LiSSA: Localized Stochastic Sensitive Autoencoders

HRadNet: A Hierarchical Radiomics-Based Network for Multicenter Breast Cancer Molecular Subtypes Prediction

Breast cancer is a heterogeneous disease, where molecular subtypes of breast cancer are closely related to the treatment and prognosis. Therefore, the goal of this work is to differentiate between luminal and non-luminal subtypes of breast cancer. The hierarchical radiomics network (HRadNet) is proposed for breast cancer molecular subtypes prediction based on dynamic contrast-enhanced magnetic resonance imaging. HRadNet fuses multilayer features with the metadata of images to take advantage of conventional radiomics methods and general convolutional neural networks. A two-stage training mechanism is adopted to improve the generalization capability of the network for multicenter breast cancer data. The ablation study shows the effectiveness of each component of HRadNet. Furthermore, the influence of features from different layers and metadata fusion are also analyzed. It reveals that selecting certain layers of features for a specified domain can make further performance improvements. Experimental results on three data sets from different devices demonstrate the effectiveness of the proposed network. HRadNet also has good performance when transferring to other domains without fine-tuning.

BASS: Broad Network Based on Localized Stochastic Sensitivity

The training of the standard broad learning system (BLS) concerns the optimization of its output weights via the minimization of both training mean square error (MSE) and a penalty term. However, it degrades the generalization capability and robustness of BLS when facing complex and noisy environments, especially when small perturbations or noise appear in input data. Therefore, this work proposes a broad network based on localized stochastic sensitivity (BASS) algorithm to tackle the issue of noise or input perturbations from a local perturbation perspective. The localized stochastic sensitivity (LSS) prompts an increase in the network's noise robustness by considering unseen samples located within a Q -neighborhood of training samples, which enhances the generalization capability of BASS with respect to noisy and perturbed data. Then, three incremental learning algorithms are derived to update BASS quickly when new samples arrive or the network is deemed to be expanded, without retraining the entire model. Due to the inherent superiorities of the LSS, extensive experimental results on 13 benchmark datasets show that BASS yields better accuracies on various regression and classification problems. For instance, BASS uses fewer parameters (12.6 million) to yield 1% higher Top-1 accuracy in comparison to AlexNet (60 million) on the large-scale ImageNet (ILSVRC2012) dataset.

Fast and Efficient Design of Deep Neural Networks for Predicting N7-Methylguanosine Sites Using autoBioSeqpy

N⁷-Methylguanosine (m⁷G) is a crucial post-transcriptional RNA modification that plays a pivotal role in regulating gene expression. Accurately identifying m⁷G sites is a fundamental step in understanding the biological functions and regulatory mechanisms associated with this modification. While whole-genome sequencing is the gold standard for RNA modification site detection, it is a time-consuming, expensive, and intricate process. Recently, computational approaches, especially deep learning (DL) techniques, have gained popularity in achieving this objective. Convolutional neural networks and recurrent neural networks are examples of DL algorithms that have emerged as versatile tools for modeling biological sequence data. However, developing an efficient network architecture with superior performance remains a challenging task, requiring significant expertise, time, and effort. To address this, we previously introduced a tool called autoBioSeqpy, which streamlines the design and implementation of DL networks for biological sequence classification. In this study, we utilized autoBioSeqpy to develop, train, evaluate, and fine-tune sequence-level DL models for predicting m⁷G sites. We provided detailed descriptions of these models, along with a step-by-step guide on their execution. The same methodology can be applied to other systems dealing with similar biological questions. The benchmark data and code utilized in this study can be accessed for free at http://github.com/jingry/autoBioSeeqpy/tree/2.0/examples/m7G.

Radial Basis Function Neural Network with Localized Stochastic-Sensitive Autoencoder for Home-Based Activity Recognition

Over the past few years, the Internet of Things (IoT) has been greatly developed with one instance being smart home devices gradually entering into people's lives. To maximize the impact of such deployments, home-based activity recognition is required to initially recognize behaviors within smart home environments and to use this information to provide better health and social care services. Activity recognition has the ability to recognize people's activities from the information about their interaction with the environment collected by sensors embedded within the home. In this paper, binary data collected by anonymous binary sensors such as pressure sensors, contact sensors, passive infrared sensors etc. are used to recognize activities. A radial basis function neural network (RBFNN) with localized stochastic-sensitive autoencoder (LiSSA) method is proposed for the purposes of home-based activity recognition. An autoencoder (AE) is introduced to extract useful features from the binary sensor data by converting binary inputs into continuous inputs to extract increased levels of hidden information. The generalization capability of the proposed method is enhanced by minimizing both the training error and the stochastic sensitivity measure in an attempt to improve the ability of the classifier to tolerate uncertainties in the sensor data. Four binary home-based activity recognition datasets including OrdonezA, OrdonezB, Ulster, and activities of daily living data from van Kasteren (vanKasterenADL) are used to evaluate the effectiveness of the proposed method. Compared with well-known benchmarking approaches including support vector machine (SVM), multilayer perceptron neural network (MLPNN), random forest and an RBFNN-based method, the proposed method yielded the best performance with 98.35%, 86.26%, 96.31%, 92.31% accuracy on four datasets, respectively.