In the field of materials science, microscopy is the first and often only accessible method for structural characterization. There is a growing interest in the development of machine learning methods that can automate the analysis and interpretation of microscopy images. Typically training of machine learning models requires large numbers of images with associated structural labels, however, manual labeling of images requires domain knowledge and is prone to human error and subjectivity. To overcome these limitations, we present a semi-supervised transfer learning approach that uses a small number of labeled microscopy images for training and performs as effectively as methods trained on significantly larger image datasets. Specifically, we train an image encoder with unlabeled images using self-supervised learning methods and use that encoder for transfer learning of different downstream image tasks (classification and segmentation) with a minimal number of labeled images for training. We test the transfer learning ability of two self-supervised learning methods: SimCLR and Barlow-Twins on transmission electron microscopy (TEM) images. We demonstrate in detail how this machine learning workflow applied to TEM images of protein nanowires enables automated classification of nanowire morphologies (e.g., single nanowires, nanowire bundles, phase separated) as well as segmentation tasks that can serve as groundwork for quantification of nanowire domain sizes and shape analysis. We also extend the application of the machine learning workflow to classification of nanoparticle morphologies and identification of different type of viruses from TEM images.
Self-training is a simple semi-supervised learning approach: Unlabelled examples that attract high-confidence predictions are labelled with their predictions and added to the training set, with this process being repeated multiple times. Recently, self-supervision -- learning without manual supervision by solving an automatically-generated pretext task -- has gained prominence in deep learning. This paper investigates three different ways of incorporating self-supervision into self-training to improve accuracy in image classification: self-supervision as pretraining only, self-supervision performed exclusively in the first iteration of self-training, and self-supervision added to every iteration of self-training. Empirical results on the SVHN, CIFAR-10, and PlantVillage datasets, using both training from scratch, and Imagenet-pretrained weights, show that applying self-supervision only in the first iteration of self-training can greatly improve accuracy, for a modest increase in computation time.
Acquisition of data in task-specific applications of machine learning like plant disease recognition is a costly endeavor owing to the requirements of professional human diligence and time constraints. In this paper, we present a simple pipeline that uses GANs in an unsupervised image translation environment to improve learning with respect to the data distribution in a plant disease dataset, reducing the partiality introduced by acute class imbalance and hence shifting the classification decision boundary towards better performance. The empirical analysis of our method is demonstrated on a limited dataset of 2789 tomato plant disease images, highly corrupted with an imbalance in the 9 disease categories. First, we extend the state of the art for the GAN-based image-to-image translation method by enhancing the perceptual quality of the generated images and preserving the semantics. We introduce AR-GAN, where in addition to the adversarial loss, our synthetic image generator optimizes on Activation Reconstruction loss (ARL) function that optimizes feature activations against the natural image. We present visually more compelling synthetic images in comparison to most prominent existing models and evaluate the performance of our GAN framework in terms of various datasets and metrics. Second, we evaluate the performance of a baseline convolutional neural network classifier for improved recognition using the resulting synthetic samples to augment our training set and compare it with the classical data augmentation scheme. We observe a significant improvement in classification accuracy (+5.2%) using generated synthetic samples as compared to (+0.8%) increase using classic augmentation in an equal class distribution environment.
Humans are able to explain their reasoning. On the contrary, deep neural networks are not. This paper attempts to bridge this gap by introducing a new way to design interpretable neural networks for classification, inspired by physiological evidence of the human visual system's inner-workings. This paper proposes a neural network design paradigm, termed InterpNET, which can be combined with any existing classification architecture to generate natural language explanations of the classifications. The success of the module relies on the assumption that the network's computation and reasoning is represented in its internal layer activations. While in principle InterpNET could be applied to any existing classification architecture, it is evaluated via an image classification and explanation task. Experiments on a CUB bird classification and explanation dataset show qualitatively and quantitatively that the model is able to generate high-quality explanations. While the current state-of-the-art METEOR score on this dataset is 29.2, InterpNET achieves a much higher METEOR score of 37.9.
