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The transformer architecture has catalyzed revolutionary advances in language modeling. However, recent architectural recipes, such as state-space models, have bridged the performance gap. Motivated by this, we examine the benefits of Convolution-Augmented Transformer (CAT) for recall, copying, and length generalization tasks. CAT incorporates convolutional filters in the K/Q/V embeddings of an attention layer. Through CAT, we show that the locality of the convolution synergizes with the global view of the attention. Unlike comparable architectures, such as Mamba or transformer, CAT can provably solve the associative recall (AR) and copying tasks using a single layer while also enjoying guaranteed length generalization. We also establish computational tradeoffs between convolution and attention by characterizing how convolution can mitigate the need for full attention by summarizing the context window and creating salient summary tokens to attend. Evaluations on real datasets corroborate our findings and demonstrate that CAT and its variations indeed enhance the language modeling performance.

Medical Large Language Models (LLMs) such as ClinicalCamel 70B, Llama3-OpenBioLLM 70B have demonstrated impressive performance on a wide variety of medical NLP task.However, there still lacks a large language model (LLM) specifically designed for cancer domain. Moreover, these LLMs typically have billions of parameters, making them computationally expensive for healthcare systems.Thus, in this study, we propose CancerLLM, a model with 7 billion parameters and a Mistral-style architecture, pre-trained on 2,676,642 clinical notes and 515,524 pathology reports covering 17 cancer types, followed by fine-tuning on three cancer-relevant tasks, including cancer phenotypes extraction, and cancer diagnosis generation. Our evaluation demonstrated that CancerLLM achieves state-of-the-art results compared to other existing LLMs, with an average F1 score improvement of 7.61 %. Additionally, CancerLLM outperforms other models on two proposed robustness testbeds. This illustrates that CancerLLM can be effectively applied to clinical AI systems, enhancing clinical research and healthcare delivery in the field of cancer., Comment: add the diagnosis evaluation of ICD code

Large language models (LLM) have demonstrated remarkable capabilities in various biomedical natural language processing (NLP) tasks, leveraging the demonstration within the input context to adapt to new tasks. However, LLM is sensitive to the selection of demonstrations. To address the hallucination issue inherent in LLM, retrieval-augmented LLM (RAL) offers a solution by retrieving pertinent information from an established database. Nonetheless, existing research work lacks rigorous evaluation of the impact of retrieval-augmented large language models on different biomedical NLP tasks. This deficiency makes it challenging to ascertain the capabilities of RAL within the biomedical domain. Moreover, the outputs from RAL are affected by retrieving the unlabeled, counterfactual, or diverse knowledge that is not well studied in the biomedical domain. However, such knowledge is common in the real world. Finally, exploring the self-awareness ability is also crucial for the RAL system. So, in this paper, we systematically investigate the impact of RALs on 5 different biomedical tasks (triple extraction, link prediction, classification, question answering, and natural language inference). We analyze the performance of RALs in four fundamental abilities, including unlabeled robustness, counterfactual robustness, diverse robustness, and negative awareness. To this end, we proposed an evaluation framework to assess the RALs' performance on different biomedical NLP tasks and establish four different testbeds based on the aforementioned fundamental abilities. Then, we evaluate 3 representative LLMs with 3 different retrievers on 5 tasks over 9 datasets.

Large Language Models (LLMs) have swiftly emerged as vital resources for different applications in the biomedical and healthcare domains; however, these models encounter issues such as generating inaccurate information or hallucinations. Retrieval-augmented generation provided a solution for these models to update knowledge and enhance their performance. In contrast to previous retrieval-augmented LMs, which utilize specialized cross-attention mechanisms to help LLM encode retrieved text, BiomedRAG adopts a simpler approach by directly inputting the retrieved chunk-based documents into the LLM. This straightforward design is easily applicable to existing retrieval and language models, effectively bypassing noise information in retrieved documents, particularly in noise-intensive tasks. Moreover, we demonstrate the potential for utilizing the LLM to supervise the retrieval model in the biomedical domain, enabling it to retrieve the document that assists the LM in improving its predictions. Our experiments reveal that with the tuned scorer,\textsc{ BiomedRAG} attains superior performance across 5 biomedical NLP tasks, encompassing information extraction (triple extraction, relation extraction), text classification, link prediction, and question-answering, leveraging over 9 datasets. For instance, in the triple extraction task, \textsc{BiomedRAG} outperforms other triple extraction systems with micro-F1 scores of 81.42 and 88.83 on GIT and ChemProt corpora, respectively.

