Metagenomic studies have increasingly utilized sequencing technologies in order to analyze DNA fragments found in environmental samples.One important step in this analysis is the taxonomic classification of the DNA fragments. Conventional read classification methods require large databases and vast amounts of memory to run, with recent deep learning methods suffering from very large model sizes. We therefore aim to develop a more memory-efficient technique for taxonomic classification. A task of particular interest is abundance estimation in metagenomic samples. Current attempts rely on classifying single DNA reads independently from each other and are therefore agnostic to co-occurence patterns between taxa. In this work, we also attempt to take these patterns into account. We develop a novel memory-efficient read classification technique, combining deep learning and locality-sensitive hashing. We show that this approach outperforms conventional mapping-based and other deep learning methods for single-read taxonomic classification when restricting all methods to a fixed memory footprint. Moreover, we formulate the task of abundance estimation as a Multiple Instance Learning (MIL) problem and we extend current deep learning architectures with two different types of permutation-invariant MIL pooling layers: a) deepsets and b) attention-based pooling. We illustrate that our architectures can exploit the co-occurrence of species in metagenomic read sets and outperform the single-read architectures in predicting the distribution over taxa at higher taxonomic ranks.
LSTMs have a proven track record in analyzing sequential data. But what about unordered instance bags, as found under a Multiple Instance Learning (MIL) setting? While not often used for this, we show LSTMs excell under this setting too. In addition, we show thatLSTMs are capable of indirectly capturing instance-level information us-ing only bag-level annotations. Thus, they can be used to learn instance-level models in a weakly supervised manner. Our empirical evaluation on both simplified (MNIST) and realistic (Lookbook and Histopathology) datasets shows that LSTMs are competitive with or even surpass state-of-the-art methods specially designed for handling specific MIL problems. Moreover, we show that their performance on instance-level prediction is close to that of fully-supervised methods.
We propose a supervised anomaly detection method for data with inexact anomaly labels, where each label, which is assigned to a set of instances, indicates that at least one instance in the set is anomalous. Although many anomaly detection methods have been proposed, they cannot handle inexact anomaly labels. To measure the performance with inexact anomaly labels, we define the inexact AUC, which is our extension of the area under the ROC curve (AUC) for inexact labels. The proposed method trains an anomaly score function so that the smooth approximation of the inexact AUC increases while anomaly scores for non-anomalous instances become low. We model the anomaly score function by a neural network-based unsupervised anomaly detection method, e.g., autoencoders. The proposed method performs well even when only a small number of inexact labels are available by incorporating an unsupervised anomaly detection mechanism with inexact AUC maximization. Using various datasets, we experimentally demonstrate that our proposed method improves the anomaly detection performance with inexact anomaly labels, and outperforms existing unsupervised and supervised anomaly detection and multiple instance learning methods.
In remote sensing, it is often challenging to acquire or collect a large dataset that is accurately labeled. This difficulty is usually due to several issues, including but not limited to the study site's spatial area and accessibility, errors in the global positioning system (GPS), and mixed pixels caused by an image's spatial resolution. We propose an approach, with two variations, that estimates multiple target signatures from training samples with imprecise labels: Multi-Target Multiple Instance Adaptive Cosine Estimator (Multi-Target MI-ACE) and Multi-Target Multiple Instance Spectral Match Filter (Multi-Target MI-SMF). The proposed methods address the problems above by directly considering the multiple-instance, imprecisely labeled dataset. They learn a dictionary of target signatures that optimizes detection against a background using the Adaptive Cosine Estimator (ACE) and Spectral Match Filter (SMF). Experiments were conducted to test the proposed algorithms using a simulated hyperspectral dataset, the MUUFL Gulfport hyperspectral dataset collected over the University of Southern Mississippi-Gulfpark Campus, and the AVIRIS hyperspectral dataset collected over Santa Barbara County, California. Both simulated and real hyperspectral target detection experiments show the proposed algorithms are effective at learning target signatures and performing target detection.
