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Jimeng Sun

Publications and source records attributed to Jimeng Sun.

At least 109 records · Page 6Linked to original sources
arXiv2024

TriSum: Learning Summarization Ability from Large Language Models with Structured Rationale

The advent of large language models (LLMs) has significantly advanced natural language processing tasks like text summarization. However, their large size and computational demands, coupled with privacy concerns in data transmission, limit their use in resource-constrained and privacy-centric settings. To overcome this, we introduce TriSum, a framework for distilling LLMs' text summarization abilities into a compact, local model. Initially, LLMs extract a set of aspect-triple rationales and summaries, which are refined using a dual-scoring method for quality. Next, a smaller local model is trained with these tasks, employing a curriculum learning strategy that evolves from simple to complex tasks. Our method enhances local model performance on various benchmarks (CNN/DailyMail, XSum, and ClinicalTrial), outperforming baselines by 4.5%, 8.5%, and 7.4%, respectively. It also improves interpretability by providing insights into the summarization rationale.

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arXiv2024

Making Pre-trained Language Models Great on Tabular Prediction

The transferability of deep neural networks (DNNs) has made significant progress in image and language processing. However, due to the heterogeneity among tables, such DNN bonus is still far from being well exploited on tabular data prediction (e.g., regression or classification tasks). Condensing knowledge from diverse domains, language models (LMs) possess the capability to comprehend feature names from various tables, potentially serving as versatile learners in transferring knowledge across distinct tables and diverse prediction tasks, but their discrete text representation space is inherently incompatible with numerical feature values in tables. In this paper, we present TP-BERTa, a specifically pre-trained LM for tabular data prediction. Concretely, a novel relative magnitude tokenization converts scalar numerical feature values to finely discrete, high-dimensional tokens, and an intra-feature attention approach integrates feature values with the corresponding feature names. Comprehensive experiments demonstrate that our pre-trained TP-BERTa leads the performance among tabular DNNs and is competitive with Gradient Boosted Decision Tree models in typical tabular data regime.

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arXiv2024

Molecular De Novo Design through Transformer-based Reinforcement Learning

In this work, we introduce a method to fine-tune a Transformer-based generative model for molecular de novo design. Leveraging the superior sequence learning capacity of Transformers over Recurrent Neural Networks (RNNs), our model can generate molecular structures with desired properties effectively. In contrast to the traditional RNN-based models, our proposed method exhibits superior performance in generating compounds predicted to be active against various biological targets, capturing long-term dependencies in the molecular structure sequence. The model's efficacy is demonstrated across numerous tasks, including generating analogues to a query structure and producing compounds with particular attributes, outperforming the baseline RNN-based methods. Our approach can be used for scaffold hopping, library expansion starting from a single molecule, and generating compounds with high predicted activity against biological targets.

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arXiv2024

MindMap: Knowledge Graph Prompting Sparks Graph of Thoughts in Large Language Models

Large language models (LLMs) have achieved remarkable performance in natural language understanding and generation tasks. However, they often suffer from limitations such as difficulty in incorporating new knowledge, generating hallucinations, and explaining their reasoning process. To address these challenges, we propose a novel prompting pipeline, named \method, that leverages knowledge graphs (KGs) to enhance LLMs' inference and transparency. Our method enables LLMs to comprehend KG inputs and infer with a combination of implicit and external knowledge. Moreover, our method elicits the mind map of LLMs, which reveals their reasoning pathways based on the ontology of knowledge. We evaluate our method on diverse question \& answering tasks, especially in medical domains, and show significant improvements over baselines. We also introduce a new hallucination evaluation benchmark and analyze the effects of different components of our method. Our results demonstrate the effectiveness and robustness of our method in merging knowledge from LLMs and KGs for combined inference. To reproduce our results and extend the framework further, we make our codebase available at https://github.com/wyl-willing/MindMap.

