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Prevalent solution for BioNER involves using representation learning techniques coupled with sequence labeling. However, such methods are inherently task-specific, demonstrate poor generalizability, and often require dedicated model for each dataset. To leverage the versatile capabilities of recently remarkable large language models (LLMs), several endeavors have explored generative approaches to entity extraction. Yet, these approaches often fall short of the effectiveness of previouly sequence labeling approaches. In this paper, we utilize the open-sourced LLM LLaMA2 as the backbone model, and design specific instructions to distinguish between different types of entities and datasets. By combining the LLM's understanding of instructions with sequence labeling techniques, we use mix of datasets to train a model capable of extracting various types of entities. Given that the backbone LLMs lacks specialized medical knowledge, we also integrate external entity knowledge bases and employ instruction tuning to compel the model to densely recognize carefully curated entities. Our model VANER, trained with a small partition of parameters, significantly outperforms previous LLMs-based models and, for the first time, as a model based on LLM, surpasses the majority of conventional state-of-the-art BioNER systems, achieving the highest F1 scores across three datasets.

As a common approach to learning English, reading comprehension primarily entails reading articles and answering related questions. However, the complexity of designing effective exercises results in students encountering standardized questions, making it challenging to align with individualized learners' reading comprehension ability. By leveraging the advanced capabilities offered by large language models, exemplified by ChatGPT, this paper presents a novel personalized support system for reading comprehension, referred to as ChatPRCS, based on the Zone of Proximal Development theory. ChatPRCS employs methods including reading comprehension proficiency prediction, question generation, and automatic evaluation, among others, to enhance reading comprehension instruction. First, we develop a new algorithm that can predict learners' reading comprehension abilities using their historical data as the foundation for generating questions at an appropriate level of difficulty. Second, a series of new ChatGPT prompt patterns is proposed to address two key aspects of reading comprehension objectives: question generation, and automated evaluation. These patterns further improve the quality of generated questions. Finally, by integrating personalized ability and reading comprehension prompt patterns, ChatPRCS is systematically validated through experiments. Empirical results demonstrate that it provides learners with high-quality reading comprehension questions that are broadly aligned with expert-crafted questions at a statistical level., Comment: We are very sorry, we found a problem in the article and will resubmit it after modification

Extracting summaries from long documents can be regarded as sentence classification using the structural information of the documents. How to use such structural information to summarize a document is challenging. In this paper, we propose GoSum, a novel graph and reinforcement learning based extractive model for long-paper summarization. In particular, GoSum encodes sentence states in reinforcement learning by building a heterogeneous graph for each input document at different discourse levels. An edge in the graph reflects the discourse hierarchy of a document for restraining the semantic drifts across section boundaries. We evaluate GoSum on two datasets of scientific articles summarization: PubMed and arXiv. The experimental results have demonstrated that GoSum achieve state-of-the-art results compared with strong baselines of both extractive and abstractive models. The ablation studies further validate that the performance of our GoSum benefits from the use of discourse information.

Weak supervision learning on classification labels has demonstrated high performance in various tasks, while a few pixel-level fine annotations are also affordable. Naturally a question comes to us that whether the combination of pixel-level (e.g., segmentation) and image level (e.g., classification) annotation can introduce further improvement. However in computational pathology this is a difficult task for this reason: High resolution of whole slide images makes it difficult to do end-to-end classification model training, which is challenging to research of weak or hybrid supervision learning in the past. To handle this problem, we propose a hybrid supervision learning framework for this kind of high resolution images with sufficient image-level coarse annotations and a few pixel-level fine labels. This framework, when applied in training patch model, can carefully make use of coarse image-level labels to refine generated pixel-level pseudo labels. Complete strategy is proposed to suppress pixel-level false positives and false negatives. A large hybrid annotated dataset is used to evaluate the effectiveness of hybrid supervision learning. By extracting pixel-level pseudo labels in initially image-level labeled samples, we achieve 5.2% higher specificity than purely training on existing labels while retaining 100% sensitivity, in the task of image-level classification to be positive or negative., Comment: Accepted in MICCAI2021

Clinical research on smart health has an increasing demand for intelligent and clinic-oriented medical image computing algorithms and platforms that support various applications. To this end, we have developed SenseCare research platform, which is designed to facilitate translational research on intelligent diagnosis and treatment planning in various clinical scenarios. To enable clinical research with Artificial Intelligence (AI), SenseCare provides a range of AI toolkits for different tasks, including image segmentation, registration, lesion and landmark detection from various image modalities ranging from radiology to pathology. In addition, SenseCare is clinic-oriented and supports a wide range of clinical applications such as diagnosis and surgical planning for lung cancer, pelvic tumor, coronary artery disease, etc. SenseCare provides several appealing functions and features such as advanced 3D visualization, concurrent and efficient web-based access, fast data synchronization and high data security, multi-center deployment, support for collaborative research, etc. In this report, we present an overview of SenseCare as an efficient platform providing comprehensive toolkits and high extensibility for intelligent image analysis and clinical research in different application scenarios. We also summarize the research outcome through the collaboration with multiple hospitals., Comment: 15 pages, 16 figures

Gastric cancer is one of the most common cancers, which ranks third among the leading causes of cancer death. Biopsy of gastric mucosa is a standard procedure in gastric cancer screening test. However, manual pathological inspection is labor-intensive and time-consuming. Besides, it is challenging for an automated algorithm to locate the small lesion regions in the gigapixel whole-slide image and make the decision correctly.To tackle these issues, we collected large-scale whole-slide image dataset with detailed lesion region annotation and designed a whole-slide image analyzing framework consisting of 3 networks which could not only determine the screening result but also present the suspicious areas to the pathologist for reference. Experiments demonstrated that our proposed framework achieves sensitivity of 97.05% and specificity of 92.72% in screening task and Dice coefficient of 0.8331 in segmentation task. Furthermore, we tested our best model in real-world scenario on 10,315 whole-slide images collected from 4 medical centers., Comment: under minor revision

Signet ring cell carcinoma is a type of rare adenocarcinoma with poor prognosis. Early detection leads to huge improvement of patients' survival rate. However, pathologists can only visually detect signet ring cells under the microscope. This procedure is not only laborious but also prone to omission. An automatic and accurate signet ring cell detection solution is thus important but has not been investigated before. In this paper, we take the first step to present a semi-supervised learning framework for the signet ring cell detection problem. Self-training is proposed to deal with the challenge of incomplete annotations, and cooperative-training is adapted to explore the unlabeled regions. Combining the two techniques, our semi-supervised learning framework can make better use of both labeled and unlabeled data. Experiments on large real clinical data demonstrate the effectiveness of our design. Our framework achieves accurate signet ring cell detection and can be readily applied in the clinical trails. The dataset will be released soon to facilitate the development of the area., Comment: Published in The 26th international conference on Information Processing in Medical Imaging (IPMI)