Most popular deep models for action recognition in videos generate independent predictions for short clips, which are then pooled heuristically to assign an action label to the full video segment. As not all frames may characterize the underlying action---many are common across multiple actions---pooling schemes that impose equal importance on all frames might be unfavorable. In an attempt to tackle this problem, we propose discriminative pooling, based on the notion that among the deep features generated on all short clips, there is at least one that characterizes the action. To identify these useful features, we resort to a negative bag consisting of features that are known to be irrelevant, for example, they are sampled either from datasets that are unrelated to our actions of interest or are CNN features produced via random noise as input. With the features from the video as a positive bag and the irrelevant features as the negative bag, we cast an objective to learn a (nonlinear) hyperplane that separates the unknown useful features from the rest in a multiple instance learning formulation within a support vector machine setup. We use the parameters of this separating hyperplane as a descriptor for the full video segment. Since these parameters are directly related to the support vectors in a max-margin framework, they can be treated as a weighted average pooling of the features from the bags, with zero weights given to non-support vectors. Our pooling scheme is end-to-end trainable within a deep learning framework. We report results from experiments on eight computer vision benchmark datasets spanning a variety of video-related tasks and demonstrate state-of-the-art performance across these tasks.
Hip and pelvic fractures are serious injuries with life-threatening complications. However, diagnostic errors of fractures in pelvic X-rays (PXRs) are very common, driving the demand for computer-aided diagnosis (CAD) solutions. A major challenge lies in the fact that fractures are localized patterns that require localized analyses. Unfortunately, the PXRs residing in hospital picture archiving and communication system do not typically specify region of interests. In this paper, we propose a two-stage hip and pelvic fracture detection method that executes localized fracture classification using weakly supervised ROI mining. The first stage uses a large capacity fully-convolutional network, i.e., deep with high levels of abstraction, in a multiple instance learning setting to automatically mine probable true positive and definite hard negative ROIs from the whole PXR in the training data. The second stage trains a smaller capacity model, i.e., shallower and more generalizable, with the mined ROIs to perform localized analyses to classify fractures. During inference, our method detects hip and pelvic fractures in one pass by chaining the probability outputs of the two stages together. We evaluate our method on 4 410 PXRs, reporting an area under the ROC curve value of 0.975, the highest among state-of-the-art fracture detection methods. Moreover, we show that our two-stage approach can perform comparably to human physicians (even outperforming emergency physicians and surgeons), in a preliminary reader study of 23 readers.
Histopathology image analysis plays a critical role in cancer diagnosis and treatment. To automatically segment the cancerous regions, fully supervised segmentation algorithms require labor-intensive and time-consuming labeling at the pixel level. In this research, we propose CAMEL, a weakly supervised learning framework for histopathology image segmentation using only image-level labels. Using multiple instance learning (MIL)-based label enrichment, CAMEL splits the image into latticed instances and automatically generates instance-level labels. After label enrichment, the instance-level labels are further assigned to the corresponding pixels, producing the approximate pixel-level labels and making fully supervised training of segmentation models possible. CAMEL achieves comparable performance with the fully supervised approaches in both instance-level classification and pixel-level segmentation on CAMELYON16 and a colorectal adenoma dataset. Moreover, the generality of the automatic labeling methodology may benefit future weakly supervised learning studies for histopathology image analysis.
Weakly supervised instance labeling using only image-level labels, in lieu of expensive fine-grained pixel annotations, is crucial in several applications including medical image analysis. In contrast to conventional instance segmentation scenarios in computer vision, the problems that we consider are characterized by a small number of training images and non-local patterns that lead to the diagnosis. In this paper, we explore the use of multiple instance learning (MIL) to design an instance label generator under this weakly supervised setting. Motivated by the observation that an MIL model can handle bags of varying sizes, we propose to repurpose an MIL model originally trained for bag-level classification to produce reliable predictions for single instances, i.e., bags of size $1$. To this end, we introduce a novel regularization strategy based on virtual adversarial training for improving MIL training, and subsequently develop a knowledge distillation technique for repurposing the trained MIL model. Using empirical studies on colon cancer and breast cancer detection from histopathological images, we show that the proposed approach produces high-quality instance-level prediction and significantly outperforms state-of-the MIL methods.
In this paper we introduce domain detection as a new natural language processing task. We argue that the ability to detect textual segments which are domain-heavy, i.e., sentences or phrases which are representative of and provide evidence for a given domain could enhance the robustness and portability of various text classification applications. We propose an encoder-detector framework for domain detection and bootstrap classifiers with multiple instance learning (MIL). The model is hierarchically organized and suited to multilabel classification. We demonstrate that despite learning with minimal supervision, our model can be applied to text spans of different granularities, languages, and genres. We also showcase the potential of domain detection for text summarization.
Motivated by our observation that motion information is the key to good anomaly detection performance in video, we propose a temporal augmented network to learn a motion-aware feature. This feature alone can achieve competitive performance with previous state-of-the-art methods, and when combined with them, can achieve significant performance improvements. Furthermore, we incorporate temporal context into the Multiple Instance Learning (MIL) ranking model by using an attention block. The learned attention weights can help to differentiate between anomalous and normal video segments better. With the proposed motion-aware feature and the temporal MIL ranking model, we outperform previous approaches by a large margin on both anomaly detection and anomalous action recognition tasks in the UCF Crime dataset.
