Mujeen Sung

Mujeen Sung, Jungsoo Park, Jaewoo Kang et al. · princeton

Recent developments of dense retrieval rely on quality representations of queries and contexts from pre-trained query and context encoders. In this paper, we introduce TOUR (Test-Time Optimization of Query Representations), which further optimizes instance-level query representations guided by signals from test-time retrieval results. We leverage a cross-encoder re-ranker to provide fine-grained pseudo labels over retrieval results and iteratively optimize query representations with gradient descent. Our theoretical analysis reveals that TOUR can be viewed as a generalization of the classical Rocchio algorithm for pseudo relevance feedback, and we present two variants that leverage pseudo-labels as hard binary or soft continuous labels. We first apply TOUR on phrase retrieval with our proposed phrase re-ranker, and also evaluate its effectiveness on passage retrieval with an off-the-shelf re-ranker. TOUR greatly improves end-to-end open-domain question answering accuracy, as well as passage retrieval performance. TOUR also consistently improves direct re-ranking by up to 2.0% while running 1.3-2.4x faster with an efficient implementation.

Chanhwi Kim, Hyunjae Kim, Sihyeon Park et al.

Generative models have become widely used in biomedical entity linking (BioEL) due to their excellent performance and efficient memory usage. However, these models are usually trained only with positive samples, i.e., entities that match the input mention's identifier, and do not explicitly learn from hard negative samples, which are entities that look similar but have different meanings. To address this limitation, we introduce ANGEL (Learning from Negative Samples in Biomedical Generative Entity Linking), the first framework that trains generative BioEL models using negative samples. Specifically, a generative model is initially trained to generate positive entity names from the knowledge base for given input entities. Subsequently, both correct and incorrect outputs are gathered from the model's top-k predictions. Finally, the model is updated to prioritize the correct predictions through preference optimization. Our models outperform the previous best baseline models by up to an average top-1 accuracy of 1.4% on five benchmarks. When incorporating our framework into pre-training, the performance improvement increases further to 1.7%, demonstrating its effectiveness in both the pre-training and fine-tuning stages. The code and model weights are available at https://github.com/dmis-lab/ANGEL.

Gangwoo Kim, Hajung Kim, Lei Ji et al.

In this paper, we introduce CheXOFA, a new pre-trained vision-language model (VLM) for the chest X-ray domain. Our model is initially pre-trained on various multimodal datasets within the general domain before being transferred to the chest X-ray domain. Following a prominent VLM, we unify various domain-specific tasks into a simple sequence-to-sequence schema. It enables the model to effectively learn the required knowledge and skills from limited resources in the domain. Demonstrating superior performance on the benchmark datasets provided by the BioNLP shared task, our model benefits from its training across multiple tasks and domains. With subtle techniques including ensemble and factual calibration, our system achieves first place on the RadSum23 leaderboard for the hidden test set.

Jiwoong Sohn, Yein Park, Chanwoong Yoon et al.

Large language models (LLM) hold significant potential for applications in biomedicine, but they struggle with hallucinations and outdated knowledge. While retrieval-augmented generation (RAG) is generally employed to address these issues, it also has its own set of challenges: (1) LLMs are vulnerable to irrelevant or incorrect context, (2) medical queries are often not well-targeted for helpful information, and (3) retrievers are prone to bias toward the specific source corpus they were trained on. In this study, we present RAG$^2$ (RAtionale-Guided RAG), a new framework for enhancing the reliability of RAG in biomedical contexts. RAG$^2$ incorporates three key innovations: a small filtering model trained on perplexity-based labels of rationales, which selectively augments informative snippets of documents while filtering out distractors; LLM-generated rationales as queries to improve the utility of retrieved snippets; a structure designed to retrieve snippets evenly from a comprehensive set of four biomedical corpora, effectively mitigating retriever bias. Our experiments demonstrate that RAG$^2$ improves the state-of-the-art LLMs of varying sizes, with improvements of up to 6.1\%, and it outperforms the previous best medical RAG model by up to 5.6\% across three medical question-answering benchmarks. Our code is available at https://github.com/dmis-lab/RAG2.

