Linhai Ma

Samah Fodeh, Sreeraj Ramachandran, Elyas Irankhah et al.

Secure patient-provider messages contain clinically important communication behaviors that are difficult to characterize manually at scale. The Electronic Patient-Provider Communication (EPPC) framework provides an ontology for coding these behaviors, but automated extraction remains challenging because predictions must preserve fine-grained code/sub-code structure while grounding annotations in message text. We developed EPPC-OASIS, an ontology-aware adaptation approach for structured EPPC extraction, and combined it with deployable inference-refinement procedures designed to improve the coherence of final annotations. EPPC-OASIS augments supervised fine-tuning with a Wasserstein alignment objective that encourages alignment between model representation neighborhoods and EPPC ontology-derived neighborhoods, while inference refinement uses verification, self-consistency, hybrid correction, and selection or ensembling to address residual prediction errors. We evaluated the framework on a de-identified corpus of secure patient-provider messages against prompting, supervised fine-tuning, preference-based, and robustness-oriented baselines across multiple open-weight language models. Across model families, the best deployable pipeline achieved 77.13% Code+Sub-code F1 and 63.83% Triplet F1, corresponding to modest but consistent absolute gains of +1.39 and +2.12 F1 points over the strongest supervised fine-tuning baseline. These results suggest that ontology-aware adaptation with structured inference refinement can support scalable retrospective EPPC mining, although external validation is needed before operational use.

Samah Fodeh, Linhai Ma, Yan Wang et al.

Patient-generated text such as secure messages, surveys, and interviews contains rich expressions of the patient voice (PV), reflecting communicative behaviors and social determinants of health (SDoH). Traditional qualitative coding frameworks are labor intensive and do not scale to large volumes of patient-authored messages across health systems. Existing machine learning (ML) and natural language processing (NLP) approaches provide partial solutions but often treat patient-centered communication (PCC) and SDoH as separate tasks or rely on models not well suited to patient-facing language. We introduce PVminer, a domain-adapted NLP framework for structuring patient voice in secure patient-provider communication. PVminer formulates PV detection as a multi-label, multi-class prediction task integrating patient-specific BERT encoders (PV-BERT-base and PV-BERT-large), unsupervised topic modeling for thematic augmentation (PV-Topic-BERT), and fine-tuned classifiers for Code, Subcode, and Combo-level labels. Topic representations are incorporated during fine-tuning and inference to enrich semantic inputs. PVminer achieves strong performance across hierarchical tasks and outperforms biomedical and clinical pre-trained baselines, achieving F1 scores of 82.25% (Code), 80.14% (Subcode), and up to 77.87% (Combo). An ablation study further shows that author identity and topic-based augmentation each contribute meaningful gains. Pre-trained models, source code, and documentation will be publicly released, with annotated datasets available upon request for research use.

Linhai Ma, Liang Liang

It is known that Deep Neural networks (DNNs) are vulnerable to adversarial attacks, and the adversarial robustness of DNNs could be improved by adding adversarial noises to training data (e.g., the standard adversarial training (SAT)). However, inappropriate noises added to training data may reduce a model's performance, which is termed the trade-off between accuracy and robustness. This problem has been sufficiently studied for the classification of whole images but has rarely been explored for image analysis tasks in the medical application domain, including image segmentation, landmark detection, and object detection tasks. In this study, we show that, for those medical image analysis tasks, the SAT method has a severe issue that limits its practical use: it generates a fixed and unified level of noise for all training samples for robust DNN training. A high noise level may lead to a large reduction in model performance and a low noise level may not be effective in improving robustness. To resolve this issue, we design an adaptive-margin adversarial training (AMAT) method that generates sample-wise adaptive adversarial noises for robust DNN training. In contrast to the existing, classification-oriented adversarial training methods, our AMAT method uses a loss-defined-margin strategy so that it can be applied to different tasks as long as the loss functions are well-defined. We successfully apply our AMAT method to state-of-the-art DNNs, using five publicly available datasets. The experimental results demonstrate that: (1) our AMAT method can be applied to the three seemingly different tasks in the medical image application domain; (2) AMAT outperforms the SAT method in adversarial robustness; (3) AMAT has a minimal reduction in prediction accuracy on clean data, compared with the SAT method; and (4) AMAT has almost the same training time cost as SAT.

