Mei Liu

Lingyao Li, Deyi Li, Chen Chen et al.

Large language models (LLMs) are increasingly deployed across healthcare applications, including clinical documentation, diagnostic reasoning, medicine recommendation, and medical education. Their outputs are largely unstructured clinical text, which is difficult to reliably evaluate at scale. LLM-as-a-Judge, in which an LLM evaluates another system's output against task-specific criteria, offers a scalable alternative and is increasingly used in clinical evaluation, yet its validity in healthcare remains underexamined. Existing reviews focus on general-purpose LLM evaluation or on risk framework, rather than systematically characterizing how LLM-as-a-Judge is applied in healthcare and how well their judgments align with human experts. We therefore conduct a PRISMA-guided comprehensive review of LLM-as-a-Judge applications in healthcare, searching five databases for studies published between January 2023 and February 2026. After screening 541 records, 134 studies meet the eligibility and are coded by health scenario, judge configuration, technical approach, and validation design. LLM-as-a-Judge is concentrated in clinical decision support, clinical natural language processing (NLP), medical knowledge and question answering (QA), and medical communication. OpenAI models are the most frequently used judges, and prompt engineering appears in nearly all studies, with ensemble, multi-agent, and retrieval-augmented designs as common extensions. Among studies reporting human validation, LLM judges often show moderate to strong alignment with expert judgments, although reliability varies substantially across tasks. Overall, this review positions LLM-as-a-Judge as a promising framework for scalable healthcare AI evaluation, while emphasizing that its clinical value depends on model design and rigorous validation.

Mohsen Nayebi Kerdabadi, Arya Hadizadeh Moghaddam, Bin Liu et al.

Survival analysis plays a crucial role in many healthcare decisions, where the risk prediction for the events of interest can support an informative outlook for a patient's medical journey. Given the existence of data censoring, an effective way of survival analysis is to enforce the pairwise temporal concordance between censored and observed data, aiming to utilize the time interval before censoring as partially observed time-to-event labels for supervised learning. Although existing studies mostly employed ranking methods to pursue an ordering objective, contrastive methods which learn a discriminative embedding by having data contrast against each other, have not been explored thoroughly for survival analysis. Therefore, in this paper, we propose a novel Ontology-aware Temporality-based Contrastive Survival (OTCSurv) analysis framework that utilizes survival durations from both censored and observed data to define temporal distinctiveness and construct negative sample pairs with adjustable hardness for contrastive learning. Specifically, we first use an ontological encoder and a sequential self-attention encoder to represent the longitudinal EHR data with rich contexts. Second, we design a temporal contrastive loss to capture varying survival durations in a supervised setting through a hardness-aware negative sampling mechanism. Last, we incorporate the contrastive task into the time-to-event predictive task with multiple loss components. We conduct extensive experiments using a large EHR dataset to forecast the risk of hospitalized patients who are in danger of developing acute kidney injury (AKI), a critical and urgent medical condition. The effectiveness and explainability of the proposed model are validated through comprehensive quantitative and qualitative studies.

Yunfei Zhao, Mei Liu, Shuowei Liu et al.

High-resolution range profile (HRRP)-based radar automatic target recognition suffers from severe performance degradation in composite jamming environments. Active jamming introduces suppression- and deception-related components into the received range profile. After pulse compression, these components are coupled with target echoes in the HRRP domain, making target-related scattering peaks difficult to distinguish and weakening feature separability. To address this problem, this paper proposes JointHRRP-Net, a unified framework for joint target-jamming recognition. A statistically constrained decoupling module is first developed to generate target-dominant and jamming-dominant latent branches from the mixed HRRP representation. Correlation-guided statistical constraints are imposed to suppress redundant cross-branch information and alleviate target-jamming feature entanglement. A multi-scale temporal encoding module is then designed to model local scattering structures and long-range range-cell dependencies, followed by a dual-expert decision module for single-label target classification and multi-label jamming classification. Experiments under diverse signal-to-jamming ratio (SJR) and signal-to-noise ratio (SNR) levels demonstrate that JointHRRP-Net outperforms representative baseline methods in both target recognition and composite jamming recognition. Open-set evaluation further shows that the learned target representation remains discriminative for unknown-target rejection. These results demonstrate the effectiveness and robustness of JointHRRP-Net in composite jamming scenarios.

Deyi Li, Zijun Yao, Qi Xu et al.

