Enhancing generalizability and performance in drug-target interaction identification by integrating pharmacophore and pre-trained models.

MOTIVATION: In drug discovery, it is crucial to assess the drug-target binding affinity (DTA). Although molecular docking is widely used, computational efficiency limits its application in large-scale virtual screening. Deep learning-based methods learn virtual scoring functions from labeled datasets and can quickly predict affinity. However, there are three limitations. First, existing methods only consider the atom-bond graph or one-dimensional sequence representations of compounds, ignoring the information about functional groups (pharmacophores) with specific biological activities. Second, relying on limited labeled datasets fails to learn comprehensive embedding representations of compounds and proteins, resulting in poor generalization performance in complex scenarios. Third, existing feature fusion methods cannot adequately capture contextual interaction information. RESULTS: Therefore, we propose a novel DTA prediction method named HeteroDTA. Specifically, a multi-view compound feature extraction module is constructed to model the atom-bond graph and pharmacophore graph. The residue concat graph and protein sequence are also utilized to model protein structure and function. Moreover, to enhance the generalization capability and reduce the dependence on task-specific labeled data, pre-trained models are utilized to initialize the atomic features of the compounds and the embedding representations of the protein sequence. A context-aware nonlinear feature fusion method is also proposed to learn interaction patterns between compounds and proteins. Experimental results on public benchmark datasets show that HeteroDTA significantly outperforms existing methods. In addition, HeteroDTA shows excellent generalization performance in cold-start experiments and superiority in the representation learning ability of drug-target pairs. Finally, the effectiveness of HeteroDTA is demonstrated in a real-world drug discovery study. AVAILABILITY AND IMPLEMENTATION: The source code and data are available at https://github.com/daydayupzzl/HeteroDTA.

Collaborative Modality Fusion for Mitigating Language Bias in Visual Question Answering.

Language bias stands as a noteworthy concern in visual question answering (VQA), wherein models tend to rely on spurious correlations between questions and answers for prediction. This prevents the models from effectively generalizing, leading to a decrease in performance. In order to address this bias, we propose a novel modality fusion collaborative de-biasing algorithm (CoD). In our approach, bias is considered as the model's neglect of information from a particular modality during prediction. We employ a collaborative training approach to facilitate mutual modeling between different modalities, achieving efficient feature fusion and enabling the model to fully leverage multimodal knowledge for prediction. Our experiments on various datasets, including VQA-CP v2, VQA v2, and VQA-VS, using different validation strategies, demonstrate the effectiveness of our approach. Notably, employing a basic baseline model resulted in an accuracy of 60.14% on VQA-CP v2.

Small- and medium-sized rice fields identification in hilly areas using all available sentinel-1/2 images.

BACKGROUND: Mastering the spatial distribution and planting area of paddy can provide a scientific basis for monitoring rice production, and planning grain production layout. Previous remote sensing studies on paddy concentrated in the plain areas with large-sized fields, ignored the fact that rice is also widely planted in vast hilly regions. In addition, the land cover types here are diverse, rice fields are characterized by a scattered and fragmented distribution with small- or medium-sized, which pose difficulties for high-precision rice recognition. METHODS: In the paper, we proposed a solution based on Sentinel-1 SAR, Sentinel-2 MSI, DEM, and rice calendar data to focus on the rice fields identification in hilly areas. This solution mainly included the construction of rice feature dataset at four crucial phenological periods, the generation of rice standard spectral curve, and the proposal of spectral similarity algorithm for rice identification. RESULTS: The solution, integrating topographical and rice phenological characteristics, manifested its effectiveness with overall accuracy exceeding 0.85. Comparing the results with UAV, it presented that rice fields with an area exceeding 400 m2 (equivalent to 4 pixels) exhibited a recognition success rate of over 79%, which reached to 89% for fields exceeding 800 m2. CONCLUSIONS: The study illustrated that the proposed solution, integrating topographical and rice phenological characteristics, has the capability for charting various rice field sizes with fragmented and dispersed distribution. It also revealed that the synergy of Sentinel-1 SAR and Sentinel-2 MSI data significantly enhanced the recognition ability of rice paddy fields ranging from 400 m2 to 2000 m2.

Classification of high-grade glioblastoma and single brain metastases using a new SCAT-inception model trained with MRI images.

Background and objectives: Glioblastoma (GBM) and brain metastasis (MET) are the two most common intracranial tumors. However, the different pathogenesis of the two tumors leads to completely different treatment options. In terms of magnetic resonance imaging (MRI), GBM and MET are extremely similar, which makes differentiation by imaging extremely challenging. Therefore, this study explores an improved deep learning algorithm to assist in the differentiation of GBM and MET. Materials and methods: For this study, axial contrast-enhanced T1 weight (ceT1W) MRI images from 321 cases of high-grade gliomas and solitary brain metastasis were collected. Among these, 251 out of 270 cases were selected for the experimental dataset (127 glioblastomas and 124 metastases), 207 cases were chosen as the training dataset, and 44 cases as the testing dataset. We designed a new deep learning algorithm called SCAT-inception (Spatial Convolutional Attention inception) and used five-fold cross-validation to verify the results. Results: By employing the newly designed SCAT-inception model to predict glioblastomas and brain metastasis, the prediction accuracy reached 92.3%, and the sensitivity and specificity reached 93.5 and 91.1%, respectively. On the external testing dataset, our model achieved an accuracy of 91.5%, which surpasses other model performances such as VGG, UNet, and GoogLeNet. Conclusion: This study demonstrated that the SCAT-inception architecture could extract more subtle features from ceT1W images, provide state-of-the-art performance in the differentiation of GBM and MET, and surpass most existing approaches.

Deep learning models for rapid discrimination of high-grade gliomas from solitary brain metastases using multi-plane T1-weighted contrast-enhanced (T1CE) images.

Background: High-grade gliomas (HGG) and solitary brain metastases (SBM) are two common types of brain tumors in middle-aged and elderly patients. HGG and SBM display a high degree of similarity on magnetic resonance imaging (MRI) images. Consequently, differential diagnosis using preoperative MRI remains challenging. This study developed deep learning models that used pre-operative T1-weighted contrast-enhanced (T1CE) MRI images to differentiate between HGG and SBM before surgery. Methods: By comparing various convolutional neural network models using T1CE image data from The First Medical Center of the Chinese PLA General Hospital and The Second People's Hospital of Yibin (Data collection for this study spanned from January 2016 to December 2023), it was confirmed that the GoogLeNet model exhibited the highest discriminative performance. Additionally, we evaluated the individual impact of the tumoral core and peritumoral edema regions on the network's predictive performance. Finally, we adopted a slice-based voting method to assess the accuracy of the validation dataset and evaluated patient prediction performance on an additional test dataset. Results: The GoogLeNet model, in a five-fold cross-validation using multi-plane T1CE slices (axial, coronal, and sagittal) from 180 patients, achieved an average patient accuracy of 92.78%, a sensitivity of 95.56%, and a specificity of 90.00%. Moreover, on an external test set of 29 patients, the model achieved an accuracy of 89.66%, a sensitivity of 90.91%, and a specificity of 83.33%, with an area under the curve of 0.939 [95% confidence interval (CI): 0.842-1.000]. Conclusions: GoogLeNet performed better than previous methods at differentiating HGG from SBM, even for core and peritumoral edema in both. HGG and SBM could be fast screened using this end-to-end approach, improving workflow for both tumor treatments.