We present a latent variable model for classification that provides a novel probabilistic interpretation of neural network softmax classifiers. We derive a variational objective to train the model, analogous to the evidence lower bound (ELBO) used to train variational auto-encoders, that generalises the softmax cross-entropy loss. Treating inputs to the softmax layer as samples of a latent variable, our abstracted perspective reveals a potential inconsistency between their anticipated distribution, required for accurate label predictions, and their empirical distribution found in practice. We augment the variational objective to mitigate such inconsistency and induce a chosen latent distribution, instead of the implicit assumption found in a standard softmax layer. Overall, we provide new theoretical insight into the inner workings of widely-used softmax classifiers. Empirical evaluation on image and text classification datasets demonstrates that our proposed approach, variational classification, maintains classification accuracy while the reshaped latent space improves other desirable properties of a classifier, such as calibration, adversarial robustness, robustness to distribution shift and sample efficiency useful in low data settings.
Cardiac Magnetic Resonance Imaging (CMR) is the gold standard for diagnosing cardiovascular diseases. Clinical diagnoses predominantly rely on magnitude-only Digital Imaging and Communications in Medicine (DICOM) images, omitting crucial phase information that might provide additional diagnostic benefits. In contrast, k-space is complex-valued and encompasses both magnitude and phase information, while humans cannot directly perceive. In this work, we propose KMAE, a Transformer-based model specifically designed to process k-space data directly, eliminating conventional intermediary conversion steps to the image domain. KMAE can handle critical cardiac disease classification, relevant phenotype regression, and cardiac morphology segmentation tasks. We utilize this model to investigate the potential of k-space-based diagnosis in cardiac MRI. Notably, this model achieves competitive classification and regression performance compared to image-domain methods e.g. Masked Autoencoders (MAEs) and delivers satisfactory segmentation performance with a myocardium dice score of 0.884. Last but not least, our model exhibits robust performance with consistent results even when the k-space is 8* undersampled. We encourage the MR community to explore the untapped potential of k-space and pursue end-to-end, automated diagnosis with reduced human intervention.
Skin lesion datasets consist predominantly of normal samples with only a small percentage of abnormal ones, giving rise to the class imbalance problem. Also, skin lesion images are largely similar in overall appearance owing to the low inter-class variability. In this paper, we propose a two-stage framework for automatic classification of skin lesion images using adversarial training and transfer learning toward melanoma detection. In the first stage, we leverage the inter-class variation of the data distribution for the task of conditional image synthesis by learning the inter-class mapping and synthesizing under-represented class samples from the over-represented ones using unpaired image-to-image translation. In the second stage, we train a deep convolutional neural network for skin lesion classification using the original training set combined with the newly synthesized under-represented class samples. The training of this classifier is carried out by minimizing the focal loss function, which assists the model in learning from hard examples, while down-weighting the easy ones. Experiments conducted on a dermatology image benchmark demonstrate the superiority of our proposed approach over several standard baseline methods, achieving significant performance improvements. Interestingly, we show through feature visualization and analysis that our method leads to context based lesion assessment that can reach an expert dermatologist level.
Spike Timing-Dependent Plasticity (STDP) is a promising substitute to backpropagation for local training of Spiking Neural Networks (SNNs) on neuromorphic hardware. STDP allows SNNs to address classification tasks by combining unsupervised STDP for feature extraction and supervised STDP for classification. Unsupervised STDP is usually employed with Winner-Takes-All (WTA) competition to learn distinct patterns. However, WTA for supervised STDP classification faces unbalanced competition challenges. In this paper, we propose a method to effectively implement WTA competition in a spiking classification layer employing first-spike coding and supervised STDP training. We introduce the Neuronal Competition Group (NCG), an architecture that improves classification capabilities by promoting the learning of various patterns per class. An NCG is a group of neurons mapped to a specific class, implementing intra-class WTA and a novel competition regulation mechanism based on two-compartment thresholds. We incorporate our proposed architecture into spiking classification layers trained with state-of-the-art supervised STDP rules. On top of two different unsupervised feature extractors, we obtain significant accuracy improvements on image recognition datasets such as CIFAR-10 and CIFAR-100. We show that our competition regulation mechanism is crucial for ensuring balanced competition and improved class separation.