The growing adoption of electronic health record (EHR) systems has provided unprecedented opportunities for predictive modeling to guide clinical decision making. Structured EHRs contain longitudinal observations of patients across hospital visits, where each visit is represented by a set of medical codes. While sequence-based, graph-based, and graph-enhanced sequence approaches have been developed to capture rich code interactions over time or within the same visits, they often overlook the inherent heterogeneous roles of medical codes arising from distinct clinical characteristics and contexts. To this end, in this study we propose the Disease Trajectory-aware Transformer for EHR (DT-BEHRT), a graph-enhanced sequential architecture that disentangles disease trajectories by explicitly modeling diagnosis-centric interactions within organ systems and capturing asynchronous progression patterns. To further enhance the representation robustness, we design a tailored pre-training methodology that combines trajectory-level code masking with ontology-informed ancestor prediction, promoting semantic alignment across multiple modeling modules. Extensive experiments on multiple benchmark datasets demonstrate that DT-BEHRT achieves strong predictive performance and provides interpretable patient representations that align with clinicians' disease-centered reasoning. The source code is publicly accessible at https://github.com/GatorAIM/DT-BEHRT.git.

Qiang Hu, Zhenyu Yi, Ying Zhou et al.

We propose MonoBox, an innovative box-supervised segmentation method constrained by monotonicity to liberate its training from the user-unfriendly box-tightness assumption. In contrast to conventional box-supervised segmentation, where the box edges must precisely touch the target boundaries, MonoBox leverages imprecisely-annotated boxes to achieve robust pixel-wise segmentation. The 'linchpin' is that, within the noisy zones around box edges, MonoBox discards the traditional misguiding multiple-instance learning loss, and instead optimizes a carefully-designed objective, termed monotonicity constraint. Along directions transitioning from the foreground to background, this new constraint steers responses to adhere to a trend of monotonically decreasing values. Consequently, the originally unreliable learning within the noisy zones is transformed into a correct and effective monotonicity optimization. Moreover, an adaptive label correction is introduced, enabling MonoBox to enhance the tightness of box annotations using predicted masks from the previous epoch and dynamically shrink the noisy zones as training progresses. We verify MonoBox in the box-supervised segmentation task of polyps, where satisfying box-tightness is challenging due to the vague boundaries between the polyp and normal tissues. Experiments on both public synthetic and in-house real noisy datasets demonstrate that MonoBox exceeds other anti-noise state-of-the-arts by improving Dice by at least 5.5% and 3.3%, respectively. Codes are at https://github.com/Huster-Hq/MonoBox.

Zhiwei Wang, Qiang Hu, Hongkuan Shi et al.

Box-supervised polyp segmentation attracts increasing attention for its cost-effective potential. Existing solutions often rely on learning-free methods or pretrained models to laboriously generate pseudo masks, triggering Dice constraint subsequently. In this paper, we found that a model guided by the simplest box-filled masks can accurately predict polyp locations/sizes, but suffers from shape collapsing. In response, we propose two innovative learning fashions, Improved Box-dice (IBox) and Contrastive Latent-Anchors (CLA), and combine them to train a robust box-supervised model IBoxCLA. The core idea behind IBoxCLA is to decouple the learning of location/size and shape, allowing for focused constraints on each of them. Specifically, IBox transforms the segmentation map into a proxy map using shape decoupling and confusion-region swapping sequentially. Within the proxy map, shapes are disentangled, while locations/sizes are encoded as box-like responses. By constraining the proxy map instead of the raw prediction, the box-filled mask can well supervise IBoxCLA without misleading its shape learning. Furthermore, CLA contributes to shape learning by generating two types of latent anchors, which are learned and updated using momentum and segmented polyps to steadily represent polyp and background features. The latent anchors facilitate IBoxCLA to capture discriminative features within and outside boxes in a contrastive manner, yielding clearer boundaries. We benchmark IBoxCLA on five public polyp datasets. The experimental results demonstrate the competitive performance of IBoxCLA compared to recent fully-supervised polyp segmentation methods, and its superiority over other box-supervised state-of-the-arts with a relative increase of overall mDice and mIoU by at least 6.5% and 7.5%, respectively.

Arya Hadizadeh Moghaddam, Mohsen Nayebi Kerdabadi, Mei Liu et al.

