Jiwoo Lee

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.

Jueon Park, Wonjune Jang, Jiwoo Lee et al.

Large Language Models (LLMs) and Vision Language Models (VLMs) have recently shown promising capabilities in various scientific domain. In particular, these advances have opened new opportunities in drug discovery, where the ability to understand and modify molecular structures is critical for optimizing drug properties such as efficacy and toxicity. However, existing models and benchmarks often overlook toxicity-related challenges, focusing primarily on general property optimization without adequately addressing safety concerns. In addition, even existing toxicity repair benchmarks suffer from limited data diversity, low structural validity of generated molecules, and heavy reliance on proxy models for toxicity assessment. To address these limitations, we propose MolDeTox, a novel benchmark for molecular detoxification, designed to enable fine-grained and reliable evaluation of toxicity-aware molecular optimization across stepwise tasks. We evaluate a wide range of general-purpose LLMs and VLMs under diverse settings, and demonstrate that understanding and generating molecules at the fragment-level improves structural validity and enhances the quality of generated molecules. Moreover, through detailed task-level performance analysis, MolDeTox provides an interpretable benchmark that enables a deeper understanding of the detoxification process. Our dataset is available at : https://huggingface.co/datasets/MolDeTox/MolDeTox

Hyunjae Kim, Hyeon Hwang, Jiwoo Lee et al.

While recent advancements in commercial large language models (LM) have shown promising results in medical tasks, their closed-source nature poses significant privacy and security concerns, hindering their widespread use in the medical field. Despite efforts to create open-source models, their limited parameters often result in insufficient multi-step reasoning capabilities required for solving complex medical problems. To address this, we introduce Meerkat, a new family of medical AI systems ranging from 7 to 70 billion parameters. The models were trained using our new synthetic dataset consisting of high-quality chain-of-thought reasoning paths sourced from 18 medical textbooks, along with diverse instruction-following datasets. Our systems achieved remarkable accuracy across six medical benchmarks, surpassing the previous best models such as MediTron and BioMistral, and GPT-3.5 by a large margin. Notably, Meerkat-7B surpassed the passing threshold of the United States Medical Licensing Examination (USMLE) for the first time for a 7B-parameter model, while Meerkat-70B outperformed GPT-4 by an average of 1.3%. Additionally, Meerkat-70B correctly diagnosed 21 out of 38 complex clinical cases, outperforming humans' 13.8 and closely matching GPT-4's 21.8. Our systems offered more detailed free-form responses to clinical queries compared to existing small models, approaching the performance level of large commercial models. This significantly narrows the performance gap with large LMs, showcasing its effectiveness in addressing complex medical challenges.

Heedou Kim, Dain Kim, Jiwoo Lee et al.

Crime situations are race against time. An AI-assisted criminal investigation system, providing prompt but precise legal counsel is in need for police officers. We introduce LAPIS (Language Model Augmented Police Investigation System), an automated system that assists police officers to perform rational and legal investigative actions. We constructed a finetuning dataset and retrieval knowledgebase specialized in crime investigation legal reasoning task. We extended the dataset's quality by incorporating manual curation efforts done by a group of domain experts. We then finetuned the pretrained weights of a smaller Korean language model to the newly constructed dataset and integrated it with the crime investigation knowledgebase retrieval approach. Experimental results show LAPIS' potential in providing reliable legal guidance for police officers, even better than the proprietary GPT-4 model. Qualitative analysis on the rationales generated by LAPIS demonstrate the model's reasoning ability to leverage the premises and derive legally correct conclusions.

Dain Kim, Jiwoo Lee, Jaehoon Yun et al.

Large Vision-Language Models (LVLMs) hold significant promise for medical applications, yet their deployment is often constrained by insufficient alignment and reliability. While Direct Preference Optimization (DPO) has emerged as a potent framework for refining model responses, its efficacy in high-stakes medical contexts remains underexplored, lacking the rigorous empirical groundwork necessary to guide future methodological advances. To bridge this gap, we present the first comprehensive examination of diverse DPO variants within the medical domain, evaluating nine distinct formulations across two medical LVLMs: LLaVA-Med and HuatuoGPT-Vision. Our results reveal several critical limitations: current DPO approaches often yield inconsistent gains over supervised fine-tuning, with their efficacy varying significantly across different tasks and backbones. Furthermore, they frequently fail to resolve fundamental visual misinterpretation errors. Building on these insights, we present a targeted preference construction strategy as a proof-of-concept that explicitly addresses visual misinterpretation errors frequently observed in existing DPO models. This design yields a 3.6% improvement over the strongest existing DPO baseline on visual question-answering tasks. To support future research, we release our complete framework, including all training data, model checkpoints, and our codebase at https://github.com/dmis-lab/med-vlm-dpo.

