This article offers a comprehensive review of the research on Natural Language Generation (NLG) over the past two decades, especially in relation to data-to-text generation and text-to-text generation deep learning methods, as well as new applications of NLG technology. This survey aims to (a) give the latest synthesis of deep learning research on the NLG core tasks, as well as the architectures adopted in the field; (b) detail meticulously and comprehensively various NLG tasks and datasets, and draw attention to the challenges in NLG evaluation, focusing on different evaluation methods and their relationships; (c) highlight some future emphasis and relatively recent research issues that arise due to the increasing synergy between NLG and other artificial intelligence areas, such as computer vision, text, and computational creativity.

Medical visual question answering (VQA) aims to correctly answer a clinical question related to a given medical image. Nevertheless, owing to the expensive manual annotations of medical data, the lack of labeled data limits the development of medical VQA. In this paper, we propose a simple yet effective data augmentation method, VQAMix, to mitigate the data limitation problem. Specifically, VQAMix generates more labeled training samples by linearly combining a pair of VQA samples, which can be easily embedded into any visual-language model to boost performance. However, mixing two VQA samples would construct new connections between images and questions from different samples, which will cause the answers for those new fabricated image-question pairs to be missing or meaningless. To solve the missing answer problem, we first develop the Learning with Missing Labels (LML) strategy, which roughly excludes the missing answers. To alleviate the meaningless answer issue, we design the Learning with Conditional-mixed Labels (LCL) strategy, which further utilizes language-type prior to forcing the mixed pairs to have reasonable answers that belong to the same category. Experimental results on the VQA-RAD and PathVQA benchmarks show that our proposed method significantly improves the performance of the baseline by about 7% and 5% on the averaging result of two backbones, respectively. More importantly, VQAMix could improve confidence calibration and model interpretability, which is significant for medical VQA models in practical applications. All code and models are available at https://github.com/haifangong/VQAMix .

In biomedical image analysis, developing architectures that effectively capture long-range dependencies is crucial. Traditional Convolutional Neural Networks (CNNs) are constrained by their local receptive fields, while Transformers, though proficient in global context integration, are computationally demanding for high-dimensional medical images. Here, we present nnMamba, a novel architecture that combines the strengths of CNNs with the long-range modeling capabilities of State Space Models (SSMs). We introduce the Mamba-In-Convolution with Channel-Spatial Siamese learning (MICCSS) block to model long-range voxel relationships. Additionally, we implement channel scaling and channel-sequential learning methods to enhance performance in dense prediction and classification tasks. Extensive experiments on seven datasets demonstrate that nnMamba outperforms current state-of-the-art methods in 3D image segmentation, classification, and landmark detection. nnMamba effectively integrates CNNs' local representation with SSMs' global con-text processing, establishing a new benchmark for long-range dependency modeling in medical image analysis. Code is available at https://github.com/lhaof/nnMamba.

Background: Pathway-based analysis of transcriptomic data has shown greater stability and better performance than traditional gene-based analysis. Until now, some pathway-based deep learning models have been developed for bioinformatic analysis, but these models have not fully considered the topological features of pathways, which limits the performance of the final prediction result. Results: To address this issue, we propose a novel model, called PathGNN, which constructs a Graph Neural Networks (GNNs) model that can capture topological features of pathways. As a case, PathGNN was applied to predict long-term survival of four types of cancer and achieved promising predictive performance when compared to other common methods. Furthermore, the adoption of an interpretation algorithm enabled the identification of plausible pathways associated with survival. Conclusion: PathGNN demonstrates that GNN can be effectively applied to build a pathway-based model, resulting in promising predictive power.