Simplicial Embeddings (SEM) are representations learned through self-supervised learning (SSL), wherein a representation is projected into $L$ simplices of $V$ dimensions each using a softmax operation. This procedure conditions the representation onto a constrained space during pretraining and imparts an inductive bias for group sparsity. For downstream classification, we formally prove that the SEM representation leads to better generalization than an unnormalized representation. Furthermore, we empirically demonstrate that SSL methods trained with SEMs have improved generalization on natural image datasets such as CIFAR-100 and ImageNet. Finally, when used in a downstream classification task, we show that SEM features exhibit emergent semantic coherence where small groups of learned features are distinctly predictive of semantically-relevant classes.
Classification on smartphone-captured chest X-ray (CXR) photos to detect pathologies is challenging due to the projective transformation caused by the non-ideal camera position. Recently, various rectification methods have been proposed for different photo rectification tasks such as document photos, license plate photos, etc. Unfortunately, we found that none of them is suitable for CXR photos, due to their specific transformation type, image appearance, annotation type, etc. In this paper, we propose an innovative deep learning-based Projective Transformation Rectification Network (PTRN) to automatically rectify CXR photos by predicting the projective transformation matrix. To the best of our knowledge, it is the first work to predict the projective transformation matrix as the learning goal for photo rectification. Additionally, to avoid the expensive collection of natural data, synthetic CXR photos are generated under the consideration of natural perturbations, extra screens, etc. We evaluate the proposed approach in the CheXphoto smartphone-captured CXR photos classification competition hosted by the Stanford University Machine Learning Group, our approach won first place with a huge performance improvement (ours 0.850, second-best 0.762, in AUC). A deeper study demonstrates that the use of PTRN successfully achieves the classification performance on the spatially transformed CXR photos to the same level as on the high-quality digital CXR images, indicating PTRN can eliminate all negative impacts of projective transformation on the CXR photos.
We present new Recurrent Neural Network (RNN) cells for image classification using a Neural Architecture Search (NAS) approach called DARTS. We are interested in the ReNet architecture, which is a RNN based approach presented as an alternative for convolutional and pooling steps. ReNet can be defined using any standard RNN cells, such as LSTM and GRU. One limitation is that standard RNN cells were designed for one dimensional sequential data and not for two dimensions like it is the case for image classification. We overcome this limitation by using DARTS to find new cell designs. We compare our results with ReNet that uses GRU and LSTM cells. Our found cells outperform the standard RNN cells on CIFAR-10 and SVHN. The improvements on SVHN indicate generalizability, as we derived the RNN cell designs from CIFAR-10 without performing a new cell search for SVHN.
Deep neural networks face many problems in the field of hyperspectral image classification, lack of effective utilization of spatial spectral information, gradient disappearance and overfitting as the model depth increases. In order to accelerate the deployment of the model on edge devices with strict latency requirements and limited computing power, we introduce a lightweight model based on the improved 3D-Densenet model and designs DGCNet. It improves the disadvantage of group convolution. Referring to the idea of dynamic network, dynamic group convolution(DGC) is designed on 3d convolution kernel. DGC introduces small feature selectors for each grouping to dynamically decide which part of the input channel to connect based on the activations of all input channels. Multiple groups can capture different and complementary visual and semantic features of input images, allowing convolution neural network(CNN) to learn rich features. 3D convolution extracts high-dimensional and redundant hyperspectral data, and there is also a lot of redundant information between convolution kernels. DGC module allows 3D-Densenet to select channel information with richer semantic features and discard inactive regions. The 3D-CNN passing through the DGC module can be regarded as a pruned network. DGC not only allows 3D-CNN to complete sufficient feature extraction, but also takes into account the requirements of speed and calculation amount. The inference speed and accuracy have been improved, with outstanding performance on the IN, Pavia and KSC datasets, ahead of the mainstream hyperspectral image classification methods.
