While high-resolution pathology images lend themselves well to `data hungry' deep learning algorithms, obtaining exhaustive annotations on these images is a major challenge. In this paper, we propose a self-supervised CNN approach to leverage unlabeled data for learning generalizable and domain invariant representations in pathology images. The proposed approach, which we term as Self-Path, is a multi-task learning approach where the main task is tissue classification and pretext tasks are a variety of self-supervised tasks with labels inherent to the input data. We introduce novel domain specific self-supervision tasks that leverage contextual, multi-resolution and semantic features in pathology images for semi-supervised learning and domain adaptation. We investigate the effectiveness of Self-Path on 3 different pathology datasets. Our results show that Self-Path with the domain-specific pretext tasks achieves state-of-the-art performance for semi-supervised learning when small amounts of labeled data are available. Further, we show that Self-Path improves domain adaptation for classification of histology image patches when there is no labeled data available for the target domain. This approach can potentially be employed for other applications in computational pathology, where annotation budget is often limited or large amount of unlabeled image data is available.
We propose algorithms to create adversarial attacks to assess model robustness in text classification problems. They can be used to create white box attacks and black box attacks while at the same time preserving the semantics and syntax of the original text. The attacks cause significant number of flips in white-box setting and same rule based can be used in black-box setting. In a black-box setting, the attacks created are able to reverse decisions of transformer based architectures.
Supervised deep learning methods are enjoying enormous success in many practical applications of computer vision and have the potential to revolutionize robotics. However, the marked performance degradation to biases and imbalanced data questions the reliability of these methods. In this work we address these questions from the perspective of dataset imbalance resulting out of severe under-representation of annotated training data for certain classes and its effect on both deep classification and generation methods. We introduce a joint dataset repairment strategy by combining a neural network classifier with Generative Adversarial Networks (GAN) that makes up for the deficit of training examples from the under-representated class by producing additional training examples. We show that the combined training helps to improve the robustness of both the classifier and the GAN against severe class imbalance. We show the effectiveness of our proposed approach on three very different datasets with different degrees of imbalance in them. The code is available at https://github.com/AadSah/ImbalanceCycleGAN .
Scene graph generation aims to produce structured representations for images, which requires to understand the relations between objects. Due to the continuous nature of deep neural networks, the prediction of scene graphs is divided into object detection and relation classification. However, the independent relation classes cannot separate the visual features well. Although some methods organize the visual features into graph structures and use message passing to learn contextual information, they still suffer from drastic intra-class variations and unbalanced data distributions. One important factor is that they learn an unstructured output space that ignores the inherent structures of scene graphs. Accordingly, in this paper, we propose a Higher Order Structure Embedded Network (HOSE-Net) to mitigate this issue. First, we propose a novel structure-aware embedding-to-classifier(SEC) module to incorporate both local and global structural information of relationships into the output space. Specifically, a set of context embeddings are learned via local graph based message passing and then mapped to a global structure based classification space. Second, since learning too many context-specific classification subspaces can suffer from data sparsity issues, we propose a hierarchical semantic aggregation(HSA) module to reduces the number of subspaces by introducing higher order structural information. HSA is also a fast and flexible tool to automatically search a semantic object hierarchy based on relational knowledge graphs. Extensive experiments show that the proposed HOSE-Net achieves the state-of-the-art performance on two popular benchmarks of Visual Genome and VRD.
Recently, graph neural networks (GNNs) have become an important and active research direction in deep learning. It is worth noting that most of the existing GNN-based methods learn graph representations within the Euclidean vector space. Beyond the Euclidean space, learning representation and embeddings in hyper-complex space have also shown to be a promising and effective approach. To this end, we propose Quaternion Graph Neural Networks (QGNN) to learn graph representations within the Quaternion space. As demonstrated, the Quaternion space, a hyper-complex vector space, provides highly meaningful computations and analogical calculus through Hamilton product compared to the Euclidean and complex vector spaces. Our QGNN obtains state-of-the-art results on a range of benchmark datasets for graph classification and node classification. Besides, regarding knowledge graphs, our QGNN-based embedding model achieves state-of-the-art results on three new and challenging benchmark datasets for knowledge graph completion. Our code is available at: \url{https://github.com/daiquocnguyen/QGNN}.
