Abbreviations are unavoidable yet critical parts of the medical text. Using abbreviations, especially in clinical patient notes, can save time and space, protect sensitive information, and help avoid repetitions. However, most abbreviations might have multiple senses, and the lack of a standardized mapping system makes disambiguating abbreviations a difficult and time-consuming task. The main objective of this study is to examine the feasibility of token classification methods for medical abbreviation disambiguation. Specifically, we explore the capability of token classification methods to deal with multiple unique abbreviations in a single text. We use two public datasets to compare and contrast the performance of several transformer models pre-trained on different scientific and medical corpora. Our proposed token classification approach outperforms the more commonly used text classification models for the abbreviation disambiguation task. In particular, the SciBERT model shows a strong performance for both token and text classification tasks over the two considered datasets. Furthermore, we find that abbreviation disambiguation performance for the text classification models becomes comparable to that of token classification only when postprocessing is applied to their predictions, which involves filtering possible labels for an abbreviation based on the training data.
An accurate multiclass classification strategy is crucial to interpreting antibody tests. However, traditional methods based on confidence intervals or receiver operating characteristics lack clear extensions to settings with more than two classes. We address this problem by developing a multiclass classification based on probabilistic modeling and optimal decision theory that minimizes the convex combination of false classification rates. The classification process is challenging when the relative fraction of the population in each class, or generalized prevalence, is unknown. Thus, we also develop a method for estimating the generalized prevalence of test data that is independent of classification. We validate our approach on serological data with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) na\"ive, previously infected, and vaccinated classes. Synthetic data are used to demonstrate that (i) prevalence estimates are unbiased and converge to true values and (ii) our procedure applies to arbitrary measurement dimensions. In contrast to the binary problem, the multiclass setting offers wide-reaching utility as the most general framework and provides new insight into prevalence estimation best practices.
COVID-19 has a spectrum of disease severity, ranging from asymptomatic to requiring hospitalization. Understanding the mechanisms driving disease severity is crucial for developing effective treatments and reducing mortality rates. One way to gain such understanding is using a multi-class classification framework, in which patients' biological features are used to predict patients' severity classes. In this severity classification problem, it is beneficial to prioritize the identification of more severe classes and control the "under-classification" errors, in which patients are misclassified into less severe categories. The Neyman-Pearson (NP) classification paradigm has been developed to prioritize the designated type of error. However, current NP procedures are either for binary classification or do not provide high probability controls on the prioritized errors in multi-class classification. Here, we propose a hierarchical NP (H-NP) framework and an umbrella algorithm that generally adapts to popular classification methods and controls the under-classification errors with high probability. On an integrated collection of single-cell RNA-seq (scRNA-seq) datasets for 864 patients, we explore ways of featurization and demonstrate the efficacy of the H-NP algorithm in controlling the under-classification errors regardless of featurization. Beyond COVID-19 severity classification, the H-NP algorithm generally applies to multi-class classification problems, where classes have a priority order.
The sentiment analysis task has various applications in practice. In the sentiment analysis task, words and phrases that represent positive and negative emotions are important. Finding out the words that represent the emotion from the text can improve the performance of the classification models for the sentiment analysis task. In this paper, we propose a methodology that combines the emotion lexicon with the classification model to enhance the accuracy of the models. Our experimental results show that the emotion lexicon combined with the classification model improves the performance of models.
Recent years have witnessed great success in handling graph-related tasks with Graph Neural Networks (GNNs). Despite their great academic success, Multi-Layer Perceptrons (MLPs) remain the primary workhorse for practical industrial applications. One reason for this academic-industrial gap is the neighborhood-fetching latency incurred by data dependency in GNNs, which make it hard to deploy for latency-sensitive applications that require fast inference. Conversely, without involving any feature aggregation, MLPs have no data dependency and infer much faster than GNNs, but their performance is less competitive. Motivated by these complementary strengths and weaknesses, we propose a Graph Self-Distillation on Neighborhood (GSDN) framework to reduce the gap between GNNs and MLPs. Specifically, the GSDN framework is based purely on MLPs, where structural information is only implicitly used as prior to guide knowledge self-distillation between the neighborhood and the target, substituting the explicit neighborhood information propagation as in GNNs. As a result, GSDN enjoys the benefits of graph topology-awareness in training but has no data dependency in inference. Extensive experiments have shown that the performance of vanilla MLPs can be greatly improved with self-distillation, e.g., GSDN improves over stand-alone MLPs by 15.54% on average and outperforms the state-of-the-art GNNs on six datasets. Regarding inference speed, GSDN infers 75X-89X faster than existing GNNs and 16X-25X faster than other inference acceleration methods.
