The generation of synthetic medical records using generative adversarial networks (GANs) has become increasingly important for addressing privacy concerns and promoting data sharing in the medical field. In this paper, we propose a novel method for generating synthetic hybrid medical records consisting of chest X-ray images (CXRs) and structured tabular data (including anthropometric data and laboratory tests) using an auto-encoding GAN ({\alpha}GAN) and a conditional tabular GAN (CTGAN). Our approach involves training a {\alpha}GAN model on a large public database (pDB) to reduce the dimensionality of CXRs. We then applied the trained encoder of the GAN model to the images in original database (oDB) to obtain the latent vectors. These latent vectors were combined with tabular data in oDB, and these joint data were used to train the CTGAN model. We successfully generated diverse synthetic records of hybrid CXR and tabular data, maintaining correspondence between them. We evaluated this synthetic database (sDB) through visual assessment, distribution of interrecord distances, and classification tasks. Our evaluation results showed that the sDB captured the features of the oDB while maintaining the correspondence between the images and tabular data. Although our approach relies on the availability of a large-scale pDB containing a substantial number of images with the same modality and imaging region as those in the oDB, this method has the potential for the public release of synthetic datasets without compromising the secondary use of data.
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While machine learning (ML) interatomic potentials (IPs) are able to achieve accuracies nearing the level of noise inherent in the first-principles data to which they are trained, it remains to be shown if their increased complexities are strictly necessary for constructing high-quality IPs. In this work, we introduce a new MLIP framework which blends the simplicity of spline-based MEAM (s-MEAM) potentials with the flexibility of a neural network (NN) architecture. The proposed framework, which we call the spline-based neural network potential (s-NNP), is a simplified version of the traditional NNP that can be used to describe complex datasets in a computationally efficient manner. We demonstrate how this framework can be used to probe the boundary between classical and ML IPs, highlighting the benefits of key architectural changes. Furthermore, we show that using spline filters for encoding atomic environments results in a readily interpreted embedding layer which can be coupled with modifications to the NN to incorporate expected physical behaviors and improve overall interpretability. Finally, we test the flexibility of the spline filters, observing that they can be shared across multiple chemical systems in order to provide a convenient reference point from which to begin performing cross-system analyses.
Flow-based models are widely used in generative tasks, including normalizing flow, where a neural network transports from a data distribution $P$ to a normal distribution. This work develops a flow-based model that transports from $P$ to an arbitrary $Q$ where both distributions are only accessible via finite samples. We propose to learn the dynamic optimal transport between $P$ and $Q$ by training a flow neural network. The model is trained to find an invertible transport map between $P$ and $Q$ optimally by minimizing the transport cost. The trained optimal transport flow allows for performing many downstream tasks, including infinitesimal density ratio estimation and distribution interpolation in the latent space for generative models. The effectiveness of the proposed model on high-dimensional data is empirically demonstrated in mutual information estimation, energy-based generative models, and image-to-image translation.
This paper addresses the problem of selective classification for deep neural networks, where a model is allowed to abstain from low-confidence predictions to avoid potential errors. We focus on so-called post-hoc methods, which replace the confidence estimator of a given classifier without retraining or modifying it, thus being practically appealing. Considering neural networks with softmax outputs, our goal is to identify the best confidence estimator that can be computed directly from the unnormalized logits. This problem is motivated by the intriguing observation in recent work that many classifiers appear to have a "broken" confidence estimator, in the sense that their selective classification performance is much worse than what could be expected by their corresponding accuracies. We perform an extensive experimental study of many existing and proposed confidence estimators applied to 84 pretrained ImageNet classifiers available from popular repositories. Our results show that a simple $p$-norm normalization of the logits, followed by taking the maximum logit as the confidence estimator, can lead to considerable gains in selective classification performance, completely fixing the pathological behavior observed in many classifiers. As a consequence, the selective classification performance of any classifier becomes almost entirely determined by its corresponding accuracy. Moreover, these results are shown to be consistent under distribution shift. We also investigate why certain classifiers innately have a good confidence estimator that apparently cannot be improved by post-hoc methods.
