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.

Large language models (LLMs) have demonstrated dominating performance in many NLP tasks, especially on generative tasks. However, they often fall short in some information extraction tasks, particularly those requiring domain-specific knowledge, such as Biomedical Named Entity Recognition (NER). In this paper, inspired by Chain-of-thought, we leverage the LLM to solve the Biomedical NER step-by-step: break down the NER task into entity span extraction and entity type determination. Additionally, for entity type determination, we inject entity knowledge to address the problem that LLM's lack of domain knowledge when predicting entity category. Experimental results show a significant improvement in our two-step BioNER approach compared to previous few-shot LLM baseline. Additionally, the incorporation of external knowledge significantly enhances entity category determination performance.

Biomedical named entity recognition (BNER) serves as the foundation for numerous biomedical text mining tasks. Unlike general NER, BNER require a comprehensive grasp of the domain, and incorporating external knowledge beyond training data poses a significant challenge. In this study, we propose a novel BNER framework called DMNER. By leveraging existing entity representation models SAPBERT, we tackle BNER as a two-step process: entity boundary detection and biomedical entity matching. DMNER exhibits applicability across multiple NER scenarios: 1) In supervised NER, we observe that DMNER effectively rectifies the output of baseline NER models, thereby further enhancing performance. 2) In distantly supervised NER, combining MRC and AutoNER as span boundary detectors enables DMNER to achieve satisfactory results. 3) For training NER by merging multiple datasets, we adopt a framework similar to DS-NER but additionally leverage ChatGPT to obtain high-quality phrases in the training. Through extensive experiments conducted on 10 benchmark datasets, we demonstrate the versatility and effectiveness of DMNER.

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.

Extreme multi-label text classification (XMTC) addresses the problem of tagging each text with the most relevant labels from an extreme-scale label set. Traditional methods use bag-of-words (BOW) representations without context information as their features. The state-ot-the-art deep learning-based method, AttentionXML, which uses a recurrent neural network (RNN) and the multi-label attention, can hardly deal with extreme-scale (hundreds of thousands labels) problem. To address this, we propose our HAXMLNet, which uses an efficient and effective hierarchical structure with the multi-label attention. Experimental results show that HAXMLNet reaches a competitive performance with other state-of-the-art methods.

We address an ensemble clustering problem, where reliable clusters are locally embedded in given multiple partitions. We propose a new nonnegative matrix factorization (NMF)-based method, in which locally reliable clusters are explicitly considered by using instance-wise weights over clusters. Our method factorizes the input cluster assignment matrix into two matrices H and W, which are optimized by iteratively 1) updating H and W while keeping the weight matrix constant and 2) updating the weight matrix while keeping H and W constant, alternatively. The weights in the second step were updated by solving a convex problem, which makes our algorithm significantly faster than existing NMF-based ensemble clustering methods. We empirically proved that our method outperformed a lot of cutting-edge ensemble clustering methods by using a variety of datasets.

We address an ensemble clustering problem, where reliable clusters are locally embedded in given multiple partitions. We propose a new nonnegative matrix factorization (NMF)-based method, in which locally reliable clusters are explicitly considered by using instance-wise weights over clusters. Our method factorizes the input cluster assignment matrix into two matrices H and W, which are optimized by iteratively 1) updating H and W while keeping the weight matrix constant and 2) updating the weight matrix while keeping H and W constant, alternatively. The weights in the second step were updated by solving a convex problem, which makes our algorithm significantly faster than existing NMF-based ensemble clustering methods. We empirically proved that our method outperformed a lot of cutting-edge ensemble clustering methods by using a variety of datasets.

We address an ensemble clustering problem, where reliable clusters are locally embedded in given multiple partitions. We propose a new nonnegative matrix factorization (NMF)-based method, in which locally reliable clusters are explicitly considered by using instance-wise weights over clusters. Our method factorizes the input cluster assignment matrix into two matrices H and W, which are optimized by iteratively 1) updating H and W while keeping the weight matrix constant and 2) updating the weight matrix while keeping H and W constant, alternatively. The weights in the second step were updated by solving a convex problem, which makes our algorithm significantly faster than existing NMF-based ensemble clustering methods. We empirically proved that our method outperformed a lot of cutting-edge ensemble clustering methods by using a variety of datasets.

We address an ensemble clustering problem, where reliable clusters are locally embedded in given multiple partitions. We propose a new nonnegative matrix factorization (NMF)-based method, in which locally reliable clusters are explicitly considered by using instance-wise weights over clusters. Our method factorizes the input cluster assignment matrix into two matrices H and W, which are optimized by iteratively 1) updating H and W while keeping the weight matrix constant and 2) updating the weight matrix while keeping H and W constant, alternatively. The weights in the second step were updated by solving a convex problem, which makes our algorithm significantly faster than existing NMF-based ensemble clustering methods. We empirically proved that our method outperformed a lot of cutting-edge ensemble clustering methods by using a variety of datasets.

We address an ensemble clustering problem, where reliable clusters are locally embedded in given multiple partitions. We propose a new nonnegative matrix factorization (NMF)-based method, in which locally reliable clusters are explicitly considered by using instance-wise weights over clusters. Our method factorizes the input cluster assignment matrix into two matrices H and W, which are optimized by iteratively 1) updating H and W while keeping the weight matrix constant and 2) updating the weight matrix while keeping H and W constant, alternatively. The weights in the second step were updated by solving a convex problem, which makes our algorithm significantly faster than existing NMF-based ensemble clustering methods. We empirically proved that our method outperformed a lot of cutting-edge ensemble clustering methods by using a variety of datasets.