Recent advancements in sequential modeling applied to Electronic Health Records (EHR) have greatly influenced prescription recommender systems. While the recent literature on drug recommendation has shown promising performance, the study of discovering a diversity of coexisting temporal relationships at the level of medical codes over consecutive visits remains less explored. The goal of this study can be motivated from two perspectives. First, there is a need to develop a sophisticated sequential model capable of disentangling the complex relationships across sequential visits. Second, it is crucial to establish multiple and diverse health profiles for the same patient to ensure a comprehensive consideration of different medical intents in drug recommendation. To achieve this goal, we introduce Attentive Recommendation with Contrasted Intents (ARCI), a multi-level transformer-based method designed to capture the different but coexisting temporal paths across a shared sequence of visits. Specifically, we propose a novel intent-aware method with contrastive learning, that links specialized medical intents of the patients to the transformer heads for extracting distinct temporal paths associated with different health profiles. We conducted experiments on two real-world datasets for the prescription recommendation task using both ranking and classification metrics. Our results demonstrate that ARCI has outperformed the state-of-the-art prescription recommendation methods and is capable of providing interpretable insights for healthcare practitioners.

Qiang Hu, Qimei Wang, Jia Chen et al.

White Light Imaging (WLI) and Narrow Band Imaging (NBI) are the two main colonoscopic modalities for polyp classification. While NBI, as optical chromoendoscopy, offers valuable vascular details, WLI remains the most common and often the only available modality in resource-limited settings. However, WLI-based methods typically underperform, limiting their clinical applicability. Existing approaches transfer knowledge from NBI to WLI through global feature alignment but often rely on cropped lesion regions, which are susceptible to detection errors and neglect contextual and subtle diagnostic cues. To address this, this paper proposes a novel holistic classification framework that leverages full-image diagnosis without requiring polyp localization. The key innovation lies in the Alignment-free Dense Distillation (ADD) module, which enables fine-grained cross-domain knowledge distillation regardless of misalignment between WLI and NBI images. Without resorting to explicit image alignment, ADD learns pixel-wise cross-domain affinities to establish correspondences between feature maps, guiding the distillation along the most relevant pixel connections. To further enhance distillation reliability, ADD incorporates Class Activation Mapping (CAM) to filter cross-domain affinities, ensuring the distillation path connects only those semantically consistent regions with equal contributions to polyp diagnosis. Extensive results on public and in-house datasets show that our method achieves state-of-the-art performance, relatively outperforming the other approaches by at least 2.5% and 16.2% in AUC, respectively. Code is available at: https://github.com/Huster-Hq/ADD.

Qiang Hu, Zhenyu Yi, Ying Zhou et al.

Colonoscopy videos provide richer information in polyp segmentation for rectal cancer diagnosis. However, the endoscope's fast moving and close-up observing make the current methods suffer from large spatial incoherence and continuous low-quality frames, and thus yield limited segmentation accuracy. In this context, we focus on robust video polyp segmentation by enhancing the adjacent feature consistency and rebuilding the reliable polyp representation. To achieve this goal, we in this paper propose SALI network, a hybrid of Short-term Alignment Module (SAM) and Long-term Interaction Module (LIM). The SAM learns spatial-aligned features of adjacent frames via deformable convolution and further harmonizes them to capture more stable short-term polyp representation. In case of low-quality frames, the LIM stores the historical polyp representations as a long-term memory bank, and explores the retrospective relations to interactively rebuild more reliable polyp features for the current segmentation. Combing SAM and LIM, the SALI network of video segmentation shows a great robustness to the spatial variations and low-visual cues. Benchmark on the large-scale SUNSEG verifies the superiority of SALI over the current state-of-the-arts by improving Dice by 2.1%, 2.5%, 4.1% and 1.9%, for the four test sub-sets, respectively. Codes are at https://github.com/Scatteredrain/SALI.

Mei Liu, Liangming Chen, Xiaohao Du et al.

Deep neural networks often suffer from poor performance or even training failure due to the ill-conditioned problem, the vanishing/exploding gradient problem, and the saddle point problem. In this paper, a novel method by acting the gradient activation function (GAF) on the gradient is proposed to handle these challenges. Intuitively, the GAF enlarges the tiny gradients and restricts the large gradient. Theoretically, this paper gives conditions that the GAF needs to meet, and on this basis, proves that the GAF alleviates the problems mentioned above. In addition, this paper proves that the convergence rate of SGD with the GAF is faster than that without the GAF under some assumptions. Furthermore, experiments on CIFAR, ImageNet, and PASCAL visual object classes confirm the GAF's effectiveness. The experimental results also demonstrate that the proposed method is able to be adopted in various deep neural networks to improve their performance. The source code is publicly available at https://github.com/LongJin-lab/Activated-Gradients-for-Deep-Neural-Networks.