Dojun Park, Jiwoo Lee, Seohyun Park et al.

As the capabilities of Large Language Models (LLMs) expand, it becomes increasingly important to evaluate them beyond basic knowledge assessment, focusing on higher-level language understanding. This study introduces MultiPragEval, the first multilingual pragmatic evaluation of LLMs, designed for English, German, Korean, and Chinese. Comprising 1200 question units categorized according to Grice's Cooperative Principle and its four conversational maxims, MultiPragEval enables an in-depth assessment of LLMs' contextual awareness and their ability to infer implied meanings. Our findings demonstrate that Claude3-Opus significantly outperforms other models in all tested languages, establishing a state-of-the-art in the field. Among open-source models, Solar-10.7B and Qwen1.5-14B emerge as strong competitors. By analyzing pragmatic inference, we provide valuable insights into the capabilities essential for advanced language comprehension in AI systems.

Youngeun Koo, Jiwoo Lee, Dojun Park et al.

To accurately understand the intention of an utterance is crucial in conversational communication. As conversational artificial intelligence models are rapidly being developed and applied in various fields, it is important to evaluate the LLMs' capabilities of understanding the intentions of user's utterance. This study evaluates whether current LLMs can understand the intention of an utterance by considering the given conversational context, particularly in cases where the actual intention differs from the surface-leveled, literal intention of the sentence, i.e. indirect speech acts. Our findings reveal that Claude3-Opus outperformed the other competing models, with 71.94% in MCQ and 65% in OEQ, showing a clear advantage. In general, proprietary models exhibited relatively higher performance compared to open-source models. Nevertheless, no LLMs reached the level of human performance. Most LLMs, except for Claude3-Opus, demonstrated significantly lower performance in understanding indirect speech acts compared to direct speech acts, where the intention is explicitly revealed through the utterance. This study not only performs an overall pragmatic evaluation of each LLM's language use through the analysis of OEQ response patterns, but also emphasizes the necessity for further research to improve LLMs' understanding of indirect speech acts for more natural communication with humans.

Hyeon Hwang, Jiwoo Lee, Jaewoo Kang

Tool-integrated reasoning (TIR) has emerged as a dominant paradigm for mathematical problem solving in language models, combining natural language (NL) reasoning with code execution. However, this interleaved setup has three key limitations: code often acts as a post-hoc verifier, intermediate NL computations are error-prone, and NL and code play overlapping rather than clearly distinct roles. We propose ThinC (Thinking in Code), a framework in which code itself serves as the reasoner rather than as a tool invoked by NL. A ThinC trajectory begins with a brief NL planning step, after which all reasoning unfolds through code blocks connected only by their execution outputs. We distill 12.2k code-centric trajectories from a teacher model and train ThinC-1.7B and ThinC-4B with supervised fine-tuning followed by reinforcement learning. ThinC-4B consistently outperforms every TIR baseline on five competition-level math benchmarks and even surpasses the much larger Qwen3-235B-A22B-Thinking. Further analysis shows that ThinC reasons through code: 99.2% of its final answers are grounded in interpreter output, and the model recovers reliably from code execution failures without intermediate NL reasoning. Our code and models will be released soon.

Boseon Yoo, Jiwoo Lee, Janghoon Ju et al.

We introduce a novel loss function, Covariance Loss, which is conceptually equivalent to conditional neural processes and has a form of regularization so that is applicable to many kinds of neural networks. With the proposed loss, mappings from input variables to target variables are highly affected by dependencies of target variables as well as mean activation and mean dependencies of input and target variables. This nature enables the resulting neural networks to become more robust to noisy observations and recapture missing dependencies from prior information. In order to show the validity of the proposed loss, we conduct extensive sets of experiments on real-world datasets with state-of-the-art models and discuss the benefits and drawbacks of the proposed Covariance Loss.

Paul A. Ullrich, Elizabeth A. Barnes, William D. Collins et al.

