Ling Luo

Ling Luo, Chih-Hsuan Wei, Po-Ting Lai et al.

The automatic assignment of species information to the corresponding genes in a research article is a critically important step in the gene normalization task, whereby a gene mention is normalized and linked to a database record or identifier by a text-mining algorithm. Existing methods typically rely on heuristic rules based on gene and species co-occurrence in the article, but their accuracy is suboptimal. We therefore developed a high-performance method, using a novel deep learning-based framework, to classify whether there is a relation between a gene and a species. Instead of the traditional binary classification framework in which all possible pairs of genes and species in the same article are evaluated, we treat the problem as a sequence-labeling task such that only a fraction of the pairs needs to be considered. Our benchmarking results show that our approach obtains significantly higher performance compared to that of the rule-based baseline method for the species assignment task (from 65.8% to 81.3% in accuracy). The source code and data for species assignment are freely available at https://github.com/ncbi/SpeciesAssignment.

Po-Ting Lai, Chih-Hsuan Wei, Ling Luo et al.

Biomedical relation extraction (RE) is the task of automatically identifying and characterizing relations between biomedical concepts from free text. RE is a central task in biomedical natural language processing (NLP) research and plays a critical role in many downstream applications, such as literature-based discovery and knowledge graph construction. State-of-the-art methods were used primarily to train machine learning models on individual RE datasets, such as protein-protein interaction and chemical-induced disease relation. Manual dataset annotation, however, is highly expensive and time-consuming, as it requires domain knowledge. Existing RE datasets are usually domain-specific or small, which limits the development of generalized and high-performing RE models. In this work, we present a novel framework for systematically addressing the data heterogeneity of individual datasets and combining them into a large dataset. Based on the framework and dataset, we report on BioREx, a data-centric approach for extracting relations. Our evaluation shows that BioREx achieves significantly higher performance than the benchmark system trained on the individual dataset, setting a new SOTA from 74.4% to 79.6% in F-1 measure on the recently released BioRED corpus. We further demonstrate that the combined dataset can improve performance for five different RE tasks. In addition, we show that on average BioREx compares favorably to current best-performing methods such as transfer learning and multi-task learning. Finally, we demonstrate BioREx's robustness and generalizability in two independent RE tasks not previously seen in training data: drug-drug N-ary combination and document-level gene-disease RE. The integrated dataset and optimized method have been packaged as a stand-alone tool available at https://github.com/ncbi/BioREx.

Ling Luo, Pinaki Nath Chowdhury, Tao Xiang et al.

3D shape modeling is labor-intensive, time-consuming, and requires years of expertise. To facilitate 3D shape modeling, we propose a 3D shape generation network that takes a 3D VR sketch as a condition. We assume that sketches are created by novices without art training and aim to reconstruct geometrically realistic 3D shapes of a given category. To handle potential sketch ambiguity, our method creates multiple 3D shapes that align with the original sketch's structure. We carefully design our method, training the model step-by-step and leveraging multi-modal 3D shape representation to support training with limited training data. To guarantee the realism of generated 3D shapes we leverage the normalizing flow that models the distribution of the latent space of 3D shapes. To encourage the fidelity of the generated 3D shapes to an input sketch, we propose a dedicated loss that we deploy at different stages of the training process. The code is available at https://github.com/Rowl1ng/3Dsketch2shape.

Ling Luo, Yulia Gryaditskaya, Tao Xiang et al.

We study the practical task of fine-grained 3D-VR-sketch-based 3D shape retrieval. This task is of particular interest as 2D sketches were shown to be effective queries for 2D images. However, due to the domain gap, it remains hard to achieve strong performance in 3D shape retrieval from 2D sketches. Recent work demonstrated the advantage of 3D VR sketching on this task. In our work, we focus on the challenge caused by inherent inaccuracies in 3D VR sketches. We observe that retrieval results obtained with a triplet loss with a fixed margin value, commonly used for retrieval tasks, contain many irrelevant shapes and often just one or few with a similar structure to the query. To mitigate this problem, we for the first time draw a connection between adaptive margin values and shape similarities. In particular, we propose to use a triplet loss with an adaptive margin value driven by a "fitting gap", which is the similarity of two shapes under structure-preserving deformations. We also conduct a user study which confirms that this fitting gap is indeed a suitable criterion to evaluate the structural similarity of shapes. Furthermore, we introduce a dataset of 202 VR sketches for 202 3D shapes drawn from memory rather than from observation. The code and data are available at https://github.com/Rowl1ng/Structure-Aware-VR-Sketch-Shape-Retrieval.