Arya Hadizadeh Moghaddam, Mohsen Nayebi Kerdabadi, Dongjie Wang et al.

Large-scale Electronic Health Record (EHR) databases have become indispensable in supporting clinical decision-making through data-driven treatment recommendations. However, existing medication recommender methods often struggle with a user (i.e., patient) cold-start problem, where recommendations for new patients are usually unreliable due to the lack of sufficient prescription history for patient profiling. While prior studies have utilized medical knowledge graphs to connect medication concepts through pharmacological or chemical relationships, these methods primarily focus on mitigating the item cold-start issue and fall short in providing personalized recommendations that adapt to individual patient characteristics. Meta-learning has shown promise in handling new users with sparse interactions in recommender systems. However, its application to EHRs remains underexplored due to the unique sequential structure of EHR data. To tackle these challenges, we propose MetaDrug, a multi-level, uncertainty-aware meta-learning framework designed to address the patient cold-start problem in medication recommendation. MetaDrug proposes a novel two-level meta-adaptation mechanism, including self-adaptation, which adapts the model to new patients using their own medical events as support sets to capture temporal dependencies; and peer-adaptation, which adapts the model using similar visits from peer patients to enrich new patient representations. Meanwhile, to further improve meta-adaptation outcomes, we introduce an uncertainty quantification module that ranks the support visits and filters out the unrelated information for adaptation consistency. We evaluate our approach on the MIMIC-III and Acute Kidney Injury (AKI) datasets. Experimental results on both datasets demonstrate that MetaDrug consistently outperforms state-of-the-art medication recommendation methods on cold-start patients.

Mei Liu, Leon Yang

As IoT networks become more complex and generate massive amounts of dynamic data, it is difficult to monitor and detect anomalies using traditional statistical methods and machine learning methods. Deep learning algorithms can process and learn from large amounts of data and can also be trained using unsupervised learning techniques, meaning they don't require labelled data to detect anomalies. This makes it possible to detect new and unknown anomalies that may not have been detected before. Also, deep learning algorithms can be automated and highly scalable; thereby, they can run continuously in the backend and make it achievable to monitor large IoT networks instantly. In this work, we conduct a literature review on the most recent works using deep learning techniques and implement a model using ensemble techniques on the KDD Cup 99 dataset. The experimental results showcase the impressive performance of our deep anomaly detection model, achieving an accuracy of over 98\%.

Zhiwei Wang, Ying Zhou, Shiquan He et al.

Photometric constraint is indispensable for self-supervised monocular depth estimation. It involves warping a source image onto a target view using estimated depth&pose, and then minimizing the difference between the warped and target images. However, the endoscopic built-in light causes significant brightness fluctuations, and thus makes the photometric constraint unreliable. Previous efforts only mitigate this relying on extra models to calibrate image brightness. In this paper, we propose MonoPCC to address the brightness inconsistency radically by reshaping the photometric constraint into a cycle form. Instead of only warping the source image, MonoPCC constructs a closed loop consisting of two opposite forward-backward warping paths: from target to source and then back to target. Thus, the target image finally receives an image cycle-warped from itself, which naturally makes the constraint invariant to brightness changes. Moreover, MonoPCC transplants the source image's phase-frequency into the intermediate warped image to avoid structure lost, and also stabilizes the training via an exponential moving average (EMA) strategy to avoid frequent changes in the forward warping. The comprehensive and extensive experimental results on four endoscopic datasets demonstrate that our proposed MonoPCC shows a great robustness to the brightness inconsistency, and exceeds other state-of-the-arts by reducing the absolute relative error by at least 7.27%, 9.38%, 9.90% and 3.17%, respectively.

Qiang Hu, Mei Liu, Qiang Li et al.