Machine learning (ML) is a revolutionary technology with demonstrable applications across multiple disciplines. Within the Earth science community, ML has been most visible for weather forecasting, producing forecasts that rival modern physics-based models. Given the importance of deepening our understanding and improving predictions of the Earth system on all time scales, efforts are now underway to develop forecasting models into Earth-system models (ESMs), capable of representing all components of the coupled Earth system (or their aggregated behavior) and their response to external changes. Modeling the Earth system is a much more difficult problem than weather forecasting, not least because the model must represent the alternate (e.g., future) coupled states of the system for which there are no historical observations. Given that the physical principles that enable predictions about the response of the Earth system are often not explicitly coded in these ML-based models, demonstrating the credibility of ML-based ESMs thus requires us to build evidence of their consistency with the physical system. To this end, this paper puts forward five recommendations to enhance comprehensive, standardized, and independent evaluation of ML-based ESMs to strengthen their credibility and promote their wider use.

Jonghyun Lee, Dojun Park, Jiwoo Lee et al.

This study investigated whether multimodal large language models can achieve human-like sensory grounding by examining their ability to capture perceptual strength ratings across sensory modalities. We explored how model characteristics (size, multimodal capabilities, architectural generation) influence grounding performance, distributional factor dependencies (word frequency, embeddings, feature distances), and human-model processing differences. We evaluated 21 models from four families (GPT, Gemini, LLaMA, Qwen) using 3,611 words from the Lancaster Sensorimotor Norms through correlation, distance metrics, and qualitative analysis. Results showed that larger (6 out of 8 comparisons), multimodal (5 of 7), and newer models (5 of 8) generally outperformed their smaller, text-based, and older counterparts. Top models achieved 85-90% accuracy and 0.58-0.65 correlations with human ratings, demonstrating substantial similarity. Moreover, distributional factors showed minimal impact, not exceeding human dependency levels. However, despite strong alignment, models were not identical to humans, as even top performers showed differences in distance and correlation measures, with qualitative analysis revealing processing patterns related to absent sensory grounding. Additionally, it remains questionable whether introducing multimodality resolves this grounding deficit. Although multimodality improved performance, it seems to provide similar information as massive text rather than qualitatively different data, as benefits occurred across unrelated sensory dimensions and massive text-only models achieved comparable results. Our findings demonstrate that while advanced LLMs can approximate human sensory-linguistic associations through statistical learning, they still differ from human embodied cognition in processing mechanisms, even with multimodal integration.

Hajung Kim, Chanhwi Kim, Hoonick Lee et al.

Transforming natural language questions into SQL queries is crucial for precise data retrieval from electronic health record (EHR) databases. A significant challenge in this process is detecting and rejecting unanswerable questions that request information beyond the database's scope or exceed the system's capabilities. In this paper, we introduce a novel text-to-SQL framework that robustly handles out-of-domain questions and verifies the generated queries with query execution.Our framework begins by standardizing the structure of questions into a templated format. We use a powerful large language model (LLM), fine-tuned GPT-3.5 with detailed prompts involving the table schemas of the EHR database system. Our experimental results demonstrate the effectiveness of our framework on the EHRSQL-2024 benchmark benchmark, a shared task in the ClinicalNLP workshop. Although a straightforward fine-tuning of GPT shows promising results on the development set, it struggled with the out-of-domain questions in the test set. With our framework, we improve our system's adaptability and achieve competitive performances in the official leaderboard of the EHRSQL-2024 challenge.

Sehyun Kim, Hye Jun Lee, Jiwoo Lee et al.

The spinal angle is an important indicator of body balance. It is important to restore the 3D shape of the human body and estimate the spine center line. Existing mul-ti-image-based body restoration methods require expensive equipment and complex pro-cedures, and single image-based body restoration methods have limitations in that it is difficult to accurately estimate the internal structure such as the spine center line due to occlusion and viewpoint limitation. This study proposes a method to compensate for the shortcomings of the multi-image-based method and to solve the limitations of the sin-gle-image method. We propose a 3D body posture analysis system that integrates depth images from four directions to restore a 3D human model and automatically estimate the spine center line. Through hierarchical matching of global and fine registration, restora-tion to noise and occlusion is performed. Also, the Adaptive Vertex Reduction is applied to maintain the resolution and shape reliability of the mesh, and the accuracy and stabil-ity of spinal angle estimation are simultaneously secured by using the Level of Detail en-semble. The proposed method achieves high-precision 3D spine registration estimation without relying on training data or complex neural network models, and the verification confirms the improvement of matching quality.