Jiasong Chen, Linchen Qian, Linhai Ma et al.

Intervertebral disc disease, a prevalent ailment, frequently leads to intermittent or persistent low back pain, and diagnosing and assessing of this disease rely on accurate measurement of vertebral bone and intervertebral disc geometries from lumbar MR images. Deep neural network (DNN) models may assist clinicians with more efficient image segmentation of individual instances (disks and vertebrae) of the lumbar spine in an automated way, which is termed as instance image segmentation. In this work, we proposed SymTC, an innovative lumbar spine MR image segmentation model that combines the strengths of Transformer and Convolutional Neural Network (CNN). Specifically, we designed a parallel dual-path architecture to merge CNN layers and Transformer layers, and we integrated a novel position embedding into the self-attention module of Transformer, enhancing the utilization of positional information for more accurate segmentation. To further improves model performance, we introduced a new data augmentation technique to create synthetic yet realistic MR image dataset, named SSMSpine, which is made publicly available. We evaluated our SymTC and the other 15 existing image segmentation models on our private in-house dataset and the public SSMSpine dataset, using two metrics, Dice Similarity Coefficient and 95% Hausdorff Distance. The results show that our SymTC has the best performance for segmenting vertebral bones and intervertebral discs in lumbar spine MR images. The SymTC code and SSMSpine dataset are available at https://github.com/jiasongchen/SymTC.

Samah Fodeh, Linhai Ma, Ganesh Puthiaraju et al.

Motivation: Patient-generated text contains critical information about patients' lived experiences, social circumstances, and engagement in care, including factors that strongly influence adherence, care coordination, and health equity. However, these patient voice signals are rarely available in structured form, limiting their use in patient-centered outcomes research and clinical quality improvement. Reliable extraction of such information is therefore essential for understanding and addressing non-clinical drivers of health outcomes at scale. Results: We introduce PVminer, a benchmark for structured extraction of patient voice, and propose PVminerLLM, a supervised fine-tuned large language model tailored to this task. Across multiple datasets and model sizes, PVminerLLM substantially outperforms prompt-based baselines, achieving up to 83.82% F1 for Code prediction, 80.74% F1 for Sub-code prediction, and 87.03% F1 for evidence Span extraction. Notably, strong performance is achieved even with smaller models, demonstrating that reliable patient voice extraction is feasible without extreme model scale. These results enable scalable analysis of social and experiential signals embedded in patient-generated text. Availability and Implementation: Code, evaluation scripts, and trained LLMs will be released publicly. Annotated datasets will be made available upon request for research use. Keywords: Large Language Models, Supervised Fine-Tuning, Medical Annotation, Patient-Generated Text, Clinical NLP

Linchen Qian, Jiasong Chen, Linhai Ma et al.

Lumbar disc degeneration, a progressive structural wear and tear of lumbar intervertebral disc, is regarded as an essential role on low back pain, a significant global health concern. Automated lumbar spine geometry reconstruction from MR images will enable fast measurement of medical parameters to evaluate the lumbar status, in order to determine a suitable treatment. Existing image segmentation-based techniques often generate erroneous segments or unstructured point clouds, unsuitable for medical parameter measurement. In this work, we present $\textit{UNet-DeformSA}$ and $\textit{TransDeformer}$: novel attention-based deep neural networks that reconstruct the geometry of the lumbar spine with high spatial accuracy and mesh correspondence across patients, and we also present a variant of $\textit{TransDeformer}$ for error estimation. Specially, we devise new attention modules with a new attention formula, which integrate image features and tokenized contour features to predict the displacements of the points on a shape template without the need for image segmentation. The deformed template reveals the lumbar spine geometry in an image. Experiment results show that our networks generate artifact-free geometry outputs, and the variant of $\textit{TransDeformer}$ can predict the errors of a reconstructed geometry. Our code is available at https://github.com/linchenq/TransDeformer-Mesh.