Fine-tuning Pre-trained protein language models (PLMs) has emerged as a prominent strategy for enhancing downstream prediction tasks, often outperforming traditional supervised learning approaches. As a widely applied powerful technique in natural language processing, employing Parameter-Efficient Fine-Tuning techniques could potentially enhance the performance of PLMs. However, the direct transfer to life science tasks is non-trivial due to the different training strategies and data forms. To address this gap, we introduce SES-Adapter, a simple, efficient, and scalable adapter method for enhancing the representation learning of PLMs. SES-Adapter incorporates PLM embeddings with structural sequence embeddings to create structure-aware representations. We show that the proposed method is compatible with different PLM architectures and across diverse tasks. Extensive evaluations are conducted on 2 types of folding structures with notable quality differences, 9 state-of-the-art baselines, and 9 benchmark datasets across distinct downstream tasks. Results show that compared to vanilla PLMs, SES-Adapter improves downstream task performance by a maximum of 11% and an average of 3%, with significantly accelerated training speed by a maximum of 1034% and an average of 362%, the convergence rate is also improved by approximately 2 times. Moreover, positive optimization is observed even with low-quality predicted structures. The source code for SES-Adapter is available at https://github.com/tyang816/SES-Adapter., Comment: 30 pages, 4 figures, 8 tables

Zero-shot link prediction (ZSLP) on knowledge graphs aims at automatically identifying relations between given entities. Existing methods primarily employ auxiliary information to predict tail entity given head entity and its relation, yet face challenges due to the occasional unavailability of such detailed information and the inherent simplicity of predicting tail entities based on semantic similarities. Even though Large Language Models (LLMs) offer a promising solution to predict unobserved relations between the head and tail entity in a zero-shot manner, their performance is still restricted due to the inability to leverage all the (exponentially many) paths' information between two entities, which are critical in collectively indicating their relation types. To address this, in this work, we introduce a Condensed Transition Graph Framework for Zero-Shot Link Prediction (CTLP), which encodes all the paths' information in linear time complexity to predict unseen relations between entities, attaining both efficiency and information preservation. Specifically, we design a condensed transition graph encoder with theoretical guarantees on its coverage, expressiveness, and efficiency. It is learned by a transition graph contrastive learning strategy. Subsequently, we design a soft instruction tuning to learn and map the all-path embedding to the input of LLMs. Experimental results show that our proposed CTLP method achieves state-of-the-art performance on three standard ZSLP datasets

Biomedical triple extraction systems aim to automatically extract biomedical entities and relations between entities. The exploration of applying large language models (LLM) to triple extraction is still relatively unexplored. In this work, we mainly focus on sentence-level biomedical triple extraction. Furthermore, the absence of a high-quality biomedical triple extraction dataset impedes the progress in developing robust triple extraction systems. To address these challenges, initially, we compare the performance of various large language models. Additionally, we present GIT, an expert-annotated biomedical triple extraction dataset that covers a wider range of relation types., Comment: this is the onging work

Large protein language models are adept at capturing the underlying evolutionary information in primary structures, offering significant practical value for protein engineering. Compared to natural language models, protein amino acid sequences have a smaller data volume and a limited combinatorial space. Choosing an appropriate vocabulary size to optimize the pre-trained model is a pivotal issue. Moreover, despite the wealth of benchmarks and studies in the natural language community, there remains a lack of a comprehensive benchmark for systematically evaluating protein language model quality. Given these challenges, PETA trained language models with 14 different vocabulary sizes under three tokenization methods. It conducted thousands of tests on 33 diverse downstream datasets to assess the models' transfer learning capabilities, incorporating two classification heads and three random seeds to mitigate potential biases. Extensive experiments indicate that vocabulary sizes between 50 and 200 optimize the model, whereas sizes exceeding 800 detrimentally affect the model's representational performance. Our code, model weights and datasets are available at https://github.com/ginnm/ProteinPretraining., Comment: 46 pages, 4figures, 9 tables

Reinforcement learning (RL) has emerged as a powerful approach for tackling complex medical decision-making problems such as treatment planning, personalized medicine, and optimizing the scheduling of surgeries and appointments. It has gained significant attention in the field of Natural Language Processing (NLP) due to its ability to learn optimal strategies for tasks such as dialogue systems, machine translation, and question-answering. This paper presents a review of the RL techniques in NLP, highlighting key advancements, challenges, and applications in healthcare. The review begins by visualizing a roadmap of machine learning and its applications in healthcare. And then it explores the integration of RL with NLP tasks. We examined dialogue systems where RL enables the learning of conversational strategies, RL-based machine translation models, question-answering systems, text summarization, and information extraction. Additionally, ethical considerations and biases in RL-NLP systems are addressed.