Pneumothorax is a critical condition that requires timely communication and immediate action. In order to prevent significant morbidity or patient death, early detection is crucial. For the task of pneumothorax detection, we study the characteristics of three different deep learning techniques: (i) convolutional neural networks, (ii) multiple-instance learning, and (iii) fully convolutional networks. We perform a five-fold cross-validation on a dataset consisting of 1003 chest X-ray images. ROC analysis yields AUCs of 0.96, 0.93, and 0.92 for the three methods, respectively. We review the classification and localization performance of these approaches as well as an ensemble of the three aforementioned techniques.
We focus on grounding (i.e., localizing or linking) referring expressions in images, e.g., ``largest elephant standing behind baby elephant''. This is a general yet challenging vision-language task since it does not only require the localization of objects, but also the multimodal comprehension of context -- visual attributes (e.g., ``largest'', ``baby'') and relationships (e.g., ``behind'') that help to distinguish the referent from other objects, especially those of the same category. Due to the exponential complexity involved in modeling the context associated with multiple image regions, existing work oversimplifies this task to pairwise region modeling by multiple instance learning. In this paper, we propose a variational Bayesian method, called Variational Context, to solve the problem of complex context modeling in referring expression grounding. Specifically, our framework exploits the reciprocal relation between the referent and context, i.e., either of them influences estimation of the posterior distribution of the other, and thereby the search space of context can be greatly reduced. In addition to reciprocity, our framework considers the semantic information of context, i.e., the referring expression can be reproduced based on the estimated context. We also extend the model to unsupervised setting where no annotation for the referent is available. Extensive experiments on various benchmarks show consistent improvement over state-of-the-art methods in both supervised and unsupervised settings.
Deep learning for medical image classification faces three major challenges: 1) the number of annotated medical images for training are usually small; 2) regions of interest (ROIs) are relatively small with unclear boundaries in the whole medical images, and may appear in arbitrary positions across the x,y (and also z in 3D images) dimensions. However often only labels of the whole images are annotated, and localized ROIs are unavailable; and 3) ROIs in medical images often appear in varying sizes (scales). We approach these three challenges with a Multi-Instance Multi-Scale (MIMS) CNN: 1) We propose a multi-scale convolutional layer, which extracts patterns of different receptive fields with a shared set of convolutional kernels, so that scale-invariant patterns are captured by this compact set of kernels. As this layer contains only a small number of parameters, training on small datasets becomes feasible; 2) We propose a "top-k pooling" to aggregate the feature maps in varying scales from multiple spatial dimensions, allowing the model to be trained using weak annotations within the multiple instance learning (MIL) framework. Our method is shown to perform well on three classification tasks involving two 3D and two 2D medical image datasets.
Sound event detection (SED) aims at identifying audio events (audio tagging task) in recordings and then locating them temporally (localization task). This last task ends with the segmentation of the frame-level class predictions, that determines the onsets and offsets of the audio events. Yet, this step is often overlooked in scientific publications. In this paper, we focus on the post-processing algorithms used to identify the audio event boundaries. Different post-processing steps are investigated, through smoothing, thresholding, and optimization. In particular, we evaluate different approaches for temporal segmentation, namely statistic-based and parametric methods. Experiments are carried out on the DCASE 2018 challenge task 4 data. We compared post-processing algorithms on the temporal prediction curves of two models: one based on the challenge's baseline and a Multiple Instance Learning (MIL) model. Results show the crucial impact of the post-processing methods on the final detection score. Statistic-based methods yield a 22.9% event-based F-score on the evaluation set with our MIL model. Moreover, the best results were obtained using class-dependent parametric methods with 32.0% F-score.
Histopathology image analysis can be considered as a Multiple instance learning (MIL) problem, where the whole slide histopathology image (WSI) is regarded as a bag of instances (i.e, patches) and the task is to predict a single class label to the WSI. However, in many real-life applications such as computational pathology, discovering the key instances that trigger the bag label is of great interest because it provides reasons for the decision made by the system. In this paper, we propose a deep convolutional neural network (CNN) model that addresses the primary task of a bag classification on a WSI and also learns to identify the response of each instance to provide interpretable results to the final prediction. We incorporate the attention mechanism into the proposed model to operate the transformation of instances and learn attention weights to allow us to find key patches. To perform a balanced training, we introduce adaptive weighing in each training bag to explicitly adjust the weight distribution in order to concentrate more on the contribution of hard samples. Based on the learned attention weights, we further develop a solution to boost the classification performance by generating the bags with hard negative instances. We conduct extensive experiments on colon and breast cancer histopathology data and show that our framework achieves state-of-the-art performance.