Xueqing Peng, Zhuohan Xie, Yupeng Cao et al.

As AI agents improve, the central question is no longer whether they can solve isolated well-defined financial tasks, but whether they can reliably carry out financial professional work. Existing financial benchmarks offer only a partial view of this ability, as they primarily evaluate static competencies such as question answering, retrieval, summarization, and classification. We introduce Herculean, the first skilled benchmark for agentic financial intelligence spanning four representative workflows, including Trading, Hedging, Market Insights, and Auditing. Each workflow is instantiated as a standardized MCP-based skill environment with its own tools, interaction dynamics, constraints, and success criteria, enabling consistent end-to-end assessment of heterogeneous agent systems. Across frontier agents, we find agents perform relatively well on Trading and Market Insights, but struggle substantially on Hedging and Auditing, where long-horizon coordination, state consistency, and structured verification are critical. Overall, our results point to a key gap in current agents in turning financial reasoning into dependable workflow execution in high-stakes financial workflows.

Samah Fodeh, Ganesh Puthiaraju, Elyas Irankhah et al.

Structured prediction requires models to generate ontology-constrained labels, grounded evidence, and valid structure under ambiguity, label skew, and heterogeneous group difficulty. We present a two-part framework for controllable inference and robust fine-tuning. First, we introduce a task-agnostic prompting strategy that combines XML-based instruction structure, disambiguation rules, verification-style reasoning, schema constraints, and self-validation to address format drift, label ambiguity, evidence hallucination, and metadata-conditioned confusion in in-context structured generation. Second, we introduce STaR-DRO, a stateful robust optimization method for group heterogeneity. It combines Tsallis mirror descent with momentum-smoothed, centered group-loss signals and bounded excess-only multipliers so that only persistently hard groups above a neutral baseline are upweighted, concentrating learning where it is most needed while avoiding volatile, dense exponentiated-gradient reweighting and unnecessary loss from downweighting easier groups. We evaluate the combined framework on EPPC Miner, a benchmark for extracting hierarchical labels and evidence spans from patient-provider secure messages. Prompt engineering improves zero-shot by +15.44 average F1 across Code, Sub-code, and Span over four Llama models. Building on supervised fine-tuning, STaR-DRO further improves the hardest semantic decisions: on Llama-3.3-70B-Instruct, Code F1 rises from 79.24 to 81.47 and Sub-code F1 from 67.78 to 69.30, while preserving Span performance and reducing group-wise validation cross-entropy by up to 29.6% on the most difficult clinical categories. Because these rare and difficult groups correspond to clinically consequential communication behaviors, these gains are not merely statistical improvements: they directly strengthen communication mining reliability for patient-centered care analysis.

Linhai Ma, Liang Liang

Electrocardiogram (ECG) is the most widely used diagnostic tool to monitor the condition of the human heart. By using deep neural networks (DNNs), interpretation of ECG signals can be fully automated for the identification of potential abnormalities in a patient's heart in a fraction of a second. Studies have shown that given a sufficiently large amount of training data, DNN accuracy for ECG classification could reach human-expert cardiologist level. However, despite of the excellent performance in classification accuracy, DNNs are highly vulnerable to adversarial noises that are subtle changes in the input of a DNN and may lead to a wrong class-label prediction. It is challenging and essential to improve robustness of DNNs against adversarial noises, which are a threat to life-critical applications. In this work, we proposed a regularization method to improve DNN robustness from the perspective of noise-to-signal ratio (NSR) for the application of ECG signal classification. We evaluated our method on PhysioNet MIT-BIH dataset and CPSC2018 ECG dataset, and the results show that our method can substantially enhance DNN robustness against adversarial noises generated from adversarial attacks, with a minimal change in accuracy on clean data.

Liang Liang, Linhai Ma, Linchen Qian et al.

Deep neural networks (DNNs), especially convolutional neural networks, have achieved superior performance on image classification tasks. However, such performance is only guaranteed if the input to a trained model is similar to the training samples, i.e., the input follows the probability distribution of the training set. Out-Of-Distribution (OOD) samples do not follow the distribution of training set, and therefore the predicted class labels on OOD samples become meaningless. Classification-based methods have been proposed for OOD detection; however, in this study we show that this type of method has no theoretical guarantee and is practically breakable by our OOD Attack algorithm because of dimensionality reduction in the DNN models. We also show that Glow likelihood-based OOD detection is breakable as well.