Machine learning techniques using neural networks have achieved promising success for time-series data classification. However, the models that they produce are challenging to verify and interpret. In this paper, we propose an explainable neural-symbolic framework for the classification of time-series behaviors. In particular, we use an expressive formal language, namely Signal Temporal Logic (STL), to constrain the search of the computation graph for a neural network. We design a novel time function and sparse softmax function to improve the soundness and precision of the neural-STL framework. As a result, we can efficiently learn a compact STL formula for the classification of time-series data through off-the-shelf gradient-based tools. We demonstrate the computational efficiency, compactness, and interpretability of the proposed method through driving scenarios and naval surveillance case studies, compared with state-of-the-art baselines.
Masked image modeling (MIM) has become a popular strategy for self-supervised learning~(SSL) of visual representations with Vision Transformers. A representative MIM model, the masked auto-encoder (MAE), randomly masks a subset of image patches and reconstructs the masked patches given the unmasked patches. Concurrently, many recent works in self-supervised learning utilize the student/teacher paradigm which provides the student with an additional target based on the output of a teacher composed of an exponential moving average (EMA) of previous students. Although common, relatively little is known about the dynamics of the interaction between the student and teacher. Through analysis on a simple linear model, we find that the teacher conditionally removes previous gradient directions based on feature similarities which effectively acts as a conditional momentum regularizer. From this analysis, we present a simple SSL method, the Reconstruction-Consistent Masked Auto-Encoder (RC-MAE) by adding an EMA teacher to MAE. We find that RC-MAE converges faster and requires less memory usage than state-of-the-art self-distillation methods during pre-training, which may provide a way to enhance the practicality of prohibitively expensive self-supervised learning of Vision Transformer models. Additionally, we show that RC-MAE achieves more robustness and better performance compared to MAE on downstream tasks such as ImageNet-1K classification, object detection, and instance segmentation.
Spectral graph convolutional neural networks (GCNNs) have been producing encouraging results in graph classification tasks. However, most spectral GCNNs utilize fixed graphs when aggregating node features, while omitting edge feature learning and failing to get an optimal graph structure. Moreover, many existing graph datasets do not provide initialized edge features, further restraining the ability of learning edge features via spectral GCNNs. In this paper, we try to address this issue by designing an edge feature scheme and an add-on layer between every two stacked graph convolution layers in GCNN. Both are lightweight while effective in filling the gap between edge feature learning and performance enhancement of graph classification. The edge feature scheme makes edge features adapt to node representations at different graph convolution layers. The add-on layers help adjust the edge features to an optimal graph structure. To test the effectiveness of our method, we take Euclidean positions as initial node features and extract graphs with semantic information from point cloud objects. The node features of our extracted graphs are more scalable for edge feature learning than most existing graph datasets (in one-hot encoded label format). Three new graph datasets are constructed based on ModelNet40, ModelNet10 and ShapeNet Part datasets. Experimental results show that our method outperforms state-of-the-art graph classification methods on the new datasets by reaching 96.56% overall accuracy on Graph-ModelNet40, 98.79% on Graph-ModelNet10 and 97.91% on Graph-ShapeNet Part. The constructed graph datasets will be released to the community.
Classifying pill categories from real-world images is crucial for various smart healthcare applications. Although existing approaches in image classification might achieve a good performance on fixed pill categories, they fail to handle novel instances of pill categories that are frequently presented to the learning algorithm. To this end, a trivial solution is to train the model with novel classes. However, this may result in a phenomenon known as catastrophic forgetting, in which the system forgets what it learned in previous classes. In this paper, we address this challenge by introducing the class incremental learning (CIL) ability to traditional pill image classification systems. Specifically, we propose a novel incremental multi-stream intermediate fusion framework enabling incorporation of an additional guidance information stream that best matches the domain of the problem into various state-of-the-art CIL methods. From this framework, we consider color-specific information of pill images as a guidance stream and devise an approach, namely "Color Guidance with Multi-stream intermediate fusion"(CG-IMIF) for solving CIL pill image classification task. We conduct comprehensive experiments on real-world incremental pill image classification dataset, namely VAIPE-PCIL, and find that the CG-IMIF consistently outperforms several state-of-the-art methods by a large margin in different task settings. Our code, data, and trained model are available at https://github.com/vinuni-vishc/CG-IMIF.