Neural Machine Translation (NMT) models have become successful, but their performance remains poor when translating on new domains with a limited number of data. In this paper, we present a novel approach Epi-Curriculum to address low-resource domain adaptation (DA), which contains a new episodic training framework along with denoised curriculum learning. Our episodic training framework enhances the model's robustness to domain shift by episodically exposing the encoder/decoder to an inexperienced decoder/encoder. The denoised curriculum learning filters the noised data and further improves the model's adaptability by gradually guiding the learning process from easy to more difficult tasks. Experiments on English-German and English-Romanian translation show that: (i) Epi-Curriculum improves both model's robustness and adaptability in seen and unseen domains; (ii) Our episodic training framework enhances the encoder and decoder's robustness to domain shift.

Generative large language models (LLMs) have shown great success in various applications, including question-answering (QA) and dialogue systems. However, in specialized domains like traditional Chinese medical QA, these models may perform unsatisfactorily without fine-tuning on domain-specific datasets. To address this, we introduce MedChatZH, a dialogue model designed specifically for traditional Chinese medical QA. Our model is pre-trained on Chinese traditional medical books and fine-tuned with a carefully curated medical instruction dataset. It outperforms several solid baselines on a real-world medical dialogue dataset. We release our model, code, and dataset on https://github.com/tyang816/MedChatZH to facilitate further research in the domain of traditional Chinese medicine and LLMs., Comment: 7 pages, 3 figures

Recent advancements in language models (LMs) have led to the emergence of powerful models such as Small LMs (e.g., T5) and Large LMs (e.g., GPT-4). These models have demonstrated exceptional capabilities across a wide range of tasks, such as name entity recognition (NER) in the general domain. (We define SLMs as pre-trained models with fewer parameters compared to models like GPT-3/3.5/4, such as T5, BERT, and others.) Nevertheless, their efficacy in the medical section remains uncertain and the performance of medical NER always needs high accuracy because of the particularity of the field. This paper aims to provide a thorough investigation to compare the performance of LMs in medical few-shot NER and answer How far is LMs from 100\% Few-shot NER in Medical Domain, and moreover to explore an effective entity recognizer to help improve the NER performance. Based on our extensive experiments conducted on 16 NER models spanning from 2018 to 2023, our findings clearly indicate that LLMs outperform SLMs in few-shot medical NER tasks, given the presence of suitable examples and appropriate logical frameworks. Despite the overall superiority of LLMs in few-shot medical NER tasks, it is important to note that they still encounter some challenges, such as misidentification, wrong template prediction, etc. Building on previous findings, we introduce a simple and effective method called \textsc{RT} (Retrieving and Thinking), which serves as retrievers, finding relevant examples, and as thinkers, employing a step-by-step reasoning process. Experimental results show that our proposed \textsc{RT} framework significantly outperforms the strong open baselines on the two open medical benchmark datasets, Comment: Published as a journal paper at Journal of the American Medical Informatics Association (JAMIA). arXiv admin note: text overlap with arXiv:2305.18624

Contrastive learning has become a popular solution for few-shot Name Entity Recognization (NER). The conventional configuration strives to reduce the distance between tokens with the same labels and increase the distance between tokens with different labels. The effect of this setup may, however, in the medical domain, there are a lot of entities annotated as OUTSIDE (O), and they are undesirably pushed apart to other entities that are not labeled as OUTSIDE (O) by the current contrastive learning method end up with a noisy prototype for the semantic representation of the label, though there are many OUTSIDE (O) labeled entities are relevant to the labeled entities. To address this challenge, we propose a novel method named Weighted Prototypical Contrastive Learning for Medical Few Shot Named Entity Recognization (W-PROCER). Our approach primarily revolves around constructing the prototype-based contractive loss and weighting network. These components play a crucial role in assisting the model in differentiating the negative samples from OUTSIDE (O) tokens and enhancing the discrimination ability of contrastive learning. Experimental results show that our proposed W-PROCER framework significantly outperforms the strong baselines on the three medical benchmark datasets., Comment: Under Review