Hyogun Lee, Soyeon Hong, Mujeen Sung et al.

In this work, we tackle the problem of long-form video-language grounding (VLG). Given a long-form video and a natural language query, a model should temporally localize the precise moment that answers the query. Humans can easily solve VLG tasks, even with arbitrarily long videos, by discarding irrelevant moments using extensive and robust knowledge gained from experience. Unlike humans, existing VLG methods are prone to fall into superficial cues learned from small-scale datasets, even when they are within irrelevant frames. To overcome this challenge, we propose EI-VLG, a VLG method that leverages richer textual information provided by a Multi-modal Large Language Model (MLLM) as a proxy for human experiences, helping to effectively exclude irrelevant frames. We validate the effectiveness of the proposed method via extensive experiments on a challenging EgoNLQ benchmark.

Minbyul Jeong, Jiwoong Sohn, Mujeen Sung et al.

Recent proprietary large language models (LLMs), such as GPT-4, have achieved a milestone in tackling diverse challenges in the biomedical domain, ranging from multiple-choice questions to long-form generations. To address challenges that still cannot be handled with the encoded knowledge of LLMs, various retrieval-augmented generation (RAG) methods have been developed by searching documents from the knowledge corpus and appending them unconditionally or selectively to the input of LLMs for generation. However, when applying existing methods to different domain-specific problems, poor generalization becomes apparent, leading to fetching incorrect documents or making inaccurate judgments. In this paper, we introduce Self-BioRAG, a framework reliable for biomedical text that specializes in generating explanations, retrieving domain-specific documents, and self-reflecting generated responses. We utilize 84k filtered biomedical instruction sets to train Self-BioRAG that can assess its generated explanations with customized reflective tokens. Our work proves that domain-specific components, such as a retriever, domain-related document corpus, and instruction sets are necessary for adhering to domain-related instructions. Using three major medical question-answering benchmark datasets, experimental results of Self-BioRAG demonstrate significant performance gains by achieving a 7.2% absolute improvement on average over the state-of-the-art open-foundation model with a parameter size of 7B or less. Overall, we analyze that Self-BioRAG finds the clues in the question, retrieves relevant documents if needed, and understands how to answer with information from retrieved documents and encoded knowledge as a medical expert does. We release our data and code for training our framework components and model weights (7B and 13B) to enhance capabilities in biomedical and clinical domains.

Hajung Kim, Chanhwi Kim, Jiwoong Sohn et al.

The objective of BioCreative8 Track 3 is to extract phenotypic key medical findings embedded within EHR texts and subsequently normalize these findings to their Human Phenotype Ontology (HPO) terms. However, the presence of diverse surface forms in phenotypic findings makes it challenging to accurately normalize them to the correct HPO terms. To address this challenge, we explored various models for named entity recognition and implemented data augmentation techniques such as synonym marginalization to enhance the normalization step. Our pipeline resulted in an exact extraction and normalization F1 score 2.6\% higher than the mean score of all submissions received in response to the challenge. Furthermore, in terms of the normalization F1 score, our approach surpassed the average performance by 1.9\%. These findings contribute to the advancement of automated medical data extraction and normalization techniques, showcasing potential pathways for future research and application in the biomedical domain.

Donghee Choi, Mogan Gim, Donghyeon Park et al.

This paper introduces CookingSense, a descriptive collection of knowledge assertions in the culinary domain extracted from various sources, including web data, scientific papers, and recipes, from which knowledge covering a broad range of aspects is acquired. CookingSense is constructed through a series of dictionary-based filtering and language model-based semantic filtering techniques, which results in a rich knowledgebase of multidisciplinary food-related assertions. Additionally, we present FoodBench, a novel benchmark to evaluate culinary decision support systems. From evaluations with FoodBench, we empirically prove that CookingSense improves the performance of retrieval augmented language models. We also validate the quality and variety of assertions in CookingSense through qualitative analysis.