Ling Luo, Po-Ting Lai, Chih-Hsuan Wei et al.

Automated relation extraction (RE) from biomedical literature is critical for many downstream text mining applications in both research and real-world settings. However, most existing benchmarking datasets for bio-medical RE only focus on relations of a single type (e.g., protein-protein interactions) at the sentence level, greatly limiting the development of RE systems in biomedicine. In this work, we first review commonly used named entity recognition (NER) and RE datasets. Then we present BioRED, a first-of-its-kind biomedical RE corpus with multiple entity types (e.g., gene/protein, disease, chemical) and relation pairs (e.g., gene-disease; chemical-chemical) at the document level, on a set of 600 PubMed abstracts. Further, we label each relation as describing either a novel finding or previously known background knowledge, enabling automated algorithms to differentiate between novel and background information. We assess the utility of BioRED by benchmarking several existing state-of-the-art methods, including BERT-based models, on the NER and RE tasks. Our results show that while existing approaches can reach high performance on the NER task (F-score of 89.3%), there is much room for improvement for the RE task, especially when extracting novel relations (F-score of 47.7%). Our experiments also demonstrate that such a rich dataset can successfully facilitate the development of more accurate, efficient, and robust RE systems for biomedicine. The BioRED dataset and annotation guideline are freely available at https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/.

Ling Luo, Chih-Hsuan Wei, Po-Ting Lai et al.

Biomedical named entity recognition (BioNER) seeks to automatically recognize biomedical entities in natural language text, serving as a necessary foundation for downstream text mining tasks and applications such as information extraction and question answering. Manually labeling training data for the BioNER task is costly, however, due to the significant domain expertise required for accurate annotation. The resulting data scarcity causes current BioNER approaches to be prone to overfitting, to suffer from limited generalizability, and to address a single entity type at a time (e.g., gene or disease). We therefore propose a novel all-in-one (AIO) scheme that uses external data from existing annotated resources to enhance the accuracy and stability of BioNER models. We further present AIONER, a general-purpose BioNER tool based on cutting-edge deep learning and our AIO schema. We evaluate AIONER on 14 BioNER benchmark tasks and show that AIONER is effective, robust, and compares favorably to other state-of-the-art approaches such as multi-task learning. We further demonstrate the practical utility of AIONER in three independent tasks to recognize entity types not previously seen in training data, as well as the advantages of AIONER over existing methods for processing biomedical text at a large scale (e.g., the entire PubMed data).

Ling Luo, Yulia Gryaditskaya, Yongxin Yang et al.

Growing free online 3D shapes collections dictated research on 3D retrieval. Active debate has however been had on (i) what the best input modality is to trigger retrieval, and (ii) the ultimate usage scenario for such retrieval. In this paper, we offer a different perspective towards answering these questions -- we study the use of 3D sketches as an input modality and advocate a VR-scenario where retrieval is conducted. Thus, the ultimate vision is that users can freely retrieve a 3D model by air-doodling in a VR environment. As a first stab at this new 3D VR-sketch to 3D shape retrieval problem, we make four contributions. First, we code a VR utility to collect 3D VR-sketches and conduct retrieval. Second, we collect the first set of $167$ 3D VR-sketches on two shape categories from ModelNet. Third, we propose a novel approach to generate a synthetic dataset of human-like 3D sketches of different abstract levels to train deep networks. At last, we compare the common multi-view and volumetric approaches: We show that, in contrast to 3D shape to 3D shape retrieval, volumetric point-based approaches exhibit superior performance on 3D sketch to 3D shape retrieval due to the sparse and abstract nature of 3D VR-sketches. We believe these contributions will collectively serve as enablers for future attempts at this problem. The VR interface, code and datasets are available at https://tinyurl.com/3DSketch3DV.

Ling Luo, Yulia Gryaditskaya, Yongxin Yang et al.