Linhai Ma, Liang Liang

Electrocardiogram (ECG) is the most widely used diagnostic tool to monitor the condition of the cardiovascular system. Deep neural networks (DNNs), have been developed in many research labs for automatic interpretation of ECG signals to identify potential abnormalities in patient hearts. Studies have shown that given a sufficiently large amount of data, the classification accuracy of DNNs could reach human-expert cardiologist level. However, despite of the excellent performance in classification accuracy, it has been shown that DNNs are highly vulnerable to adversarial noises which are subtle changes in input of a DNN and lead to a wrong class-label prediction with a high confidence. Thus, it is challenging and essential to improve robustness of DNNs against adversarial noises for ECG signal classification, a life-critical application. In this work, we designed a CNN for classification of 12-lead ECG signals with variable length, and we applied three defense methods to improve robustness of this CNN for this classification task. The ECG data in this study is very challenging because the sample size is limited, and the length of each ECG recording varies in a large range. The evaluation results show that our customized CNN reached satisfying F1 score and average accuracy, comparable to the top-6 entries in the CPSC2018 ECG classification challenge, and the defense methods enhanced robustness of our CNN against adversarial noises and white noises, with a minimal reduction in accuracy on clean data.

Linhai Ma, Liang Liang

Deep neural networks (DNNs) are vulnerable to adversarial noises. Adversarial training is a general and effective strategy to improve DNN robustness (i.e., accuracy on noisy data) against adversarial noises. However, DNN models trained by the current existing adversarial training methods may have much lower standard accuracy (i.e., accuracy on clean data), compared to the same models trained by the standard method on clean data, and this phenomenon is known as the trade-off between accuracy and robustness and is considered unavoidable. This issue prevents adversarial training from being used in many application domains, such as medical image analysis, as practitioners do not want to sacrifice standard accuracy too much in exchange for adversarial robustness. Our objective is to lift (i.e., alleviate or even avoid) this trade-off between standard accuracy and adversarial robustness for medical image classification and segmentation. We propose a novel adversarial training method, named Increasing-Margin Adversarial (IMA) Training, which is supported by an equilibrium state analysis about the optimality of adversarial training samples. Our method aims to preserve accuracy while improving robustness by generating optimal adversarial training samples. We evaluate our method and the other eight representative methods on six publicly available image datasets corrupted by noises generated by AutoAttack and white-noise attack. Our method achieves the highest adversarial robustness for image classification and segmentation with the smallest reduction in accuracy on clean data. For one of the applications, our method improves both accuracy and robustness. Our study has demonstrated that our method can lift the trade-off between standard accuracy and adversarial robustness for the image classification and segmentation applications.

Linhai Ma, Liang Liang

Electrocardiogram (ECG) is the most widely used diagnostic tool to monitor the condition of the cardiovascular system. Deep neural networks (DNNs), have been developed in many research labs for automatic interpretation of ECG signals to identify potential abnormalities in patient hearts. Studies have shown that given a sufficiently large amount of data, the classification accuracy of DNNs could reach human-expert cardiologist level. A DNN-based automated ECG diagnostic system would be an affordable solution for patients in developing countries where human-expert cardiologist are lacking. However, despite of the excellent performance in classification accuracy, it has been shown that DNNs are highly vulnerable to adversarial attacks: subtle changes in input of a DNN can lead to a wrong classification output with high confidence. Thus, it is challenging and essential to improve adversarial robustness of DNNs for ECG signal classification, a life-critical application. In this work, we proposed to improve DNN robustness from the perspective of noise-to-signal ratio (NSR) and developed two methods to minimize NSR during training process. We evaluated the proposed methods on PhysionNets MIT-BIH dataset, and the results show that our proposed methods lead to an enhancement in robustness against PGD adversarial attack and SPSA attack, with a minimal change in accuracy on clean data.