MIL) has become the standard learning paradigm for distantly supervised relation extraction (DSRE). However, due to relation extraction being performed at bag level, MIL has significant hardware requirements for training when coupled with large sentence encoders such as deep transformer neural networks. In this paper, we propose a novel sampling method for DSRE that relaxes these hardware requirements. In the proposed method, we limit the number of sentences in a batch by randomly sampling sentences from the bags in the batch. However, this comes at the cost of losing valid sentences from bags. To alleviate the issues caused by random sampling, we use an ensemble of trained models for prediction. We demonstrate the effectiveness of our approach by using our proposed learning setting to fine-tuning BERT on the widely NYT dataset. Our approach significantly outperforms previous state-of-the-art methods in terms of AUC and P@N metrics.
As modern complex neural networks keep breaking records and solving harder problems, their predictions also become less and less intelligible. The current lack of interpretability often undermines the deployment of accurate machine learning tools in sensitive settings. In this work, we present a model-agnostic explanation method for image classification based on a hierarchical extension of Shapley coefficients--Hierarchical Shap (h-Shap)--that resolves some of the limitations of current approaches. Unlike other Shapley-based explanation methods, h-Shap is scalable and can be computed without the need of approximation. Under certain distributional assumptions, such as those common in multiple instance learning, h-Shap retrieves the exact Shapley coefficients with an exponential improvement in computational complexity. We compare our hierarchical approach with popular Shapley-based and non-Shapley-based methods on a synthetic dataset, a medical imaging scenario, and a general computer vision problem, showing that h-Shap outperforms the state of the art in both accuracy and runtime. Code and experiments are made publicly available.
In this paper, we present a novel approach to the audio-visual video parsing (AVVP) task that demarcates events from a video separately for audio and visual modalities. The proposed parsing approach simultaneously detects the temporal boundaries in terms of start and end times of such events. We show how AVVP can benefit from the following techniques geared towards effective cross-modal learning: (i) adversarial training and skip connections (ii) global context aware attention and, (iii) self-supervised pretraining using an audio-video grounding objective to obtain cross-modal audio-video representations. We present extensive experimental evaluations on the Look, Listen, and Parse (LLP) dataset and show that we outperform the state-of-the-art Hybrid Attention Network (HAN) on all five metrics proposed for AVVP. We also present several ablations to validate the effect of pretraining, global attention and adversarial training.