Steady-state visual evoked potentials (SSVEPs) based brain-computer interface (BCI) has received considerable attention due to its high information transfer rate (ITR) and available quantity of targets. However, the performance of frequency identification methods heavily hinges on the amount of user calibration data and data length, which hinders the deployment in real-world applications. Recently, generative adversarial networks (GANs)-based data generation methods have been widely adopted to create synthetic electroencephalography (EEG) data, holds promise to address these issues. In this paper, we proposed a GAN-based end-to-end signal transformation network for Time-window length Extension, termed as TEGAN. TEGAN transforms short-length SSVEP signals into long-length artificial SSVEP signals. By incorporating a novel U-Net generator architecture and an auxiliary classifier into the network architecture, the TEGAN could produce conditioned features in the synthetic data. Additionally, we introduced a two-stage training strategy and the LeCam-divergence regularization term to regularize the training process of GAN during the network implementation. The proposed TEGAN was evaluated on two public SSVEP datasets (a 4-class dataset and a 12-class dataset). With the assistance of TEGAN, the performance of traditional frequency recognition methods and deep learning-based methods have been significantly improved under limited calibration data. And the classification performance gap of various frequency recognition methods has been narrowed. This study substantiates the feasibility of the proposed method to extend the data length for short-time SSVEP signals for developing a high-performance BCI system. The proposed GAN-based methods have the great potential of shortening the calibration time and cutting down the budget for various real-world BCI-based applications.
In this article, the performance of a fixed grid network is examined for various modulation formats to estimate the system's capacity and spectral efficiency. The optical In-phase Quadrature Modulator structure is used to build a fixed grid network modulation, and the homodyne detection approach is used for the receiver. Data multiplexing is accomplished using the Polarization Division Multiplexed technology. 100 Gbps, 150 Gbps, and 200 Gbps data rates are transmitted under these circumstances utilizing various modulation formats. Various pre-processing and signal recovery steps are explained by using modern digital signal processing systems. The achieved spectrum efficiencies for PM-QPSK, PM-8 QAM, and PM-16 QAM, respectively, were 2, 3, and 4 bits/s/Hz. Different modulation like PM-QPSK, PM-8-QAM, and PM-16-QAM each has system capacities of 8-9, 12-13.5, and 16-18 Tbps and it reaches transmission distances of 3000, 1300, and 700 kilometers with acceptable Bit Error Rate less than equal to 2*10-3 respectively. Peak optical power for received signal detection and full width at half maximum is noted for the different modulations under a fixed grind network.
Reservoir Computing (RC) is a type of recursive neural network (RNN), and there can be no doubt that the RC will be more and more widely used for building future prediction models for time-series data, with low training cost, high speed and high computational power. However, research into the mathematical structure of RC neural networks has only recently begun. Bollt (2021) clarified the necessity of the autoregressive (AR) model for gaining the insight into the mathematical structure of RC neural networks, and indicated that the Wold decomposition theorem is the milestone for understanding of these. Keeping this celebrated result in mind, in this paper, we clarify hidden structures of input and recurrent weight matrices in RC neural networks, and show that such structures attain perfect prediction for the AR type of time series data.
Hopfield networks are widely used in neuroscience as simplified theoretical models of biological associative memory. The original Hopfield networks store memories by encoding patterns of binary associations, which result in a synaptic learning mechanism known as Hebbian learning rule. Modern Hopfield networks can achieve exponential capacity scaling by using highly non-linear energy functions. However, the energy function of these newer models cannot be straightforwardly compressed into binary synaptic couplings and it does not directly provide new synaptic learning rules. In this work we show that generative diffusion models can be interpreted as energy-based models and that, when trained on discrete patterns, their energy function is equivalent to that of modern Hopfield networks. This equivalence allows us to interpret the supervised training of diffusion models as a synaptic learning process that encodes the associative dynamics of a modern Hopfield network in the weight structure of a deep neural network. Accordingly, in our experiments we show that the storage capacity of a continuous modern Hopfield network is identical to the capacity of a diffusion model. Our results establish a strong link between generative modeling and the theoretical neuroscience of memory, which provide a powerful computational foundation for the reconstructive theory of memory, where creative generation and memory recall can be seen as parts of a unified continuum.
This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of the root and reticulation vertices, can be oriented as a directed nonbinary phylogenetic network. Moreover, we characterize when this is possible and show that, in such instances, the resulting directed nonbinary phylogenetic network is unique. In addition, without being given the location of the root and the reticulation vertices, we describe an algorithm for deciding whether an undirected binary phylogenetic network $N$ can be oriented as a directed binary phylogenetic network of a certain class. The algorithm is fixed-parameter tractable (FPT) when the parameter is the level of $N$ and is applicable to classes of directed phylogenetic networks that satisfy certain conditions. As an example, we show that the well-studied class of binary tree-child networks satisfies these conditions.
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.
Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.
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