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arXiv2024

GenRES: Rethinking Evaluation for Generative Relation Extraction in the Era of Large Language Models

The field of relation extraction (RE) is experiencing a notable shift towards generative relation extraction (GRE), leveraging the capabilities of large language models (LLMs). However, we discovered that traditional relation extraction (RE) metrics like precision and recall fall short in evaluating GRE methods. This shortfall arises because these metrics rely on exact matching with human-annotated reference relations, while GRE methods often produce diverse and semantically accurate relations that differ from the references. To fill this gap, we introduce GenRES for a multi-dimensional assessment in terms of the topic similarity, uniqueness, granularity, factualness, and completeness of the GRE results. With GenRES, we empirically identified that (1) precision/recall fails to justify the performance of GRE methods; (2) human-annotated referential relations can be incomplete; (3) prompting LLMs with a fixed set of relations or entities can cause hallucinations. Next, we conducted a human evaluation of GRE methods that shows GenRES is consistent with human preferences for RE quality. Last, we made a comprehensive evaluation of fourteen leading LLMs using GenRES across document, bag, and sentence level RE datasets, respectively, to set the benchmark for future research in GRE

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arXiv2024

GraphCare: Enhancing Healthcare Predictions with Personalized Knowledge Graphs

Clinical predictive models often rely on patients' electronic health records (EHR), but integrating medical knowledge to enhance predictions and decision-making is challenging. This is because personalized predictions require personalized knowledge graphs (KGs), which are difficult to generate from patient EHR data. To address this, we propose \textsc{GraphCare}, an open-world framework that uses external KGs to improve EHR-based predictions. Our method extracts knowledge from large language models (LLMs) and external biomedical KGs to build patient-specific KGs, which are then used to train our proposed Bi-attention AugmenTed (BAT) graph neural network (GNN) for healthcare predictions. On two public datasets, MIMIC-III and MIMIC-IV, \textsc{GraphCare} surpasses baselines in four vital healthcare prediction tasks: mortality, readmission, length of stay (LOS), and drug recommendation. On MIMIC-III, it boosts AUROC by 17.6\% and 6.6\% for mortality and readmission, and F1-score by 7.9\% and 10.8\% for LOS and drug recommendation, respectively. Notably, \textsc{GraphCare} demonstrates a substantial edge in scenarios with limited data availability. Our findings highlight the potential of using external KGs in healthcare prediction tasks and demonstrate the promise of \textsc{GraphCare} in generating personalized KGs for promoting personalized medicine.

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arXiv2024

UniPredict: Large Language Models are Universal Tabular Classifiers

Tabular data prediction is a fundamental machine learning task for many applications. Existing methods predominantly employ discriminative modeling and operate under the assumption of a fixed target column, necessitating re-training for every new predictive task. Inspired by the generative power of large language models (LLMs), this paper exploits the idea of building universal tabular data predictors based on generative modeling, namely UniPredict. Here, we demonstrate the scalability of an LLM to extensive tabular datasets, enabling it to comprehend diverse tabular inputs and predict target variables following the provided instructions. Specifically, we train a single LLM on an aggregation of 169 tabular datasets with diverse targets and compare its performance against baselines that are trained on each dataset separately. We observe this versatile UniPredict model demonstrates an advantage over other models, ranging from 5.4% to 13.4%, when compared with the best tree-boosting baseline and the best neural network baseline, respectively. We further test UniPredict in few-shot learning settings on another 62 tabular datasets. Our method achieves strong performance in quickly adapting to new tasks. In low-resource few-shot setup, we observed a 100%+ performance advantage compared with XGBoost, and significant margin over all baselines. We envision that UniPredict sheds light on developing a universal tabular data prediction system that learns from data at scale and serves a wide range of prediction tasks.

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arXiv2023

ConSequence: Synthesizing Logically Constrained Sequences for Electronic Health Record Generation

Generative models can produce synthetic patient records for analytical tasks when real data is unavailable or limited. However, current methods struggle with adhering to domain-specific knowledge and removing invalid data. We present ConSequence, an effective approach to integrating domain knowledge into sequential generative neural network outputs. Our rule-based formulation includes temporal aggregation and antecedent evaluation modules, ensured by an efficient matrix multiplication formulation, to satisfy hard and soft logical constraints across time steps. Existing constraint methods often fail to guarantee constraint satisfaction, lack the ability to handle temporal constraints, and hinder the learning and computational efficiency of the model. In contrast, our approach efficiently handles all types of constraints with guaranteed logical coherence. We demonstrate ConSequence's effectiveness in generating electronic health records, outperforming competitors in achieving complete temporal and spatial constraint satisfaction without compromising runtime performance or generative quality. Specifically, ConSequence successfully prevents all rule violations while improving the model quality in reducing its test perplexity by 5% and incurring less than a 13% slowdown in generation speed compared to an unconstrained model.