Automatic video polyp segmentation plays a critical role in gastrointestinal cancer screening, but the cost of frameby-frame annotations is prohibitively high. While sparse-frame supervised methods have reduced this burden proportionately, the cost remains overwhelming for long-duration videos and large-scale datasets. In this paper, we, for the first time, reduce the annotation cost to just a single frame per polyp video, regardless of the video's length. To this end, we introduce a new task, First-Frame Supervised Video Polyp Segmentation (FSVPS), and propose a novel Propagative and Semantic Dual-Teacher Network (PSDNet). Specifically, PSDNet adopts a teacher-student framework but employs two distinct types of teachers: the propagative teacher and the semantic teacher. The propagative teacher is a universal object tracker that propagates the first-frame annotation to subsequent frames as pseudo labels. However, tracking errors may accumulate over time, gradually degrading the pseudo labels and misguiding the student model. To address this, we introduce the semantic teacher, an exponential moving average of the student model, which produces more stable and time-invariant pseudo labels. PSDNet merges the pseudo labels from both teachers using a carefully-designed back-propagation strategy. This strategy assesses the quality of the pseudo labels by tracking them backward to the first frame. High-quality pseudo labels are more likely to spatially align with the firstframe annotation after this backward tracking, ensuring more accurate teacher-to-student knowledge transfer and improved segmentation performance. Benchmarking on SUN-SEG, the largest VPS dataset, demonstrates the competitive performance of PSDNet compared to fully-supervised approaches, and its superiority over sparse-frame supervised state-of-the-arts with a minimum improvement of 4.5% in Dice score.

Deyi Li, Zijun Yao, Muxuan Liang et al.

In recent years, graph learning has gained significant interest for modeling complex interactions among medical events in structured Electronic Health Record (EHR) data. However, existing graph-based approaches often work in a static manner, either restricting interactions within individual encounters or collapsing all historical encounters into a single snapshot. As a result, when it is necessary to identify meaningful groups of medical events spanning longitudinal encounters, existing methods are inadequate in modeling interactions cross encounters while accounting for temporal dependencies. To address this limitation, we introduce Deep Patient Journey (DeepJ), a novel graph convolutional transformer model with differentiable graph pooling to effectively capture intra-encounter and inter-encounter medical event interactions. DeepJ can identify groups of temporally and functionally related medical events, offering valuable insights into key event clusters pertinent to patient outcome prediction. DeepJ significantly outperformed five state-of-the-art baseline models while enhancing interpretability, demonstrating its potential for improved patient risk stratification.

Mohsen Nayebi Kerdabadi, Arya Hadizadeh Moghaddam, Bin Liu et al.

Survival analysis (SA) models have been widely studied in mining electronic health records (EHRs), particularly in forecasting the risk of critical conditions for prioritizing high-risk patients. However, their vulnerability to adversarial attacks is much less explored in the literature. Developing black-box perturbation algorithms and evaluating their impact on state-of-the-art survival models brings two benefits to medical applications. First, it can effectively evaluate the robustness of models in pre-deployment testing. Also, exploring how subtle perturbations would result in significantly different outcomes can provide counterfactual insights into the clinical interpretation of model prediction. In this work, we introduce SurvAttack, a novel black-box adversarial attack framework leveraging subtle clinically compatible, and semantically consistent perturbations on longitudinal EHRs to degrade survival models' predictive performance. We specifically develop a greedy algorithm to manipulate medical codes with various adversarial actions throughout a patient's medical history. Then, these adversarial actions are prioritized using a composite scoring strategy based on multi-aspect perturbation quality, including saliency, perturbation stealthiness, and clinical meaningfulness. The proposed adversarial EHR perturbation algorithm is then used in an efficient SA-specific strategy to attack a survival model when estimating the temporal ranking of survival urgency for patients. To demonstrate the significance of our work, we conduct extensive experiments, including baseline comparisons, explainability analysis, and case studies. The experimental results affirm our research's effectiveness in illustrating the vulnerabilities of patient survival models, model interpretation, and ultimately contributing to healthcare quality.

Sijia Liu, Andrew Wen, Liwei Wang et al.

