Biomedical entity linking is an essential task in biomedical text processing, which aims to map entity mentions in biomedical text, such as clinical notes, to standard terms in a given knowledge base. However, this task is challenging due to the rarity of many biomedical entities in real-world scenarios, which often leads to a lack of annotated data for them. Limited by understanding these unseen entities, traditional biomedical entity linking models suffer from multiple types of linking errors. In this paper, we propose a novel latent feature generation framework BioFEG to address these challenges. Specifically, our BioFEG leverages domain knowledge to train a generative adversarial network, which generates latent semantic features of corresponding mentions for unseen entities. Utilizing these features, we fine-tune our entity encoder to capture fine-grained coherence information of unseen entities and better understand them. This allows models to make linking decisions more accurately, particularly for ambiguous mentions involving rare entities. Extensive experiments on the two benchmark datasets demonstrate the superiority of our proposed framework.

Entity linking, which aligns mentions in the text to entities in knowledge bases, is essential for many natural language processing tasks. Considering the real-world scenarios, recent research hotspot of entity linking has focused on the zero-shot setting, where mentions need to link to unseen entities and only the description of each entity is provided. This task challenges the language understanding ability of models to capture the coherence evidence between the mention context and entity description. However, entity descriptions often contain rich information from multiple views, and a mention with context only relates to a small part of the information. Other irrelevant information will introduce noise, which interferes with models to make the right judgments. Furthermore, the existence of these information also makes it difficult to synthesize key information. To solve these problems, we select key views from descriptions and propose a KVZEL framework for zero-shot entity linking. Specifically, our KVZEL first adopts unsupervised clustering to form sub views. Then, it employs a mention-aware key views selection module to iteratively accumulate mention-focused views. This puts emphasis on capturing mention-related information and allows long-range key information integration. Finally, we aggregate key views to make the final decision. Experimental results show the effectiveness of our KVZEL and it achieves the new state-of-the-art on the zero-shot entity linking dataset.

Fine-grained entity typing (FGET) aims to assign appropriate fine-grained types to entity mentions within their context, which is an important foundational task in natural language processing. Previous approaches for FGET only utilized textual context information. However, in the form of short text, the contextual semantic information is often insufficient for FGET. In many real-world scenarios, text is often accompanied by images, and the visual context is valuable for FGET. To this end, we firstly propose a new task called multimodal fine-grained entity typing (MFGET). Then we construct a large-scale dataset for multimodal fine-grained entity typing called MFIGER based on FIGER. To fully leverage both textual and visual information, we propose a novel Multimodal Object-Level Visual Context Network (MOVCNet). MOVCNet can capture fine-grained semantic information by detecting objects in images, and effectively merge both textual and visual context. Experimental results demonstrate that our approach achieves superior classification performance compared to previous text-based approaches.

Multimodal named entity recognition (MNER) on social media is a challenging task which aims to extract named entities in free text and incorporate images to classify them into user-defined types. However, the annotation for named entities on social media demands a mount of human efforts. The existing semi-supervised named entity recognition methods focus on the text modal and are utilized to reduce labeling costs in traditional NER. However, the previous methods are not efficient for semi-supervised MNER. Because the MNER task is defined to combine the text information with image one and needs to consider the mismatch between the posted text and image. To fuse the text and image features for MNER effectively under semi-supervised setting, we propose a novel span-based multimodal variational autoencoder (SMVAE) model for semi-supervised MNER. The proposed method exploits modal-specific VAEs to model text and image latent features, and utilizes product-of-experts to acquire multimodal features. In our approach, the implicit relations between labels and multimodal features are modeled by multimodal VAE. Thus, the useful information of unlabeled data can be exploited in our method under semi-supervised setting. Experimental results on two benchmark datasets demonstrate that our approach not only outperforms baselines under supervised setting, but also improves MNER performance with less labeled data than existing semi-supervised methods.

Entity linking, which aims at aligning ambiguous entity mentions to their referent entities in a knowledge base, plays a key role in multiple natural language processing tasks. Recently, zero-shot entity linking task has become a research hotspot, which links mentions to unseen entities to challenge the generalization ability. For this task, the training set and test set are from different domains, and thus entity linking models tend to be overfitting due to the tendency of memorizing the properties of entities that appear frequently in the training set. We argue that general ultra-fine-grained type information can help the linking models to learn contextual commonality and improve their generalization ability to tackle the overfitting problem. However, in the zero-shot entity linking setting, any type information is not available and entities are only identified by textual descriptions. Thus, we first extract the ultra-fine entity type information from the entity textual descriptions. Then, we propose a hierarchical multi-task model to improve the high-level zero-shot entity linking candidate generation task by utilizing the entity typing task as an auxiliary low-level task, which introduces extracted ultra-fine type information into the candidate generation task. Experimental results demonstrate the effectiveness of utilizing the ultra-fine entity type information and our proposed method achieves state-of-the-art performance.

Clinical outcome prediction is critical to the condition prediction of patients and management of hospital capacities. There are two kinds of medical data, including time series signals recorded by various devices and clinical notes in electronic health records (EHR), which are used for two common prediction targets: mortality and length of stay. Traditional methods focused on utilizing time series data but ignored clinical notes. With the development of deep learning, natural language processing (NLP) and multi-modal learning methods are exploited to jointly model the time series and clinical notes with different modals. However, the existing methods failed to fuse the multi-modal features of patients from different views. Therefore, we propose the patient multi-view multi-modal feature fusion networks for clinical outcome prediction. Firstly, from patient inner view, we propose to utilize the co-attention module to enhance the fine-grained feature interaction between time series and clinical notes from each patient. Secondly, the patient outer view is the correlation between patients, which can be reflected by the structural knowledge in clinical notes. We exploit the structural information extracted from clinical notes to construct the patient correlation graph, and fuse patients’ multi-modal features by graph neural networks (GNN). The experimental results on MIMIC-III benchmark demonstrate the superiority of our method.