Many high-performance classification models utilize complex CNN-based architectures for Alzheimer's Disease classification. We aim to investigate two relevant questions regarding classification of Alzheimer's Disease using MRI: "Do Vision Transformer-based models perform better than CNN-based models?" and "Is it possible to use a shallow 3D CNN-based model to obtain satisfying results?" To achieve these goals, we propose two models that can take in and process 3D MRI scans: Convolutional Voxel Vision Transformer (CVVT) architecture, and ConvNet3D-4, a shallow 4-block 3D CNN-based model. Our results indicate that the shallow 3D CNN-based models are sufficient to achieve good classification results for Alzheimer's Disease using MRI scans.
Training deep learning models on medical datasets that perform well for all classes is a challenging task. It is often the case that a suboptimal performance is obtained on some classes due to the natural class imbalance issue that comes with medical data. An effective way to tackle this problem is by using targeted active learning, where we iteratively add data points to the training data that belong to the rare classes. However, existing active learning methods are ineffective in targeting rare classes in medical datasets. In this work, we propose Clinical (targeted aCtive Learning for ImbalaNced medICal imAge cLassification) a framework that uses submodular mutual information functions as acquisition functions to mine critical data points from rare classes. We apply our framework to a wide-array of medical imaging datasets on a variety of real-world class imbalance scenarios - namely, binary imbalance and long-tail imbalance. We show that Clinical outperforms the state-of-the-art active learning methods by acquiring a diverse set of data points that belong to the rare classes.
Numerous real-world problems from a diverse set of application areas exist that exhibit temporal dependencies. We focus on a specific type of time series classification which we refer to as aggregated time series classification. We consider an aggregated sequence of a multi-variate time series, and propose a methodology to make predictions based solely on the aggregated information. As a case study, we apply our methodology to the challenging problem of household water end-use dissagregation when using non-intrusive water monitoring. Our methodology does not require a-priori identification of events, and to our knowledge, it is considered for the first time. We conduct an extensive experimental study using a residential water-use simulator, involving different machine learning classifiers, multi-label classification methods, and successfully demonstrate the effectiveness of our methodology.
Multi-label classification, which predicts a set of labels for an input, has many applications. However, multiple recent studies showed that multi-label classification is vulnerable to adversarial examples. In particular, an attacker can manipulate the labels predicted by a multi-label classifier for an input via adding carefully crafted, human-imperceptible perturbation to it. Existing provable defenses for multi-class classification achieve sub-optimal provable robustness guarantees when generalized to multi-label classification. In this work, we propose MultiGuard, the first provably robust defense against adversarial examples to multi-label classification. Our MultiGuard leverages randomized smoothing, which is the state-of-the-art technique to build provably robust classifiers. Specifically, given an arbitrary multi-label classifier, our MultiGuard builds a smoothed multi-label classifier via adding random noise to the input. We consider isotropic Gaussian noise in this work. Our major theoretical contribution is that we show a certain number of ground truth labels of an input are provably in the set of labels predicted by our MultiGuard when the $\ell_2$-norm of the adversarial perturbation added to the input is bounded. Moreover, we design an algorithm to compute our provable robustness guarantees. Empirically, we evaluate our MultiGuard on VOC 2007, MS-COCO, and NUS-WIDE benchmark datasets. Our code is available at: \url{https://github.com/quwenjie/MultiGuard}
For long-tailed classification, most works often pretrain a big model on a large-scale dataset, and then fine-tune the whole model for adapting to long-tailed data. Though promising, fine-tuning the whole pretrained model tends to suffer from high cost in computation and deployment of different models for different tasks, as well as weakened generalization ability for overfitting to certain features of long-tailed data. To alleviate these issues, we propose an effective Long-tailed Prompt Tuning method for long-tailed classification. LPT introduces several trainable prompts into a frozen pretrained model to adapt it to long-tailed data. For better effectiveness, we divide prompts into two groups: 1) a shared prompt for the whole long-tailed dataset to learn general features and to adapt a pretrained model into target domain; and 2) group-specific prompts to gather group-specific features for the samples which have similar features and also to empower the pretrained model with discrimination ability. Then we design a two-phase training paradigm to learn these prompts. In phase 1, we train the shared prompt via supervised prompt tuning to adapt a pretrained model to the desired long-tailed domain. In phase 2, we use the learnt shared prompt as query to select a small best matched set for a group of similar samples from the group-specific prompt set to dig the common features of these similar samples, then optimize these prompts with dual sampling strategy and asymmetric GCL loss. By only fine-tuning a few prompts while fixing the pretrained model, LPT can reduce training and deployment cost by storing a few prompts, and enjoys a strong generalization ability of the pretrained model. Experiments show that on various long-tailed benchmarks, with only ~1.1% extra parameters, LPT achieves comparable performance than previous whole model fine-tuning methods, and is more robust to domain-shift.