Deep learning requires large amounts of data to learn new tasks well, limiting its applicability to domains where such data is available. Meta-learning overcomes this limitation by learning how to learn. In 2001, Hochreiter et al. showed that an LSTM trained with backpropagation across different tasks is capable of meta-learning. Despite promising results of this approach on small problems, and more recently, also on reinforcement learning problems, the approach has received little attention in the supervised few-shot learning setting. We revisit this approach and test it on modern few-shot learning benchmarks. We find that LSTM, surprisingly, outperform the popular meta-learning technique MAML on a simple few-shot sine wave regression benchmark, but that LSTM, expectedly, fall short on more complex few-shot image classification benchmarks. We identify two potential causes and propose a new method called Outer Product LSTM (OP-LSTM) that resolves these issues and displays substantial performance gains over the plain LSTM. Compared to popular meta-learning baselines, OP-LSTM yields competitive performance on within-domain few-shot image classification, and performs better in cross-domain settings by 0.5% to 1.9% in accuracy score. While these results alone do not set a new state-of-the-art, the advances of OP-LSTM are orthogonal to other advances in the field of meta-learning, yield new insights in how LSTM work in image classification, allowing for a whole range of new research directions. For reproducibility purposes, we publish all our research code publicly.
Visual representation based on covariance matrix has demonstrates its efficacy for image classification by characterising the pairwise correlation of different channels in convolutional feature maps. However, pairwise correlation will become misleading once there is another channel correlating with both channels of interest, resulting in the ``confounding'' effect. For this case, ``partial correlation'' which removes the confounding effect shall be estimated instead. Nevertheless, reliably estimating partial correlation requires to solve a symmetric positive definite matrix optimisation, known as sparse inverse covariance estimation (SICE). How to incorporate this process into CNN remains an open issue. In this work, we formulate SICE as a novel structured layer of CNN. To ensure end-to-end trainability, we develop an iterative method to solve the above matrix optimisation during forward and backward propagation steps. Our work obtains a partial correlation based deep visual representation and mitigates the small sample problem often encountered by covariance matrix estimation in CNN. Computationally, our model can be effectively trained with GPU and works well with a large number of channels of advanced CNNs. Experiments show the efficacy and superior classification performance of our deep visual representation compared to covariance matrix based counterparts.
Deep neural networks face several challenges in hyperspectral image classification, including complex and sparse ground object distributions, small clustered structures, and elongated multi-branch features that often lead to missing detections. To better adapt to ground object distributions and achieve adaptive dynamic feature responses while skipping redundant information, this paper proposes a Spatial-Geometry Enhanced 3D Dynamic Snake Network (SG-DSCNet) based on an improved 3D-DenseNet model. The network employs Dynamic Snake Convolution (DSCConv), which introduces deformable offsets to enhance kernel flexibility through constrained self-learning, thereby improving regional perception of ground objects. Additionally, we propose a multi-view feature fusion strategy that generates multiple morphological kernel templates from DSCConv to observe target structures from different perspectives and achieve efficient feature fusion through summarizing key characteristics. This dynamic approach enables the model to focus more flexibly on critical spatial structures when processing different regions, rather than relying on fixed receptive fields of single static kernels. The DSC module enhances model representation capability through dynamic kernel aggregation without increasing network depth or width. Experimental results demonstrate superior performance on the IN, UP, and KSC datasets, outperforming mainstream hyperspectral classification methods.
While class activation map (CAM) generated by image classification network has been widely used for weakly supervised object localization (WSOL) and semantic segmentation (WSSS), such classifiers usually focus on discriminative object regions. In this paper, we propose Contrastive learning for Class-agnostic Activation Map (C$^2$AM) generation only using unlabeled image data, without the involvement of image-level supervision. The core idea comes from the observation that i) semantic information of foreground objects usually differs from their backgrounds; ii) foreground objects with similar appearance or background with similar color/texture have similar representations in the feature space. We form the positive and negative pairs based on the above relations and force the network to disentangle foreground and background with a class-agnostic activation map using a novel contrastive loss. As the network is guided to discriminate cross-image foreground-background, the class-agnostic activation maps learned by our approach generate more complete object regions. We successfully extracted from C$^2$AM class-agnostic object bounding boxes for object localization and background cues to refine CAM generated by classification network for semantic segmentation. Extensive experiments on CUB-200-2011, ImageNet-1K, and PASCAL VOC2012 datasets show that both WSOL and WSSS can benefit from the proposed C$^2$AM.