Classification and identification of the materials lying over or beneath the Earth's surface have long been a fundamental but challenging research topic in geoscience and remote sensing (RS) and have garnered a growing concern owing to the recent advancements of deep learning techniques. Although deep networks have been successfully applied in single-modality-dominated classification tasks, yet their performance inevitably meets the bottleneck in complex scenes that need to be finely classified, due to the limitation of information diversity. In this work, we provide a baseline solution to the aforementioned difficulty by developing a general multimodal deep learning (MDL) framework. In particular, we also investigate a special case of multi-modality learning (MML) -- cross-modality learning (CML) that exists widely in RS image classification applications. By focusing on "what", "where", and "how" to fuse, we show different fusion strategies as well as how to train deep networks and build the network architecture. Specifically, five fusion architectures are introduced and developed, further being unified in our MDL framework. More significantly, our framework is not only limited to pixel-wise classification tasks but also applicable to spatial information modeling with convolutional neural networks (CNNs). To validate the effectiveness and superiority of the MDL framework, extensive experiments related to the settings of MML and CML are conducted on two different multimodal RS datasets. Furthermore, the codes and datasets will be available at https://github.com/danfenghong/IEEE_TGRS_MDL-RS, contributing to the RS community.
Neural network-based approaches have become the driven forces for Natural Language Processing (NLP) tasks. Conventionally, there are two mainstream neural architectures for NLP tasks: the recurrent neural network (RNN) and the convolution neural network (ConvNet). RNNs are good at modeling long-term dependencies over input texts, but preclude parallel computation. ConvNets do not have memory capability and it has to model sequential data as un-ordered features. Therefore, ConvNets fail to learn sequential dependencies over the input texts, but it is able to carry out high-efficient parallel computation. As each neural architecture, such as RNN and ConvNets, has its own pro and con, integration of different architectures is assumed to be able to enrich the semantic representation of texts, thus enhance the performance of NLP tasks. However, few investigation explores the reconciliation of these seemingly incompatible architectures. To address this issue, we propose a hybrid architecture based on a novel hierarchical multi-granularity attention mechanism, named Multi-granularity Attention-based Hybrid Neural Network (MahNN). The attention mechanism is to assign different weights to different parts of the input sequence to increase the computation efficiency and performance of neural models. In MahNN, two types of attentions are introduced: the syntactical attention and the semantical attention. The syntactical attention computes the importance of the syntactic elements (such as words or sentence) at the lower symbolic level and the semantical attention is used to compute the importance of the embedded space dimension corresponding to the upper latent semantics. We adopt the text classification as an exemplifying way to illustrate the ability of MahNN to understand texts.
Structure determination is key to understanding protein function at a molecular level. Whilst significant advances have been made in predicting structure and function from amino acid sequence, researchers must still rely on expensive, time-consuming analytical methods to visualise detailed protein conformation. In this study, we demonstrate that it is possible to make accurate ($\geq$80%) predictions of protein class and architecture from structures determined at low ($>$3A) resolution, using a deep convolutional neural network trained on high-resolution ($\leq$3A) structures represented as 2D matrices. Thus, we provide proof of concept for high-speed, low-cost protein structure classification at low resolution, and a basis for extension to prediction of function. We investigate the impact of the input representation on classification performance, showing that side-chain information may not be necessary for fine-grained structure predictions. Finally, we confirm that high-resolution, low-resolution and NMR-determined structures inhabit a common feature space, and thus provide a theoretical foundation for boosting with single-image super-resolution.
Semi-supervised techniques have removed the barriers of large scale labelled set by exploiting unlabelled data to improve the performance of a model. In this paper, we propose a semi-supervised deep multi-task classification and localization approach HydraMix-Net in the field of medical imagining where labelling is time consuming and costly. Firstly, the pseudo labels are generated using the model's prediction on the augmented set of unlabelled image with averaging. The high entropy predictions are further sharpened to reduced the entropy and are then mixed with the labelled set for training. The model is trained in multi-task learning manner with noise tolerant joint loss for classification localization and achieves better performance when given limited data in contrast to a simple deep model. On DLBCL data it achieves 80\% accuracy in contrast to simple CNN achieving 70\% accuracy when given only 100 labelled examples.