Sehyun Kim, Hye Jun Lee, Jiwoo Lee et al.

With the development of deep learning technology, virtual try-on technology has devel-oped important application value in the fields of e-commerce, fashion, and entertainment. The recently proposed Leffa technology has addressed the texture distortion problem of diffusion-based models, but there are limitations in that the bottom detection inaccuracy and the existing clothing silhouette persist in the synthesis results. To solve this problem, this study proposes CaP-VTON (Clothing Agnostic Pre-Inpainting Virtual Try-On). CaP-VTON integrates DressCode-based multi-category masking and Stable Diffu-sion-based skin inflation preprocessing; in particular, a generated skin module was in-troduced to solve skin restoration problems that occur when long-sleeved images are con-verted to short-sleeved or sleeveless ones, introducing a preprocessing structure that im-proves the naturalness and consistency of full-body clothing synthesis, and allowing the implementation of high-quality restoration considering human posture and color. As a result, CaP-VTON achieved 92.5%, which is 15.4% better than Leffa, in short-sleeved syn-thesis accuracy, and consistently reproduced the style and shape of the reference clothing in visual evaluation. These structures maintain model-agnostic properties and are appli-cable to various diffusion-based virtual inspection systems; they can also contribute to applications that require high-precision virtual wearing, such as e-commerce, custom styling, and avatar creation.

Dojun Park, Jiwoo Lee, Hyeyun Jeong et al.

Benchmarks play a significant role in the current evaluation of Large Language Models (LLMs), yet they often overlook the models' abilities to capture the nuances of human language, primarily focusing on evaluating embedded knowledge and technical skills. To address this gap, our study evaluates how well LLMs understand context-dependent expressions from a pragmatic standpoint, specifically in Korean. We use both Multiple-Choice Questions (MCQs) for automatic evaluation and Open-Ended Questions (OEQs) assessed by human experts. Our results show that GPT-4 leads with scores of 81.11 in MCQs and 85.69 in OEQs, closely followed by HyperCLOVA X. Additionally, while few-shot learning generally improves performance, Chain-of-Thought (CoT) prompting tends to encourage literal interpretations, which may limit effective pragmatic inference. Our findings highlight the need for LLMs to better understand and generate language that reflects human communicative norms.

Baoxiang Pan, Gemma J. Anderson, AndrE Goncalves et al.

The path toward realizing the potential of seasonal forecasting and its socioeconomic benefits depends heavily on improving general circulation model based dynamical forecasting systems. To improve dynamical seasonal forecast, it is crucial to set up forecast benchmarks, and clarify forecast limitations posed by model initialization errors, formulation deficiencies, and internal climate variability. With huge cost in generating large forecast ensembles, and limited observations for forecast verification, the seasonal forecast benchmarking and diagnosing task proves challenging. In this study, we develop a probabilistic deep neural network model, drawing on a wealth of existing climate simulations to enhance seasonal forecast capability and forecast diagnosis. By leveraging complex physical relationships encoded in climate simulations, our probabilistic forecast model demonstrates favorable deterministic and probabilistic skill compared to state-of-the-art dynamical forecast systems in quasi-global seasonal forecast of precipitation and near-surface temperature. We apply this probabilistic forecast methodology to quantify the impacts of initialization errors and model formulation deficiencies in a dynamical seasonal forecasting system. We introduce the saliency analysis approach to efficiently identify the key predictors that influence seasonal variability. Furthermore, by explicitly modeling uncertainty using variational Bayes, we give a more definitive answer to how the El Nino/Southern Oscillation, the dominant mode of seasonal variability, modulates global seasonal predictability.

Sookyung Kim, Jungmin M. Lee, Jiwoo Lee et al.

Polluting fine dusts in South Korea which are mainly consisted of biomass burning and fugitive dust blown from dust belt is significant problem these days. Predicting concentrations of fine dust particles in Seoul is challenging because they are product of complicate chemical reactions among gaseous pollutants and also influenced by dynamical interactions between pollutants and multiple climate variables. Elaborating state-of-art time series analysis techniques using deep learning, non-linear interactions between multiple variables can be captured and used to predict future dust concentration. In this work, we propose the LSTM based model to predict hourly concentration of fine dust at target location in Seoul based on previous concentration of pollutants, dust concentrations and climate variables in surrounding area. Our results show that proposed model successfully predicts future dust concentrations at 25 target districts(Gu) in Seoul.