Objective: Semantic indexing of biomedical literature is usually done at the level of MeSH descriptors with several related but distinct biomedical concepts often grouped together and treated as a single topic. This study proposes a new method for the automated refinement of subject annotations at the level of MeSH concepts. Methods: Lacking labelled data, we rely on weak supervision based on concept occurrence in the abstract of an article, which is also enhanced by dictionary-based heuristics. In addition, we investigate deep learning approaches, making design choices to tackle the particular challenges of this task. The new method is evaluated on a large-scale retrospective scenario, based on concepts that have been promoted to descriptors. Results: In our experiments concept occurrence was the strongest heuristic achieving a macro-F1 score of about 0.63 across several labels. The proposed method improved it further by more than 4pp. Conclusion: The results suggest that concept occurrence is a strong heuristic for refining the coarse-grained labels at the level of MeSH concepts and the proposed method improves it further.
Given a local Hamiltonian, how difficult is it to determine the entanglement structure of its ground state? We show that this problem is computationally intractable even if one is only trying to decide if the ground state is volume-law vs near area-law entangled. We prove this by constructing strong forms of pseudoentanglement in a public-key setting, where the circuits used to prepare the states are public knowledge. In particular, we construct two families of quantum circuits which produce volume-law vs near area-law entangled states, but nonetheless the classical descriptions of the circuits are indistinguishable under the Learning with Errors (LWE) assumption. Indistinguishability of the circuits then allows us to translate our construction to Hamiltonians. Our work opens new directions in Hamiltonian complexity, for example whether it is difficult to learn certain phases of matter.
Background and objectives: Dynamic handwriting analysis, due to its non-invasive and readily accessible nature, has recently emerged as a vital adjunctive method for the early diagnosis of Parkinson's disease. In this study, we design a compact and efficient network architecture to analyse the distinctive handwriting patterns of patients' dynamic handwriting signals, thereby providing an objective identification for the Parkinson's disease diagnosis. Methods: The proposed network is based on a hybrid deep learning approach that fully leverages the advantages of both long short-term memory (LSTM) and convolutional neural networks (CNNs). Specifically, the LSTM block is adopted to extract the time-varying features, while the CNN-based block is implemented using one-dimensional convolution for low computational cost. Moreover, the hybrid model architecture is continuously refined under ablation studies for superior performance. Finally, we evaluate the proposed method with its generalization under a five-fold cross-validation, which validates its efficiency and robustness. Results: The proposed network demonstrates its versatility by achieving impressive classification accuracies on both our new DraWritePD dataset ($96.2\%$) and the well-established PaHaW dataset ($90.7\%$). Moreover, the network architecture also stands out for its excellent lightweight design, occupying a mere $0.084$M of parameters, with a total of only $0.59$M floating-point operations. It also exhibits near real-time CPU inference performance, with inference times ranging from $0.106$ to $0.220$s. Conclusions: We present a series of experiments with extensive analysis, which systematically demonstrate the effectiveness and efficiency of the proposed hybrid neural network in extracting distinctive handwriting patterns for precise diagnosis of Parkinson's disease.
Purpose: To develop biophysics-based method for estimating perfusion Q from arterial spin labeling (ASL) images using deep learning. Methods: A 3D U-Net (QTMnet) was trained to estimate perfusion from 4D tracer propagation images. The network was trained and tested on simulated 4D tracer concentration data based on artificial vasculature structure generated by constrained constructive optimization (CCO) method. The trained network was further tested in a synthetic brain ASL image based on vasculature network extracted from magnetic resonance (MR) angiography. The estimations from both trained network and a conventional kinetic model were compared in ASL images acquired from eight healthy volunteers. Results: QTMnet accurately reconstructed perfusion Q from concentration data. Relative error of the synthetic brain ASL image was 7.04% for perfusion Q, lower than the error using single-delay ASL model: 25.15% for Q, and multi-delay ASL model: 12.62% for perfusion Q. Conclusion: QTMnet provides accurate estimation on perfusion parameters and is a promising approach as a clinical ASL MRI image processing pipeline.
Despite the increasing use of deep learning in medical image segmentation, acquiring sufficient training data remains a challenge in the medical field. In response, data augmentation techniques have been proposed; however, the generation of diverse and realistic medical images and their corresponding masks remains a difficult task, especially when working with insufficient training sets. To address these limitations, we present an end-to-end architecture based on the Hamiltonian Variational Autoencoder (HVAE). This approach yields an improved posterior distribution approximation compared to traditional Variational Autoencoders (VAE), resulting in higher image generation quality. Our method outperforms generative adversarial architectures under data-scarce conditions, showcasing enhancements in image quality and precise tumor mask synthesis. We conduct experiments on two publicly available datasets, MICCAI's Brain Tumor Segmentation Challenge (BRATS), and Head and Neck Tumor Segmentation Challenge (HECKTOR), demonstrating the effectiveness of our method on different medical imaging modalities.