Exploring the expansion history of the universe, understanding its evolutionary stages, and predicting its future evolution are important goals in astrophysics. Today, machine learning tools are used to help achieving these goals by analyzing transient sources, which are modeled as uncertain time series. Although black-box methods achieve appreciable performance, existing interpretable time series methods failed to obtain acceptable performance for this type of data. Furthermore, data uncertainty is rarely taken into account in these methods. In this work, we propose an uncertaintyaware subsequence based model which achieves a classification comparable to that of state-of-the-art methods. Unlike conformal learning which estimates model uncertainty on predictions, our method takes data uncertainty as additional input. Moreover, our approach is explainable-by-design, giving domain experts the ability to inspect the model and explain its predictions. The explainability of the proposed method has also the potential to inspire new developments in theoretical astrophysics modeling by suggesting important subsequences which depict details of light curve shapes. The dataset, the source code of our experiment, and the results are made available on a public repository.
Recently, there has been increasing interest in building efficient audio neural networks for on-device scenarios. Most existing approaches are designed to reduce the size of audio neural networks using methods such as model pruning. In this work, we show that instead of reducing model size using complex methods, eliminating the temporal redundancy in the input audio features (e.g., mel-spectrogram) could be an effective approach for efficient audio classification. To do so, we proposed a family of simple pooling front-ends (SimPFs) which use simple non-parametric pooling operations to reduce the redundant information within the mel-spectrogram. We perform extensive experiments on four audio classification tasks to evaluate the performance of SimPFs. Experimental results show that SimPFs can achieve a reduction in more than half of the number of floating point operations (FLOPs) for off-the-shelf audio neural networks, with negligible degradation or even some improvements in audio classification performance.
We present a framework for cloud characterization that leverages modern unsupervised deep learning technologies. While previous neural network-based cloud classification models have used supervised learning methods, unsupervised learning allows us to avoid restricting the model to artificial categories based on historical cloud classification schemes and enables the discovery of novel, more detailed classifications. Our framework learns cloud features directly from radiance data produced by NASA's Moderate Resolution Imaging Spectroradiometer (MODIS) satellite instrument, deriving cloud characteristics from millions of images without relying on pre-defined cloud types during the training process. We present preliminary results showing that our method extracts physically relevant information from radiance data and produces meaningful cloud classes.
Quantum Neural Networks (QNNs) are an emerging technology that can be used in many applications including computer vision. In this paper, we presented a traffic sign classification system implemented using a hybrid quantum-classical convolutional neural network. Experiments on the German Traffic Sign Recognition Benchmark dataset indicate that currently QNN do not outperform classical DCNN (Deep Convolutuional Neural Networks), yet still provide an accuracy of over 90% and are a definitely promising solution for advanced computer vision.
Clouds play an important role in the Earth's energy budget and their behavior is one of the largest uncertainties in future climate projections. Satellite observations should help in understanding cloud responses, but decades and petabytes of multispectral cloud imagery have to date received only limited use. This study reduces the dimensionality of satellite cloud observations by grouping them via a novel automated, unsupervised cloud classification technique by using a convolutional neural network. Our technique combines a rotation-invariant autoencoder with hierarchical agglomerative clustering to generate cloud clusters that capture meaningful distinctions among cloud textures, using only raw multispectral imagery as input. Thus, cloud classes are defined without reliance on location, time/season, derived physical properties, or pre-designated class definitions. We use this approach to generate a unique new cloud dataset, the AI-driven cloud classification atlas (AICCA), which clusters 22 years of ocean images from the Moderate Resolution Imaging Spectroradiometer (MODIS) on NASA's Aqua and Terra instruments - 800 TB of data or 198 million patches roughly 100 km x 100 km (128 x 128 pixels) - into 42 AI-generated cloud classes. We show that AICCA classes involve meaningful distinctions that employ spatial information and result in distinct geographic distributions, capturing, for example, stratocumulus decks along the West coasts of North and South America. AICCA delivers the information in multi-spectral images in a compact form, enables data-driven diagnosis of patterns of cloud organization, provides insight into cloud evolution on timescales of hours to decades, and helps democratize climate research by facilitating access to core data.
In this paper, we explore how to utilize pre-trained language model to perform few-shot text classification where only a few annotated examples are given for each class. Since using traditional cross-entropy loss to fine-tune language model under this scenario causes serious overfitting and leads to sub-optimal generalization of model, we adopt supervised contrastive learning on few labeled data and consistency-regularization on vast unlabeled data. Moreover, we propose a novel contrastive consistency to further boost model performance and refine sentence representation. After conducting extensive experiments on four datasets, we demonstrate that our model (FTCC) can outperform state-of-the-art methods and has better robustness.