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arXiv2023

Synthesize High-dimensional Longitudinal Electronic Health Records via Hierarchical Autoregressive Language Model

Synthetic electronic health records (EHRs) that are both realistic and preserve privacy can serve as an alternative to real EHRs for machine learning (ML) modeling and statistical analysis. However, generating high-fidelity and granular electronic health record (EHR) data in its original, highly-dimensional form poses challenges for existing methods due to the complexities inherent in high-dimensional data. In this paper, we propose Hierarchical Autoregressive Language mOdel (HALO) for generating longitudinal high-dimensional EHR, which preserve the statistical properties of real EHR and can be used to train accurate ML models without privacy concerns. Our HALO method, designed as a hierarchical autoregressive model, generates a probability density function of medical codes, clinical visits, and patient records, allowing for the generation of realistic EHR data in its original, unaggregated form without the need for variable selection or aggregation. Additionally, our model also produces high-quality continuous variables in a longitudinal and probabilistic manner. We conducted extensive experiments and demonstrate that HALO can generate high-fidelity EHR data with high-dimensional disease code probabilities (d > 10,000), disease co-occurrence probabilities within visits (d > 1,000,000), and conditional probabilities across consecutive visits (d > 5,000,000) and achieve above 0.9 R2 correlation in comparison to real EHR data. This performance then enables downstream ML models trained on its synthetic data to achieve comparable accuracy to models trained on real data (0.938 AUROC with HALO data vs. 0.943 with real data). Finally, using a combination of real and synthetic data enhances the accuracy of ML models beyond that achieved by using only real EHR data.

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arXiv2023

Conformal Drug Property Prediction with Density Estimation under Covariate Shift

In drug discovery, it is vital to confirm the predictions of pharmaceutical properties from computational models using costly wet-lab experiments. Hence, obtaining reliable uncertainty estimates is crucial for prioritizing drug molecules for subsequent experimental validation. Conformal Prediction (CP) is a promising tool for creating such prediction sets for molecular properties with a coverage guarantee. However, the exchangeability assumption of CP is often challenged with covariate shift in drug discovery tasks: Most datasets contain limited labeled data, which may not be representative of the vast chemical space from which molecules are drawn. To address this limitation, we propose a method called CoDrug that employs an energy-based model leveraging both training data and unlabelled data, and Kernel Density Estimation (KDE) to assess the densities of a molecule set. The estimated densities are then used to weigh the molecule samples while building prediction sets and rectifying for distribution shift. In extensive experiments involving realistic distribution drifts in various small-molecule drug discovery tasks, we demonstrate the ability of CoDrug to provide valid prediction sets and its utility in addressing the distribution shift arising from de novo drug design models. On average, using CoDrug can reduce the coverage gap by over 35% when compared to conformal prediction sets not adjusted for covariate shift.

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arXiv2023

PromptRE: Weakly-Supervised Document-Level Relation Extraction via Prompting-Based Data Programming

Relation extraction aims to classify the relationships between two entities into pre-defined categories. While previous research has mainly focused on sentence-level relation extraction, recent studies have expanded the scope to document-level relation extraction. Traditional relation extraction methods heavily rely on human-annotated training data, which is time-consuming and labor-intensive. To mitigate the need for manual annotation, recent weakly-supervised approaches have been developed for sentence-level relation extraction while limited work has been done on document-level relation extraction. Weakly-supervised document-level relation extraction faces significant challenges due to an imbalanced number "no relation" instances and the failure of directly probing pretrained large language models for document relation extraction. To address these challenges, we propose PromptRE, a novel weakly-supervised document-level relation extraction method that combines prompting-based techniques with data programming. Furthermore, PromptRE incorporates the label distribution and entity types as prior knowledge to improve the performance. By leveraging the strengths of both prompting and data programming, PromptRE achieves improved performance in relation classification and effectively handles the "no relation" problem. Experimental results on ReDocRED, a benchmark dataset for document-level relation extraction, demonstrate the superiority of PromptRE over baseline approaches.