We present the first fine-grained dataset of 1,497 3D VR sketch and 3D shape pairs of a chair category with large shapes diversity. Our dataset supports the recent trend in the sketch community on fine-grained data analysis, and extends it to an actively developing 3D domain. We argue for the most convenient sketching scenario where the sketch consists of sparse lines and does not require any sketching skills, prior training or time-consuming accurate drawing. We then, for the first time, study the scenario of fine-grained 3D VR sketch to 3D shape retrieval, as a novel VR sketching application and a proving ground to drive out generic insights to inform future research. By experimenting with carefully selected combinations of design factors on this new problem, we draw important conclusions to help follow-on work. We hope our dataset will enable other novel applications, especially those that require a fine-grained angle such as fine-grained 3D shape reconstruction. The dataset is available at tinyurl.com/VRSketch3DV21.

Ling Luo, Jinzhong Ning, Yingwen Zhao et al.

Objective: Most existing fine-tuned biomedical large language models (LLMs) focus on enhancing performance in monolingual biomedical question answering and conversation tasks. To investigate the effectiveness of the fine-tuned LLMs on diverse biomedical NLP tasks in different languages, We present Taiyi, a bilingual fine-tuned LLM for diverse biomedical tasks. Materials and Methods: We first curated a comprehensive collection of 140 existing biomedical text mining datasets (102 English and 38 Chinese datasets) across over 10 task types. Subsequently, a two-stage strategy is proposed for supervised fine-tuning to optimize the model performance across varied tasks. Results: Experimental results on 13 test sets covering named entity recognition, relation extraction, text classification, question answering tasks demonstrate that Taiyi achieves superior performance compared to general LLMs. The case study involving additional biomedical NLP tasks further shows Taiyi's considerable potential for bilingual biomedical multi-tasking. Conclusion: Leveraging rich high-quality biomedical corpora and developing effective fine-tuning strategies can significantly improve the performance of LLMs within the biomedical domain. Taiyi shows the bilingual multi-tasking capability through supervised fine-tuning. However, those tasks such as information extraction that are not generation tasks in nature remain challenging for LLM-based generative approaches, and they still underperform the conventional discriminative approaches of smaller language models.

Feiyang Pan, Tongzhe Zhang, Ling Luo et al.

Optimal execution is a sequential decision-making problem for cost-saving in algorithmic trading. Studies have found that reinforcement learning (RL) can help decide the order-splitting sizes. However, a problem remains unsolved: how to place limit orders at appropriate limit prices? The key challenge lies in the "continuous-discrete duality" of the action space. On the one hand, the continuous action space using percentage changes in prices is preferred for generalization. On the other hand, the trader eventually needs to choose limit prices discretely due to the existence of the tick size, which requires specialization for every single stock with different characteristics (e.g., the liquidity and the price range). So we need continuous control for generalization and discrete control for specialization. To this end, we propose a hybrid RL method to combine the advantages of both of them. We first use a continuous control agent to scope an action subset, then deploy a fine-grained agent to choose a specific limit price. Extensive experiments show that our method has higher sample efficiency and better training stability than existing RL algorithms and significantly outperforms previous learning-based methods for order execution.

Juntao Li, Haobin Yuan, Ling Luo et al.

Intelligent drug recommendation based on Electronic Health Records (EHRs) is critical for improving for improving the quality and efficiency of clinical decision-making. By leveraging large-scale patient data, drug recommendation systems can assist physicians in selecting the most appropriate medications according to a patient's medical history, diagnoses, laboratory results, and comorbidities. However, the advancement of such systems is significantly hampered by the scarcity of publicly available, real-world EHR datasets, particularly in languages other than English. In this work, we present CDrugRed, a first publicly available Chinese drug recommendation dataset focused on discharge medications for metabolic diseases. The dataset includes 5,894 de-identified records from 3,190 patients, containing comprehensive information such as patient demographics, medical history, clinical course, and discharge diagnoses. We assess the utility of CDrugRed by benchmarking several state-of-the-art large language models (LLMs) on the discharge medication recommendation task. Experimental results show that while supervised fine-tuning improves model performance, there remains substantial room for improvement, with the best model achieving the F1 score of 0.5648 and Jaccard score of 0.4477. This result highlights the complexity of the clinical drug recommendation task and establishes CDrugRed as a challenging and valuable resource for developing more robust and accurate drug recommendation systems. The dataset is publicly available to the research community under the data usage agreements at https://github.com/DUTIR-BioNLP/CDrugRed.