Social media produces large amounts of contents every day. To help users quickly capture what they need, keyphrase prediction is receiving a growing attention. Nevertheless, most prior efforts focus on text modeling, largely ignoring the rich features embedded in the matching images. In this work, we explore the joint effects of texts and images in predicting the keyphrases for a multimedia post. To better align social media style texts and images, we propose: (1) a novel Multi-Modality Multi-Head Attention (M3H-Att) to capture the intricate cross-media interactions; (2) image wordings, in forms of optical characters and image attributes, to bridge the two modalities. Moreover, we design a unified framework to leverage the outputs of keyphrase classification and generation and couple their advantages. Extensive experiments on a large-scale dataset newly collected from Twitter show that our model significantly outperforms the previous state of the art based on traditional attention networks. Further analyses show that our multi-head attention is able to attend information from various aspects and boost classification or generation in diverse scenarios.
Transfer learning is a commonly used strategy for medical image classification, especially via pretraining on source data and fine-tuning on target data. There is currently no consensus on how to choose appropriate source data, and in the literature we can find both evidence of favoring large natural image datasets such as ImageNet, and evidence of favoring more specialized medical datasets. In this paper we perform a systematic study with nine source datasets with natural or medical images, and three target medical datasets, all with 2D images. We find that ImageNet is the source leading to the highest performances, but also that larger datasets are not necessarily better. We also study different definitions of data similarity. We show that common intuitions about similarity may be inaccurate, and therefore not sufficient to predict an appropriate source a priori. Finally, we discuss several steps needed for further research in this field, especially with regard to other types (for example 3D) medical images. Our experiments and pretrained models are available via \url{https://www.github.com/vcheplygina/cats-scans}
Pathological image analysis is an important process for detecting abnormalities such as cancer from cell images. However, since the image size is generally very large, the cost of providing detailed annotations is high, which makes it difficult to apply machine learning techniques. One way to improve the performance of identifying abnormalities while keeping the annotation cost low is to use only labels for each slide, or to use information from another dataset that has already been labeled. However, such weak supervisory information often does not provide sufficient performance. In this paper, we proposed a new task setting to improve the classification performance of the target dataset without increasing annotation costs. And to solve this problem, we propose a pipeline that uses multiple instance learning (MIL) and domain adaptation (DA) methods. Furthermore, in order to combine the supervisory information of both methods effectively, we propose a method to create pseudo-labels with high confidence. We conducted experiments on the pathological image dataset we created for this study and showed that the proposed method significantly improves the classification performance compared to existing methods.
Medical image segmentation is a key task in the imaging workflow, influencing many image-based decisions. Traditional, fully-supervised segmentation models rely on large amounts of labeled training data, typically obtained through manual annotation, which can be an expensive, time-consuming, and error-prone process. This signals a need for accurate, automatic, and annotation-efficient methods of training these models. We propose ADA-SAM (automated, domain-specific, and adaptive segment anything model), a novel multitask learning framework for medical image segmentation that leverages class activation maps from an auxiliary classifier to guide the predictions of the semi-supervised segmentation branch, which is based on the Segment Anything (SAM) framework. Additionally, our ADA-SAM model employs a novel gradient feedback mechanism to create a learnable connection between the segmentation and classification branches by using the segmentation gradients to guide and improve the classification predictions. We validate ADA-SAM on real-world clinical data collected during rehabilitation trials, and demonstrate that our proposed method outperforms both fully-supervised and semi-supervised baselines by double digits in limited label settings. Our code is available at: https://github.com/tbwa233/ADA-SAM.