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arXiv2023

AutoTrial: Prompting Language Models for Clinical Trial Design

Clinical trials are critical for drug development. Constructing the appropriate eligibility criteria (i.e., the inclusion/exclusion criteria for patient recruitment) is essential for the trial's success. Proper design of clinical trial protocols should consider similar precedent trials and their eligibility criteria to ensure sufficient patient coverage. In this paper, we present a method named AutoTrial to aid the design of clinical eligibility criteria using language models. It allows (1) controllable generation under instructions via a hybrid of discrete and neural prompting, (2) scalable knowledge incorporation via in-context learning, and (3) explicit reasoning chains to provide rationales for understanding the outputs. Experiments on over 70K clinical trials verify that AutoTrial generates high-quality criteria texts that are fluent and coherent and with high accuracy in capturing the relevant clinical concepts to the target trial. It is noteworthy that our method, with a much smaller parameter size, gains around 60% winning rate against the GPT-3.5 baselines via human evaluations.

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arXiv2023

PyTrial: Machine Learning Software and Benchmark for Clinical Trial Applications

Clinical trials are conducted to test the effectiveness and safety of potential drugs in humans for regulatory approval. Machine learning (ML) has recently emerged as a new tool to assist in clinical trials. Despite this progress, there have been few efforts to document and benchmark ML4Trial algorithms available to the ML research community. Additionally, the accessibility to clinical trial-related datasets is limited, and there is a lack of well-defined clinical tasks to facilitate the development of new algorithms. To fill this gap, we have developed PyTrial that provides benchmarks and open-source implementations of a series of ML algorithms for clinical trial design and operations. In this paper, we thoroughly investigate 34 ML algorithms for clinical trials across 6 different tasks, including patient outcome prediction, trial site selection, trial outcome prediction, patient-trial matching, trial similarity search, and synthetic data generation. We have also collected and prepared 23 ML-ready datasets as well as their working examples in Jupyter Notebooks for quick implementation and testing. PyTrial defines each task through a simple four-step process: data loading, model specification, model training, and model evaluation, all achievable with just a few lines of code. Furthermore, our modular API architecture empowers practitioners to expand the framework to incorporate new algorithms and tasks effortlessly. The code is available at https://github.com/RyanWangZf/PyTrial.

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arXiv2023

PIE: Simulating Disease Progression via Progressive Image Editing

Disease progression simulation is a crucial area of research that has significant implications for clinical diagnosis, prognosis, and treatment. One major challenge in this field is the lack of continuous medical imaging monitoring of individual patients over time. To address this issue, we develop a novel framework termed Progressive Image Editing (PIE) that enables controlled manipulation of disease-related image features, facilitating precise and realistic disease progression simulation. Specifically, we leverage recent advancements in text-to-image generative models to simulate disease progression accurately and personalize it for each patient. We theoretically analyze the iterative refining process in our framework as a gradient descent with an exponentially decayed learning rate. To validate our framework, we conduct experiments in three medical imaging domains. Our results demonstrate the superiority of PIE over existing methods such as Stable Diffusion Walk and Style-Based Manifold Extrapolation based on CLIP score (Realism) and Disease Classification Confidence (Alignment). Our user study collected feedback from 35 veteran physicians to assess the generated progressions. Remarkably, 76.2% of the feedback agrees with the fidelity of the generated progressions. To our best knowledge, PIE is the first of its kind to generate disease progression images meeting real-world standards. It is a promising tool for medical research and clinical practice, potentially allowing healthcare providers to model disease trajectories over time, predict future treatment responses, and improve patient outcomes.

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arXiv2023

CITING: Large Language Models Create Curriculum for Instruction Tuning

The recent advancement of large language models (LLMs) has been achieved through a combo of instruction tuning and human alignment. However, building manually crafted instruction datasets and performing human alignment become the bottleneck for scaling the development of LLMs. In this paper, we exploit the idea of leveraging AI models in lieu of humans as the teacher to train student LLMs. Our method is inspired by how human students refine their writing skills by following the rubrics and learning from the revisions offered by their tutors. Specifically, we employ a teacher LLM to create a curriculum for instruction tuning of the student LLM, namely Curriculum Instruction TunING (CITING). It encompasses two main steps: (1) the teacher LLM crafts the rubrics for evaluating the answers corresponding to various types of questions, and (2) the student LLM learns to follow the rubrics and perform self-correction from the revision made by the teacher. We further iteratively carry out it to embody the procedure of CITING. We compare CITING to a series of state-of-the-art baselines on four datasets. Our method demonstrates strong improvement in terms of articulate, in-depth, and comprehensive by GPT-4 evaluation. Specifically, it achieves an average winning rate of 79.4% over SFT, 73.4% over RLHF, 78.1% over RRHF, and 76.3% over RAFT, respectively.