A weakly supervised learning based clustering framework is proposed in this paper. As the core of this framework, we introduce a novel multiple instance learning task based on a bag level label called unique class count ($ucc$), which is the number of unique classes among all instances inside the bag. In this task, no annotations on individual instances inside the bag are needed during training of the models. We mathematically prove that with a perfect $ucc$ classifier, perfect clustering of individual instances inside the bags is possible even when no annotations on individual instances are given during training. We have constructed a neural network based $ucc$ classifier and experimentally shown that the clustering performance of our framework with our weakly supervised $ucc$ classifier is comparable to that of fully supervised learning models where labels for all instances are known. Furthermore, we have tested the applicability of our framework to a real world task of semantic segmentation of breast cancer metastases in histological lymph node sections and shown that the performance of our weakly supervised framework is comparable to the performance of a fully supervised Unet model.
Weakly supervised object detection (WSOD) focuses on training object detector with only image-level annotations, and is challenging due to the gap between the supervision and the objective. Most of existing approaches model WSOD as a multiple instance learning (MIL) problem. However, we observe that the result of MIL based detector is unstable, i.e., the most confident bounding boxes change significantly when using different initializations. We quantitatively demonstrate the instability by introducing a metric to measure it, and empirically analyze the reason of instability. Although the instability seems harmful for detection task, we argue that it can be utilized to improve the performance by fusing the results of differently initialized detectors. To implement this idea, we propose an end-to-end framework with multiple detection branches, and introduce a simple fusion strategy. We further propose an orthogonal initialization method to increase the difference between detection branches. By utilizing the instability, we achieve 52.6% and 48.0% mAP on the challenging PASCAL VOC 2007 and 2012 datasets, which are both the new state-of-the-arts.
Multiple instance learning (MIL) aims to learn the mapping between a bag of instances and the bag-level label. In this paper, we propose a new end-to-end graph neural network (GNN) based algorithm for MIL: we treat each bag as a graph and use GNN to learn the bag embedding, in order to explore the useful structural information among instances in bags. The final graph representation is fed into a classifier for label prediction. Our algorithm is the first attempt to use GNN for MIL. We empirically show that the proposed algorithm achieves the state of the art performance on several popular MIL data sets without losing model interpretability.
Visual-semantic embedding aims to find a shared latent space where related visual and textual instances are close to each other. Most current methods learn injective embedding functions that map an instance to a single point in the shared space. Unfortunately, injective embedding cannot effectively handle polysemous instances with multiple possible meanings; at best, it would find an average representation of different meanings. This hinders its use in real-world scenarios where individual instances and their cross-modal associations are often ambiguous. In this work, we introduce Polysemous Instance Embedding Networks (PIE-Nets) that compute multiple and diverse representations of an instance by combining global context with locally-guided features via multi-head self-attention and residual learning. To learn visual-semantic embedding, we tie-up two PIE-Nets and optimize them jointly in the multiple instance learning framework. Most existing work on cross-modal retrieval focuses on image-text data. Here, we also tackle a more challenging case of video-text retrieval. To facilitate further research in video-text retrieval, we release a new dataset of 50K video-sentence pairs collected from social media, dubbed MRW (my reaction when). We demonstrate our approach on both image-text and video-text retrieval scenarios using MS-COCO, TGIF, and our new MRW dataset.
Histology review is often used as the `gold standard' for disease diagnosis. Computer aided diagnosis tools can potentially help improve current pathology workflows by reducing examination time and interobserver variability. Previous work in cancer grading has focused mainly on classifying pre-defined regions of interest (ROIs), or relied on large amounts of fine-grained labels. In this paper, we propose a two-stage attention-based multiple instance learning model for slide-level cancer grading and weakly-supervised ROI detection and demonstrate its use in prostate cancer. Compared with existing Gleason classification models, our model goes a step further by utilizing visualized saliency maps to select informative tiles for fine-grained grade classification. The model was primarily developed on a large-scale whole slide dataset consisting of 3,521 prostate biopsy slides with only slide-level labels from 718 patients. The model achieved state-of-the-art performance for prostate cancer grading with an accuracy of 85.11\% for classifying benign, low-grade (Gleason grade 3+3 or 3+4), and high-grade (Gleason grade 4+3 or higher) slides on an independent test set.