Scalar Coupling Constant Prediction Using Graph Embedding Local Attention Encoder

Scalar coupling constant (SCC) plays a key role in the analysis of three-dimensional structure of organic matter, however, the traditional SCC prediction using quantum mechanical calculations is very time-consuming. To calculate SCC efficiently and accurately, we proposed a graph embedding local self-attention encoder (GELAE) model, in which, a novel invariant structure representation of the coupling system in terms of bond length, bond angle and dihedral angle was presented firstly, and then a local self-attention module embedded with the adjacent matrix of a graph was designed to extract effectively the features of coupling systems, finally, with a modified classification loss function, the SCC was predicted. To validate the superiority of the proposed method, we conducted a series of comparison experiments using different structure representations, different attention modules, and different losses. The experimental results demonstrate that, compared to the traditional chemical bond structure representations, the rotation and translation invariant structure representations proposed in this work can improve the SCC prediction accuracy; with the graph embedded local self-attention, the mean absolute error (MAE) of the prediction model in the validation set decreases from 0.1603 Hz to 0.1067 Hz; using the classification based loss function instead of the scaled regression loss, the MAE of the predicted SCC can be decreased to 0.0963 HZ, which is close to the quantum chemistry standard on CHAMPS dataset.

CNN-Based Invertible Wavelet Scattering for the Investigation of Diffusion Properties of the In Vivo Human Heart in Diffusion Tensor Imaging

In vivo diffusion tensor imaging (DTI) is a promising technique to investigate noninvasively the fiber structures of the in vivo human heart. However, signal loss due to motions remains a persistent problem in in vivo cardiac DTI. We propose a novel motion-compensation method for investigating in vivo myocardium structures in DTI with free-breathing acquisitions. The method is based on an invertible Wavelet Scattering achieved by means of Convolutional Neural Network (WSCNN). It consists of first extracting translation-invariant wavelet scattering features from DW images acquired at different trigger delays and then mapping the fused scattering features into motion-compensated spatial DW images by performing an inverse wavelet scattering transform achieved using CNN. The results on both simulated and acquired in vivo cardiac DW images showed that the proposed WSCNN method effectively compensates for motion-induced signal loss and produces in vivo cardiac DW images with better quality and more coherent fiber structures with respect to existing methods, which makes it an interesting method for measuring correctly the diffusion properties of the in vivo human heart in DTI under free breathing.

Convolutional Restricted Boltzmann Machine Based-Radiomics for Prediction of Pathological Complete Response to Neoadjuvant Chemotherapy in Breast Cancer

We proposed a novel convolutional restricted Boltzmann machine CRBM-based radiomic method for predicting pathologic complete response (pCR) to neoadjuvant chemotherapy treatment (NACT) in breast cancer. The method consists of extracting semantic features from CRBM network, and pCR prediction. It was evaluated on the dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) data of 57 patients and using the area under the receiver operating characteristic curve (AUC). Traditional radiomics features and the semantic features learned from CRBM network were extracted from the images acquired before and after the administration of NACT. After the feature selection, the support vector machine (SVM), logistic regression (LR) and random forest (RF) were trained to predict the pCR status. Compared to traditional radiomic methods, the proposed CRBM-based radiomic method yielded an AUC of 0.92 for the prediction with the images acquired before and after NACT, and an AUC of 0.87 for the pretreatment prediction, which was increased by about 38%. The results showed that the CRBM-based radiomic method provided a potential means for accurately predicting the pCR to NACT in breast cancer before the treatment, which is very useful for making more appropriate and personalized treatment regimens.