Data collected by different modalities can provide a wealth of complementary information, such as hyperspectral image (HSI) to offer rich spectral-spatial properties, synthetic aperture radar (SAR) to provide structural information about the Earth's surface, and light detection and ranging (LiDAR) to cover altitude information about ground elevation. Therefore, a natural idea is to combine multimodal images for refined and accurate land-cover interpretation. Although many efforts have been attempted to achieve multi-source remote sensing image classification, there are still three issues as follows: 1) indiscriminate feature representation without sufficiently considering modal heterogeneity, 2) abundant features and complex computations associated with modeling long-range dependencies, and 3) overfitting phenomenon caused by sparsely labeled samples. To overcome the above barriers, a transformer-based heterogeneously salient graph representation (THSGR) approach is proposed in this paper. First, a multimodal heterogeneous graph encoder is presented to encode distinctively non-Euclidean structural features from heterogeneous data. Then, a self-attention-free multi-convolutional modulator is designed for effective and efficient long-term dependency modeling. Finally, a mean forward is put forward in order to avoid overfitting. Based on the above structures, the proposed model is able to break through modal gaps to obtain differentiated graph representation with competitive time cost, even for a small fraction of training samples. Experiments and analyses on three benchmark datasets with various state-of-the-art (SOTA) methods show the performance of the proposed approach.
Contrastive, self-supervised learning (SSL) is used to train a model that predicts cancer type from miRNA, mRNA or RPPA expression data. This model, a pretrained FT-Transformer, is shown to outperform XGBoost and CatBoost, standard benchmarks for tabular data, when labelled samples are scarce but the number of unlabelled samples is high. This is despite the fact that the datasets we use have $\mathcal{O}(10^{1})$ classes and $\mathcal{O}(10^{2})-\mathcal{O}(10^{4})$ features. After demonstrating the efficacy of our chosen method of self-supervised pretraining, we investigate SSL for multi-modal models. A late-fusion model is proposed, where each omics is passed through its own sub-network, the outputs of which are averaged and passed to the pretraining or downstream objective function. Multi-modal pretraining is shown to improve predictions from a single omics, and we argue that this is useful for datasets with many unlabelled multi-modal samples, but few labelled unimodal samples. Additionally, we show that pretraining each omics-specific module individually is highly effective. This enables the application of the proposed model in a variety of contexts where a large amount of unlabelled data is available from each omics, but only a few labelled samples.
Redundant information transfer in a neural network can increase the complexity of the deep learning model, thus increasing its power consumption. We introduce in this paper a novel spiking neuron, termed Variable Spiking Neuron (VSN), which can reduce the redundant firing using lessons from biological neuron inspired Leaky Integrate and Fire Spiking Neurons (LIF-SN). The proposed VSN blends LIF-SN and artificial neurons. It garners the advantage of intermittent firing from the LIF-SN and utilizes the advantage of continuous activation from the artificial neuron. This property of the proposed VSN makes it suitable for regression tasks, which is a weak point for the vanilla spiking neurons, all while keeping the energy budget low. The proposed VSN is tested against both classification and regression tasks. The results produced advocate favorably towards the efficacy of the proposed spiking neuron, particularly for regression tasks.
We hypothesize that due to the greedy nature of learning in multi-modal deep neural networks, these models tend to rely on just one modality while under-fitting the other modalities. Such behavior is counter-intuitive and hurts the models' generalization, as we observe empirically. To estimate the model's dependence on each modality, we compute the gain on the accuracy when the model has access to it in addition to another modality. We refer to this gain as the conditional utilization rate. In the experiments, we consistently observe an imbalance in conditional utilization rates between modalities, across multiple tasks and architectures. Since conditional utilization rate cannot be computed efficiently during training, we introduce a proxy for it based on the pace at which the model learns from each modality, which we refer to as the conditional learning speed. We propose an algorithm to balance the conditional learning speeds between modalities during training and demonstrate that it indeed addresses the issue of greedy learning. The proposed algorithm improves the model's generalization on three datasets: Colored MNIST, Princeton ModelNet40, and NVIDIA Dynamic Hand Gesture.
Knowledge graphs (KGs) of real-world facts about entities and their relationships are useful resources for a variety of natural language processing tasks. However, because knowledge graphs are typically incomplete, it is useful to perform knowledge graph completion or link prediction, i.e. predict whether a relationship not in the knowledge graph is likely to be true. This paper serves as a comprehensive survey of embedding models of entities and relationships for knowledge graph completion, summarizing up-to-date experimental results on standard benchmark datasets and pointing out potential future research directions.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.