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arXiv2023

DRG-LLaMA : Tuning LLaMA Model to Predict Diagnosis-related Group for Hospitalized Patients

In the U.S. inpatient payment system, the Diagnosis-Related Group (DRG) is pivotal, but its assignment process is inefficient. The study introduces DRG-LLaMA, an advanced large language model (LLM) fine-tuned on clinical notes to enhance DRGs assignment. Utilizing LLaMA as the foundational model and optimizing it through Low-Rank Adaptation (LoRA) on 236,192 MIMIC-IV discharge summaries, our DRG-LLaMA-7B model exhibited a noteworthy macro-averaged F1 score of 0.327, a top-1 prediction accuracy of 52.0%, and a macro-averaged Area Under the Curve (AUC) of 0.986, with a maximum input token length of 512. This model surpassed the performance of prior leading models in DRG prediction, showing a relative improvement of 40.3% and 35.7% in macro-averaged F1 score compared to ClinicalBERT and CAML, respectively. Applied to base DRG and complication or comorbidity (CC)/major complication or comorbidity (MCC) prediction, DRG-LLaMA achieved a top-1 prediction accuracy of 67.8% and 67.5%, respectively. Additionally, our findings indicate that DRG-LLaMA's performance correlates with increased model parameters and input context lengths.

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arXiv2023

TREEMENT: Interpretable Patient-Trial Matching via Personalized Dynamic Tree-Based Memory Network

Clinical trials are critical for drug development but often suffer from expensive and inefficient patient recruitment. In recent years, machine learning models have been proposed for speeding up patient recruitment via automatically matching patients with clinical trials based on longitudinal patient electronic health records (EHR) data and eligibility criteria of clinical trials. However, they either depend on trial-specific expert rules that cannot expand to other trials or perform matching at a very general level with a black-box model where the lack of interpretability makes the model results difficult to be adopted. To provide accurate and interpretable patient trial matching, we introduce a personalized dynamic tree-based memory network model named TREEMENT. It utilizes hierarchical clinical ontologies to expand the personalized patient representation learned from sequential EHR data, and then uses an attentional beam-search query learned from eligibility criteria embedding to offer a granular level of alignment for improved performance and interpretability. We evaluated TREEMENT against existing models on real-world datasets and demonstrated that TREEMENT outperforms the best baseline by 7% in terms of error reduction in criteria-level matching and achieves state-of-the-art results in its trial-level matching ability. Furthermore, we also show TREEMENT can offer good interpretability to make the model results easier for adoption.

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arXiv2023

FRAMM: Fair Ranking with Missing Modalities for Clinical Trial Site Selection

Despite many efforts to address the disparities, the underrepresentation of gender, racial, and ethnic minorities in clinical trials remains a problem and undermines the efficacy of treatments on minorities. This paper focuses on the trial site selection task and proposes FRAMM, a deep reinforcement learning framework for fair trial site selection. We focus on addressing two real-world challenges that affect fair trial sites selection: the data modalities are often not complete for many potential trial sites, and the site selection needs to simultaneously optimize for both enrollment and diversity since the problem is necessarily a trade-off between the two with the only possible way to increase diversity post-selection being through limiting enrollment via caps. To address the missing data challenge, FRAMM has a modality encoder with a masked cross-attention mechanism for handling missing data, bypassing data imputation and the need for complete data in training. To handle the need for making efficient trade-offs, FRAMM uses deep reinforcement learning with a specifically designed reward function that simultaneously optimizes for both enrollment and fairness. We evaluate FRAMM using 4,392 real-world clinical trials ranging from 2016 to 2021 and show that FRAMM outperforms the leading baseline in enrollment-only settings while also achieving large gains in diversity. Specifically, it is able to produce a 9% improvement in diversity with similar enrollment levels over the leading baselines. That improved diversity is further manifested in achieving up to a 14% increase in Hispanic enrollment, 27% increase in Black enrollment, and 60% increase in Asian enrollment compared to selecting sites with an enrollment-only model.

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