While we pay attention to the latest advances in clinical natural language processing (NLP), we can notice some resistance in the clinical and translational research community to adopt NLP models due to limited transparency, interpretability, and usability. In this study, we proposed an open natural language processing development framework. We evaluated it through the implementation of NLP algorithms for the National COVID Cohort Collaborative (N3C). Based on the interests in information extraction from COVID-19 related clinical notes, our work includes 1) an open data annotation process using COVID-19 signs and symptoms as the use case, 2) a community-driven ruleset composing platform, and 3) a synthetic text data generation workflow to generate texts for information extraction tasks without involving human subjects. The corpora were derived from texts from three different institutions (Mayo Clinic, University of Kentucky, University of Minnesota). The gold standard annotations were tested with a single institution's (Mayo) ruleset. This resulted in performances of 0.876, 0.706, and 0.694 in F-scores for Mayo, Minnesota, and Kentucky test datasets, respectively. The study as a consortium effort of the N3C NLP subgroup demonstrates the feasibility of creating a federated NLP algorithm development and benchmarking platform to enhance multi-institution clinical NLP study and adoption. Although we use COVID-19 as a use case in this effort, our framework is general enough to be applied to other domains of interest in clinical NLP.

Liangming Chen, Long Jin, Xiujuan Du et al.

In deep learning, it is usually assumed that the optimization process is conducted on a shape-fixed loss surface. Differently, we first propose a novel concept of deformation mapping in this paper to affect the behaviour of the optimizer. Vertical deformation mapping (VDM), as a type of deformation mapping, can make the optimizer enter a flat region, which often implies better generalization performance. Moreover, we design various VDMs, and further provide their contributions to the loss surface. After defining the local M region, theoretical analyses show that deforming the loss surface can enhance the gradient descent optimizer's ability to filter out sharp minima. With visualizations of loss landscapes, we evaluate the flatnesses of minima obtained by both the original optimizer and optimizers enhanced by VDMs on CIFAR-100. The experimental results show that VDMs do find flatter regions. Moreover, we compare popular convolutional neural networks enhanced by VDMs with the corresponding original ones on ImageNet, CIFAR-10, and CIFAR-100. The results are surprising: there are significant improvements on all of the involved models equipped with VDMs. For example, the top-1 test accuracy of ResNet-20 on CIFAR-100 increases by 1.46%, with insignificant additional computational overhead.

Liangming Chen, Long Jin, Xiujuan Du et al.

In deep learning, it is usually assumed that the shape of the loss surface is fixed. Differently, a novel concept of deformation operator is first proposed in this paper to deform the loss surface, thereby improving the optimization. Deformation function, as a type of deformation operator, can improve the generalization performance. Moreover, various deformation functions are designed, and their contributions to the loss surface are further provided. Then, the original stochastic gradient descent optimizer is theoretically proved to be a flat minima filter that owns the talent to filter out the sharp minima. Furthermore, the flatter minima could be obtained by exploiting the proposed deformation functions, which is verified on CIFAR-100, with visualizations of loss landscapes near the critical points obtained by both the original optimizer and optimizer enhanced by deformation functions. The experimental results show that deformation functions do find flatter regions. Moreover, on ImageNet, CIFAR-10, and CIFAR-100, popular convolutional neural networks enhanced by deformation functions are compared with the corresponding original models, where significant improvements are observed on all of the involved models equipped with deformation functions. For example, the top-1 test accuracy of ResNet-20 on CIFAR-100 increases by 1.46%, with insignificant additional computational overhead.

Jingqi Wang, Noor Abu-el-rub, Josh Gray et al.

The COVID-19 pandemic swept across the world rapidly, infecting millions of people. An efficient tool that can accurately recognize important clinical concepts of COVID-19 from free text in electronic health records (EHRs) will be valuable to accelerate COVID-19 clinical research. To this end, this study aims at adapting the existing CLAMP natural language processing tool to quickly build COVID-19 SignSym, which can extract COVID-19 signs/symptoms and their 8 attributes (body location, severity, temporal expression, subject, condition, uncertainty, negation, and course) from clinical text. The extracted information is also mapped to standard concepts in the Observational Medical Outcomes Partnership common data model. A hybrid approach of combining deep learning-based models, curated lexicons, and pattern-based rules was applied to quickly build the COVID-19 SignSym from CLAMP, with optimized performance. Our extensive evaluation using 3 external sites with clinical notes of COVID-19 patients, as well as the online medical dialogues of COVID-19, shows COVID-19 Sign-Sym can achieve high performance across data sources. The workflow used for this study can be generalized to other use cases, where existing clinical natural language processing tools need to be customized for specific information needs within a short time. COVID-19 SignSym is freely accessible to the research community as a downloadable package (https://clamp.uth.edu/covid/nlp.php) and has been used by 16 healthcare organizations to support clinical research of COVID-19.