Open set classification (OSC) tackles the problem of determining whether the data are in-class or out-of-class during inference, when only provided with a set of in-class examples at training time. Traditional OSC methods usually train discriminative or generative models with in-class data, then utilize the pre-trained models to classify test data directly. However, these methods always suffer from embedding confusion problem, i.e., partial out-of-class instances are mixed with in-class ones of similar semantics, making it difficult to classify. To solve this problem, we unify semi-supervised learning to develop a novel OSC algorithm, S2OSC, that incorporates out-of-class instances filtering and model re-training in a transductive manner. In detail, given a pool of newly coming test data, S2OSC firstly filters distinct out-of-class instances using the pre-trained model, and annotates super-class for them. Then, S2OSC trains a holistic classification model by combing in-class and out-of-class labeled data and remaining unlabeled test data in semi-supervised paradigm, which also integrates pre-trained model for knowledge distillation to further separate mixed instances. Despite its simplicity, the experimental results show that S2OSC achieves state-of-the-art performance across a variety of OSC tasks, including 85.4% of F1 on CIFAR-10 with only 300 pseudo-labels. We also demonstrate how S2OSC can be expanded to incremental OSC setting effectively with streaming data.
Data-driven fault diagnosis is complicated by unknown fault classes and limited training data from different fault realizations. In these situations, conventional multi-class classification approaches are not suitable for fault diagnosis. One solution is the use of anomaly classifiers that are trained using only nominal data. Anomaly classifiers can be used to detect when a fault occurs but give little information about its root cause. Hybrid fault diagnosis methods combining physically-based models and available training data have shown promising results to improve fault classification performance and identify unknown fault classes. Residual generation using grey-box recurrent neural networks can be used for anomaly classification where physical insights about the monitored system are incorporated into the design of the machine learning algorithm. In this work, an automated residual design is developed using a bipartite graph representation of the system model to design grey-box recurrent neural networks and evaluated using a real industrial case study. Data from an internal combustion engine test bench is used to illustrate the potentials of combining machine learning and model-based fault diagnosis techniques.
The authors compared oversampling methods for the problem of multi-class topic classification. The SMOTE algorithm underlies one of the most popular oversampling methods. It consists in choosing two examples of a minority class and generating a new example based on them. In the paper, the authors compared the basic SMOTE method with its two modifications (Borderline SMOTE and ADASYN) and random oversampling technique on the example of one of text classification tasks. The paper discusses the k-nearest neighbor algorithm, the support vector machine algorithm and three types of neural networks (feedforward network, long short-term memory (LSTM) and bidirectional LSTM). The authors combine these machine learning algorithms with different text representations and compared synthetic oversampling methods. In most cases, the use of oversampling techniques can significantly improve the quality of classification. The authors conclude that for this task, the quality of the KNN and SVM algorithms is more influenced by class imbalance than neural networks.
In many fields of research, labeled datasets are hard to acquire. This is where data augmentation promises to overcome the lack of training data in the context of neural network engineering and classification tasks. The idea here is to reduce model over-fitting to the feature distribution of a small under-descriptive training dataset. We try to evaluate such data augmentation techniques to gather insights in the performance boost they provide for several convolutional neural networks on mel-spectrogram representations of audio data. We show the impact of data augmentation on the binary classification task of surgical mask detection in samples of human voice (ComParE Challenge 2020). Also we consider four varying architectures to account for augmentation robustness. Results show that most of the baselines given by ComParE are outperformed.
We propose PiNet, a generalised differentiable attention-based pooling mechanism for utilising graph convolution operations for graph level classification. We demonstrate high sample efficiency and superior performance over other graph neural networks in distinguishing isomorphic graph classes, as well as competitive results with state of the art methods on standard chemo-informatics datasets.
A relatively new set of transport-based transforms (CDT, R-CDT, LOT) have shown their strength and great potential in various image and data processing tasks such as parametric signal estimation, classification, cancer detection among many others. It is hence worthwhile to elucidate some of the mathematical properties that explain the successes of these transforms when they are used as tools in data analysis, signal processing or data classification. In particular, we give conditions under which classes of signals that are created by algebraic generative models are transformed into convex sets by the transport transforms. Such convexification of the classes simplify the classification and other data analysis and processing problems when viewed in the transform domain. More specifically, we study the extent and limitation of the convexification ability of these transforms under an algebraic generative modeling framework. We hope that this paper will serve as an introduction to these transforms and will encourage mathematicians and other researchers to further explore the theoretical underpinnings and algorithmic tools that will help understand the successes of these transforms and lay the groundwork for further successful applications.