Chenhao Gu, Ling Luo, Zainab Razia Zaidi et al.

The rise of echo chambers on social media platforms has heightened concerns about polarization and the reinforcement of existing beliefs. Traditional approaches for simulating echo chamber formation have often relied on predefined rules and numerical simulations, which, while insightful, may lack the nuance needed to capture complex, real-world interactions. In this paper, we present a novel framework that leverages large language models (LLMs) as generative agents to simulate echo chamber dynamics within social networks. The novelty of our approach is that it incorporates both opinion updates and network rewiring behaviors driven by LLMs, allowing for a context-aware and semantically rich simulation of social interactions. Additionally, we utilize real-world Twitter (now X) data to benchmark the LLM-based simulation against actual social media behaviors, providing insights into the accuracy and realism of the generated opinion trends. Our results demonstrate the efficacy of LLMs in modeling echo chamber formation, capturing both structural and semantic dimensions of opinion clustering. %This work contributes to a deeper understanding of social influence dynamics and offers a new tool for studying polarization in online communities.

Po-Ting Lai, Elisabeth Coudert, Lucila Aimo et al.

Expert curation is essential to capture knowledge of enzyme functions from the scientific literature in FAIR open knowledgebases but cannot keep pace with the rate of new discoveries and new publications. In this work we present EnzChemRED, for Enzyme Chemistry Relation Extraction Dataset, a new training and benchmarking dataset to support the development of Natural Language Processing (NLP) methods such as (large) language models that can assist enzyme curation. EnzChemRED consists of 1,210 expert curated PubMed abstracts in which enzymes and the chemical reactions they catalyze are annotated using identifiers from the UniProt Knowledgebase (UniProtKB) and the ontology of Chemical Entities of Biological Interest (ChEBI). We show that fine-tuning pre-trained language models with EnzChemRED can significantly boost their ability to identify mentions of proteins and chemicals in text (Named Entity Recognition, or NER) and to extract the chemical conversions in which they participate (Relation Extraction, or RE), with average F1 score of 86.30% for NER, 86.66% for RE for chemical conversion pairs, and 83.79% for RE for chemical conversion pairs and linked enzymes. We combine the best performing methods after fine-tuning using EnzChemRED to create an end-to-end pipeline for knowledge extraction from text and apply this to abstracts at PubMed scale to create a draft map of enzyme functions in literature to guide curation efforts in UniProtKB and the reaction knowledgebase Rhea. The EnzChemRED corpus is freely available at https://ftp.expasy.org/databases/rhea/nlp/.

Chih-Hsuan Wei, Alexis Allot, Po-Ting Lai et al.

PubTator 3.0 (https://www.ncbi.nlm.nih.gov/research/pubtator3/) is a biomedical literature resource using state-of-the-art AI techniques to offer semantic and relation searches for key concepts like proteins, genetic variants, diseases, and chemicals. It currently provides over one billion entity and relation annotations across approximately 36 million PubMed abstracts and 6 million full-text articles from the PMC open access subset, updated weekly. PubTator 3.0's online interface and API utilize these precomputed entity relations and synonyms to provide advanced search capabilities and enable large-scale analyses, streamlining many complex information needs. We showcase the retrieval quality of PubTator 3.0 using a series of entity pair queries, demonstrating that PubTator 3.0 retrieves a greater number of articles than either PubMed or Google Scholar, with higher precision in the top 20 results. We further show that integrating ChatGPT (GPT-4) with PubTator APIs dramatically improves the factuality and verifiability of its responses. In summary, PubTator 3.0 offers a comprehensive set of features and tools that allow researchers to navigate the ever-expanding wealth of biomedical literature, expediting research and unlocking valuable insights for scientific discovery.

Amila Silva, Ling Luo, Shanika Karunasekera et al.