Yongwoo Song, Minbyul Jeong, Mujeen Sung

Large language models (LLMs) show promise for extracting information from Electronic Health Records (EHR) and supporting clinical decisions. However, deployment in clinical settings faces challenges due to hallucination risks. We propose Hallucination Controlled Accuracy at k% (HCAcc@k%), a novel metric quantifying the accuracy-reliability trade-off at varying confidence thresholds. We introduce TrustEHRAgent, a confidence-aware agent incorporating stepwise confidence estimation for clinical question answering. Experiments on MIMIC-III and eICU datasets show TrustEHRAgent outperforms baselines under strict reliability constraints, achieving improvements of 44.23%p and 25.34%p at HCAcc@70% while baseline methods fail at these thresholds. These results highlight limitations of traditional accuracy metrics in evaluating healthcare AI agents. Our work contributes to developing trustworthy clinical agents that deliver accurate information or transparently express uncertainty when confidence is low.

Mujeen Sung, James Gung, Elman Mansimov et al.

Intent classification (IC) plays an important role in task-oriented dialogue systems. However, IC models often generalize poorly when training without sufficient annotated examples for each user intent. We propose a novel pre-training method for text encoders that uses contrastive learning with intent psuedo-labels to produce embeddings that are well-suited for IC tasks, reducing the need for manual annotations. By applying this pre-training strategy, we also introduce Pre-trained Intent-aware Encoder (PIE), which is designed to align encodings of utterances with their intent names. Specifically, we first train a tagger to identify key phrases within utterances that are crucial for interpreting intents. We then use these extracted phrases to create examples for pre-training a text encoder in a contrastive manner. As a result, our PIE model achieves up to 5.4% and 4.0% higher accuracy than the previous state-of-the-art text encoder for the N-way zero- and one-shot settings on four IC datasets.

Mujeen Sung, Minbyul Jeong, Yonghwa Choi et al.

In biomedical natural language processing, named entity recognition (NER) and named entity normalization (NEN) are key tasks that enable the automatic extraction of biomedical entities (e.g. diseases and drugs) from the ever-growing biomedical literature. In this article, we present BERN2 (Advanced Biomedical Entity Recognition and Normalization), a tool that improves the previous neural network-based NER tool by employing a multi-task NER model and neural network-based NEN models to achieve much faster and more accurate inference. We hope that our tool can help annotate large-scale biomedical texts for various tasks such as biomedical knowledge graph construction.

Hyunjae Kim, Mujeen Sung, Wonjin Yoon et al.

This paper is a technical report on our system submitted to the chemical identification task of the BioCreative VII Track 2 challenge. The main feature of this challenge is that the data consists of full-text articles, while current datasets usually consist of only titles and abstracts. To effectively address the problem, we aim to improve tagging consistency and entity coverage using various methods such as majority voting within the same articles for named entity recognition (NER) and a hybrid approach that combines a dictionary and a neural model for normalization. In the experiments on the NLM-Chem dataset, we show that our methods improve models' performance, particularly in terms of recall. Finally, in the official evaluation of the challenge, our system was ranked 1st in NER by significantly outperforming the baseline model and more than 80 submissions from 16 teams.

Mujeen Sung, Jinhyuk Lee, Sean Yi et al.

Pre-trained language models (LMs) have become ubiquitous in solving various natural language processing (NLP) tasks. There has been increasing interest in what knowledge these LMs contain and how we can extract that knowledge, treating LMs as knowledge bases (KBs). While there has been much work on probing LMs in the general domain, there has been little attention to whether these powerful LMs can be used as domain-specific KBs. To this end, we create the BioLAMA benchmark, which is comprised of 49K biomedical factual knowledge triples for probing biomedical LMs. We find that biomedical LMs with recently proposed probing methods can achieve up to 18.51% Acc@5 on retrieving biomedical knowledge. Although this seems promising given the task difficulty, our detailed analyses reveal that most predictions are highly correlated with prompt templates without any subjects, hence producing similar results on each relation and hindering their capabilities to be used as domain-specific KBs. We hope that BioLAMA can serve as a challenging benchmark for biomedical factual probing.

Jinhyuk Lee, Mujeen Sung, Jaewoo Kang et al.