Due to the incompleteness of knowledge graphs (KGs), zero-shot link prediction (ZSLP) which aims to predict unobserved relations in KGs has attracted recent interest from researchers. A common solution is to use textual features of relations (e.g., surface name or textual descriptions) as auxiliary information to bridge the gap between seen and unseen relations. Current approaches learn an embedding for each word token in the text. These methods lack robustness as they suffer from the out-of-vocabulary (OOV) problem. Meanwhile, models built on character n-grams have the capability of generating expressive representations for OOV words. Thus, in this paper, we propose a Hierarchical N-Gram framework for Zero-Shot Link Prediction (HNZSLP), which considers the dependencies among character n-grams of the relation surface name for ZSLP. Our approach works by first constructing a hierarchical n-gram graph on the surface name to model the organizational structure of n-grams that leads to the surface name. A GramTransformer, based on the Transformer is then presented to model the hierarchical n-gram graph to construct the relation embedding for ZSLP. Experimental results show the proposed HNZSLP achieved state-of-the-art performance on two ZSLP datasets., Comment: Published as a conference paper at EMNLP Findings 2022

Building query graphs from natural language questions is an important step in complex question answering over knowledge graph (Complex KGQA). In general, a question can be correctly answered if its query graph is built correctly and the right answer is then retrieved by issuing the query graph against the KG. Therefore, this paper focuses on query graph generation from natural language questions. Existing approaches for query graph generation ignore the semantic structure of a question, resulting in a large number of noisy query graph candidates that undermine prediction accuracies. In this paper, we define six semantic structures from common questions in KGQA and develop a novel Structure-BERT to predict the semantic structure of a question. By doing so, we can first filter out noisy candidate query graphs, and then rank the remaining candidates with a BERT-based ranking model. Extensive experiments on two popular benchmarks MetaQA and WebQuestionsSP (WSP) demonstrate the effectiveness of our method as compared to state-of-the-arts., Comment: Published as a conference paper at COLING 2022

Short text is becoming more and more popular on the web, such as Chat Message, SMS and Product Reviews. Accurately classifying short text is an important and challenging task. A number of studies have difficulties in addressing this problem because of the word ambiguity and data sparsity. To address this issue, we propose a knowledge powered attention with similarity matrix based convolutional neural network (KASM) model, which can compute comprehensive information by utilizing the knowledge and deep neural network. We use knowledge graph (KG) to enrich the semantic representation of short text, specially, the information of parent-entity is introduced in our model. Meanwhile, we consider the word interaction in the literal-level between short text and the representation of label, and utilize similarity matrix based convolutional neural network (CNN) to extract it. For the purpose of measuring the importance of knowledge, we introduce the attention mechanisms to choose the important information. Experimental results on five standard datasets show that our model significantly outperforms state-of-the-art methods., Comment: there is an error in this paper

Princeton WordNet (PWN) is a lexicon-semantic network based on cognitive linguistics, which promotes the development of natural language processing. Based on PWN, five Chinese wordnets have been developed to solve the problems of syntax and semantics. They include: Northeastern University Chinese WordNet (NEW), Sinica Bilingual Ontological WordNet (BOW), Southeast University Chinese WordNet (SEW), Taiwan University Chinese WordNet (CWN), Chinese Open WordNet (COW). By using them, we found that these word networks have low accuracy and coverage, and cannot completely portray the semantic network of PWN. So we decided to make a new Chinese wordnet called Multi-Fusion Chinese Wordnet (MCW) to make up those shortcomings. The key idea is to extend the SEW with the help of Oxford bilingual dictionary and Xinhua bilingual dictionary, and then correct it. More specifically, we used machine learning and manual adjustment in our corrections. Two standards were formulated to help our work. We conducted experiments on three tasks including relatedness calculation, word similarity and word sense disambiguation for the comparison of lemma's accuracy, at the same time, coverage also was compared. The results indicate that MCW can benefit from coverage and accuracy via our method. However, it still has room for improvement, especially with lemmas. In the future, we will continue to enhance the accuracy of MCW and expand the concepts in it., Comment: 7 pages. CICLing 2019: International Conference on Computational Linguistics and Intelligent Text Processing