When performing classification tasks, raw high dimensional features often contain redundant information, and lead to increased computational complexity and overfitting. In this paper, we assume the data samples lie on a single underlying smooth manifold, and define intra-class and inter-class similarities using pairwise local kernel distances. We aim to find a linear projection to maximize the intra-class similarities and minimize the inter-class similarities simultaneously, so that the projected low dimensional data has optimized pairwise distances based on the label information, which is more suitable for a Diffusion Map to do further dimensionality reduction. Numerical experiments on several benchmark datasets show that our proposed approaches are able to extract low dimensional discriminate features that could help us achieve higher classification accuracy.
Breast cancer is the most common invasive cancer in women. Besides the primary B-mode ultrasound screening, sonographers have explored the inclusion of Doppler, strain and shear-wave elasticity imaging to advance the diagnosis. However, recognizing useful patterns in all types of images and weighing up the significance of each modality can elude less-experienced clinicians. In this paper, we explore, for the first time, an automatic way to combine the four types of ultrasonography to discriminate between benign and malignant breast nodules. A novel multimodal network is proposed, along with promising learnability and simplicity to improve classification accuracy. The key is using a weight-sharing strategy to encourage interactions between modalities and adopting an additional cross-modalities objective to integrate global information. In contrast to hardcoding the weights of each modality in the model, we embed it in a Reinforcement Learning framework to learn this weighting in an end-to-end manner. Thus the model is trained to seek the optimal multimodal combination without handcrafted heuristics. The proposed framework is evaluated on a dataset contains 1616 set of multimodal images. Results showed that the model scored a high classification accuracy of 95.4%, which indicates the efficiency of the proposed method.
One of the most efficient methods to solve L2-regularized primal problems, such as logistic regression and linear support vector machine (SVM) classification, is the widely used trust region Newton algorithm, TRON. While TRON has recently been shown to enjoy substantial speedups on shared-memory multi-core systems, exploiting graphical processing units (GPUs) to speed up the method is significantly more difficult, owing to the highly complex and heavily sequential nature of the algorithm. In this work, we show that using judicious GPU-optimization principles, TRON training time for different losses and feature representations may be drastically reduced. For sparse feature sets, we show that using GPUs to train logistic regression classifiers in LIBLINEAR is up to an order-of-magnitude faster than solely using multithreading. For dense feature sets--which impose far more stringent memory constraints--we show that GPUs substantially reduce the lengthy SVM learning times required for state-of-the-art proteomics analysis, leading to dramatic improvements over recently proposed speedups. Furthermore, we show how GPU speedups may be mixed with multithreading to enable such speedups when the dataset is too large for GPU memory requirements; on a massive dense proteomics dataset of nearly a quarter-billion data instances, these mixed-architecture speedups reduce SVM analysis time from over half a week to less than a single day while using limited GPU memory.
Deep neural networks often degrade significantly when training data suffer from class imbalance problems. Existing approaches, e.g., re-sampling and re-weighting, commonly address this issue by rearranging the label distribution of training data to train the networks fitting well to the implicit balanced label distribution. However, most of them hinder the representative ability of learned features due to insufficient use of intra/inter-sample information of training data. To address this issue, we propose meta feature modulator (MFM), a meta-learning framework to model the difference between the long-tailed training data and the balanced meta data from the perspective of representation learning. Concretely, we employ learnable hyper-parameters (dubbed modulation parameters) to adaptively scale and shift the intermediate features of classification networks, and the modulation parameters are optimized together with the classification network parameters guided by a small amount of balanced meta data. We further design a modulator network to guide the generation of the modulation parameters, and such a meta-learner can be readily adapted to train the classification network on other long-tailed datasets. Extensive experiments on benchmark vision datasets substantiate the superiority of our approach on long-tailed recognition tasks beyond other state-of-the-art methods.
Speech is a critical biomarker for Huntington Disease (HD), with changes in speech increasing in severity as the disease progresses. Speech analyses are currently conducted using either transcriptions created manually by trained professionals or using global rating scales. Manual transcription is both expensive and time-consuming and global rating scales may lack sufficient sensitivity and fidelity. Ultimately, what is needed is an unobtrusive measure that can cheaply and continuously track disease progression. We present first steps towards the development of such a system, demonstrating the ability to automatically differentiate between healthy controls and individuals with HD using speech cues. The results provide evidence that objective analyses can be used to support clinical diagnoses, moving towards the tracking of symptomatology outside of laboratory and clinical environments.