Open-domain question answering can be reformulated as a phrase retrieval problem, without the need for processing documents on-demand during inference (Seo et al., 2019). However, current phrase retrieval models heavily depend on sparse representations and still underperform retriever-reader approaches. In this work, we show for the first time that we can learn dense representations of phrases alone that achieve much stronger performance in open-domain QA. We present an effective method to learn phrase representations from the supervision of reading comprehension tasks, coupled with novel negative sampling methods. We also propose a query-side fine-tuning strategy, which can support transfer learning and reduce the discrepancy between training and inference. On five popular open-domain QA datasets, our model DensePhrases improves over previous phrase retrieval models by 15%-25% absolute accuracy and matches the performance of state-of-the-art retriever-reader models. Our model is easy to parallelize due to pure dense representations and processes more than 10 questions per second on CPUs. Finally, we directly use our pre-indexed dense phrase representations for two slot filling tasks, showing the promise of utilizing DensePhrases as a dense knowledge base for downstream tasks.

Minbyul Jeong, Mujeen Sung, Gangwoo Kim et al.

Biomedical question answering (QA) is a challenging task due to the scarcity of data and the requirement of domain expertise. Pre-trained language models have been used to address these issues. Recently, learning relationships between sentence pairs has been proved to improve performance in general QA. In this paper, we focus on applying BioBERT to transfer the knowledge of natural language inference (NLI) to biomedical QA. We observe that BioBERT trained on the NLI dataset obtains better performance on Yes/No (+5.59%), Factoid (+0.53%), List type (+13.58%) questions compared to performance obtained in a previous challenge (BioASQ 7B Phase B). We present a sequential transfer learning method that significantly performed well in the 8th BioASQ Challenge (Phase B). In sequential transfer learning, the order in which tasks are fine-tuned is important. We measure an unanswerable rate of the extractive QA setting when the formats of factoid and list type questions are converted to the format of the Stanford Question Answering Dataset (SQuAD).

Jinhyuk Lee, Sean S. Yi, Minbyul Jeong et al.

The recent outbreak of the novel coronavirus is wreaking havoc on the world and researchers are struggling to effectively combat it. One reason why the fight is difficult is due to the lack of information and knowledge. In this work, we outline our effort to contribute to shrinking this knowledge vacuum by creating covidAsk, a question answering (QA) system that combines biomedical text mining and QA techniques to provide answers to questions in real-time. Our system also leverages information retrieval (IR) approaches to provide entity-level answers that are complementary to QA models. Evaluation of covidAsk is carried out by using a manually created dataset called COVID-19 Questions which is based on information from various sources, including the CDC and the WHO. We hope our system will be able to aid researchers in their search for knowledge and information not only for COVID-19, but for future pandemics as well.

Mujeen Sung, Hwisang Jeon, Jinhyuk Lee et al.

Biomedical named entities often play important roles in many biomedical text mining tools. However, due to the incompleteness of provided synonyms and numerous variations in their surface forms, normalization of biomedical entities is very challenging. In this paper, we focus on learning representations of biomedical entities solely based on the synonyms of entities. To learn from the incomplete synonyms, we use a model-based candidate selection and maximize the marginal likelihood of the synonyms present in top candidates. Our model-based candidates are iteratively updated to contain more difficult negative samples as our model evolves. In this way, we avoid the explicit pre-selection of negative samples from more than 400K candidates. On four biomedical entity normalization datasets having three different entity types (disease, chemical, adverse reaction), our model BioSyn consistently outperforms previous state-of-the-art models almost reaching the upper bound on each dataset.

Jungsoo Park, Mujeen Sung, Jinhyuk Lee et al.

Exposing diverse subword segmentations to neural machine translation (NMT) models often improves the robustness of machine translation as NMT models can experience various subword candidates. However, the diversification of subword segmentations mostly relies on the pre-trained subword language models from which erroneous segmentations of unseen words are less likely to be sampled. In this paper, we present adversarial subword regularization (ADVSR) to study whether gradient signals during training can be a substitute criterion for exposing diverse subword segmentations. We experimentally show that our model-based adversarial samples effectively encourage NMT models to be less sensitive to segmentation errors and improve the performance of NMT models in low-resource and out-domain datasets.