The emergence of social media as one of the main platforms for people to access news has enabled the wide dissemination of fake news. This has motivated numerous studies on automating fake news detection. Although there have been limited attempts at unsupervised fake news detection, their performance suffers due to not exploiting the knowledge from various modalities related to news records and due to the presence of various latent biases in the existing news datasets. To address these limitations, this work proposes an effective framework for unsupervised fake news detection, which first embeds the knowledge available in four modalities in news records and then proposes a novel noise-robust self-supervised learning technique to identify the veracity of news records from the multi-modal embeddings. Also, we propose a novel technique to construct news datasets minimizing the latent biases in existing news datasets. Following the proposed approach for dataset construction, we produce a Large-scale Unlabelled News Dataset consisting 419,351 news articles related to COVID-19, acronymed as LUND-COVID. We trained the proposed unsupervised framework using LUND-COVID to exploit the potential of large datasets, and evaluate it using a set of existing labelled datasets. Our results show that the proposed unsupervised framework largely outperforms existing unsupervised baselines for different tasks such as multi-modal fake news detection, fake news early detection and few-shot fake news detection, while yielding notable improvements for unseen domains during training.

Amila Silva, Ling Luo, Shanika Karunasekera et al.

With the rapid evolution of social media, fake news has become a significant social problem, which cannot be addressed in a timely manner using manual investigation. This has motivated numerous studies on automating fake news detection. Most studies explore supervised training models with different modalities (e.g., text, images, and propagation networks) of news records to identify fake news. However, the performance of such techniques generally drops if news records are coming from different domains (e.g., politics, entertainment), especially for domains that are unseen or rarely-seen during training. As motivation, we empirically show that news records from different domains have significantly different word usage and propagation patterns. Furthermore, due to the sheer volume of unlabelled news records, it is challenging to select news records for manual labelling so that the domain-coverage of the labelled dataset is maximized. Hence, this work: (1) proposes a novel framework that jointly preserves domain-specific and cross-domain knowledge in news records to detect fake news from different domains; and (2) introduces an unsupervised technique to select a set of unlabelled informative news records for manual labelling, which can be ultimately used to train a fake news detection model that performs well for many domains while minimizing the labelling cost. Our experiments show that the integration of the proposed fake news model and the selective annotation approach achieves state-of-the-art performance for cross-domain news datasets, while yielding notable improvements for rarely-appearing domains in news datasets.

Ling Luo, Shankai Yan, Po-Ting Lai et al.

Automatic phenotype concept recognition from unstructured text remains a challenging task in biomedical text mining research. Previous works that address the task typically use dictionary-based matching methods, which can achieve high precision but suffer from lower recall. Recently, machine learning-based methods have been proposed to identify biomedical concepts, which can recognize more unseen concept synonyms by automatic feature learning. However, most methods require large corpora of manually annotated data for model training, which is difficult to obtain due to the high cost of human annotation. In this paper, we propose PhenoTagger, a hybrid method that combines both dictionary and machine learning-based methods to recognize Human Phenotype Ontology (HPO) concepts in unstructured biomedical text. We first use all concepts and synonyms in HPO to construct a dictionary, which is then used to automatically build a distantly supervised training dataset for machine learning. Next, a cutting-edge deep learning model is trained to classify each candidate phrase (n-gram from input sentence) into a corresponding concept label. Finally, the dictionary and machine learning-based prediction results are combined for improved performance. Our method is validated with two HPO corpora, and the results show that PhenoTagger compares favorably to previous methods. In addition, to demonstrate the generalizability of our method, we retrained PhenoTagger using the disease ontology MEDIC for disease concept recognition to investigate the effect of training on different ontologies. Experimental results on the NCBI disease corpus show that PhenoTagger without requiring manually annotated training data achieves competitive performance as compared with state-of-the-art supervised methods.

Jianfeng Liu, Feiyang Pan, Ling Luo

A chatbot that converses like a human should be goal-oriented (i.e., be purposeful in conversation), which is beyond language generation. However, existing dialogue systems often heavily rely on cumbersome hand-crafted rules or costly labelled datasets to reach the goals. In this paper, we propose Goal-oriented Chatbots (GoChat), a framework for end-to-end training chatbots to maximize the longterm return from offline multi-turn dialogue datasets. Our framework utilizes hierarchical reinforcement learning (HRL), where the high-level policy guides the conversation towards the final goal by determining some sub-goals, and the low-level policy fulfills the sub-goals by generating the corresponding utterance for response. In our experiments on a real-world dialogue dataset for anti-fraud in financial, our approach outperforms previous methods on both the quality of response generation as well as the success rate of accomplishing the goal.