Dang Nguyen, Arun Kumar A, Taylor A. Braund +8cs.LG
University students experience disproportionately high rates of common mental health conditions, such as depression, which can impair learning, social functioning, and overall well-being. Although lifestyle interventions such as mindfulness and physical activity can reduce the symptoms, many do not achieve symptomatic remission. Developing new approaches to identify students with poor outcomes could enable earlier and more targeted intervention. Machine learning (ML) methods have increasingly been used to predict remission in depressive patients. However, these ML models often suffer from class imbalance, where there may be an unequal proportion of people in the remitted group relative to the non-remitted group. This imbalance can reduce model accuracy and bias predictions. To address this, studies commonly employ the popular oversampling strategy SMOTE. However, SMOTE has a notable limitation: it may generate invalid synthetic minority samples. In a clinical context, these false positives can lead to incorrect risk stratification, potentially delaying necessary escalated care for patients unlikely to remit. In this paper, we introduce a novel and effective oversampling method that addresses this shortcoming. Our approach leverages the variance function of a Gaussian process to estimate the uncertainty of generated minority samples to reduce false positives. We validate our method on a depression dataset collected from university students and demonstrate that it is better than existing oversampling approaches in predicting remission (i.e., treatment outcome). By improving the reliable identification of non-responders, our method provides a robust computational tool to help clinicians rapidly pivot to adjunctive therapies, thereby personalizing and optimizing mental health care pathways.
Olivera Kotevska, Ian Goethert, Michael McGee +11cs.CV
Lung cancer remains a leading cause of cancer-related mortality worldwide, and early diagnosis is critical for improving survival. However, early-stage malignancies can be subtle on chest X-rays, creating challenges for radiologists. This study evaluates Vision Transformers (ViTs) for predicting lung cancer one to two years before clinical diagnosis. We analyzed 259,361 chest X-rays from 91,020 imaging studies at the Jamaica Plains VA Hospital in Boston, MA. The dataset showed extreme class imbalance, approximately 1:150 cancer to non-cancer, which was addressed using hybrid under- and over-sampling and class-weighted loss optimization. Three ViT configurations were evaluated: a model trained from scratch, an ImageNet-pretrained model, and a Corona-pretrained model fine-tuned on the lung cancer dataset. Transfer learning improved performance, with pretrained models exceeding the scratch baseline by 6-10 percentage points in AUC and about 10-12 percent in balanced accuracy. ImageNet-pretrained models showed the most stable overall performance, while Corona-pretrained models achieved higher sensitivity in some settings but greater variability. Moderate resampling ratios, including 1:1 undersampling and 1.5:2 oversampling, provided favorable trade-offs between sensitivity, precision, and computational efficiency, reducing runtime by up to 70 percent without major performance loss. These findings demonstrate the potential of ViTs for early lung cancer risk prediction from routine chest X-rays. Although performance remains below clinical deployment thresholds, the results support further development of ViT-based triage systems to flag high-risk patients for earlier evaluation.
Medical image classification often suffers from class imbalance due to the inherent disparities in disease incidence. Existing approaches, such as class resampling and loss reweighting, mainly improve learning within the observed feature distribution, but do not explicitly enlarge the latent support region of tail classes. As a result, tail-class representations remain overly compact and are easily encroached upon by head classes, leading to biased decision boundaries. In this work, we propose Recurrent Contrastive Learning (RCL) for imbalanced medical image classification. RCL progressively expands the support region of tail classes by recurrently reusing historical feature states across training phases. Specifically, we adopt DINOv3 with LoRA adapters as the backbone to provide robust feature embeddings. We then devise a Temporal Memory Queue (TMQ) to preserve corpus-level features across training phases and provide diversified global references for contrastive learning. Based on TMQ, we construct Temporal Anchors (TARs) to form an anchor field around tail classes. This field enlarges the support region of tail classes, suppresses head-class encroachment, and improves inter-class separation. Extensive experiments on three imbalanced medical datasets demonstrate that RCL achieves consistent improvements over strong baselines. The code is available at https://github.com/dndins/RCL.
Personalized neoantigen prediction is challenging due to the scarcity of positive samples, the noise of the experimental data, the severe class imbalance trait and the complex of immunogenicity features. Prior arts, such as linear regression and XGBoost fail to model long-range dependencies and contextual relationships within peptide features, therefore the performance of neoantigen positive recall rate is limited. In this paper, we present a novel deep learning framework based on Transformer, coined as TransNRank. By leveraging the self-attention mechanism, our model captures both local and global feature contexts, enabling more accurate recognition of immunogenic neoantigens. A positive-aware training objective is utilized to handle the class imbalance problem, assigning more weights to those few positive samples. Extensive experiments are performed on NCI, TESLA and HiTIDE datasets. Notably, our TransNRank can push the upper bound top 20 recall rate of neoantigen prediction from 46.9% (45 from 96) to 53.1% (51 from 96), while reducing the training epochs from 200 epochs to 20 epochs. Furthermore, we analyze the features contribution based on TransNRank and find that the mutation at anchor and TCGA expression level play an unexpected important role in neoantigen prediction, and removing insignificant features to reduce the input dimensionality of peptides does not drastically impair the overall performance of the model. Our paradigm not only streamlines the prediction pipeline but also sets a new state-of-the-art for neoantigen discovery, with broad implications for accurate immuno-oncology.
Priya Tomar, Aditya Parikh, Christian Bauckhage +1cs.CV cs.LG
Effective multi-organ segmentation in surgical data requires learning the intricate anatomical features and alleviating the challenge of class imbalance, which results from relatively lower proportions of small and limitedly exposed structures. Recent works on laparoscopic multi-organ segmentation focus on learning structure-specific features through class-specific decoder architectures and report favorable results. This work extends the decoder-focused architectures to investigate knowledge sharing in the cross-surgical domain. We utilize two datasets representing different surgical domains, rectal and cholecystectomy surgeries, to explore how surgical conceptual knowledge transfers under partially common anatomical representations. Additionally, we compare the feature adaptation for the encoder and decoder at different training stages to analyse the knowledge adaptation and retention in the network. Our results corroborate previous findings on decoder-specific architectures and demonstrate that the organ-specific decoder model (CEMD), fully fine-tuned after cross-domain pre-training, achieves the highest segmentation performance (62.4\% dice) while converging substantially faster than training from scratch. However, we also find that class imbalance in surgical data remains a persistent challenge that transfer learning does not fully resolve for underrepresented anatomical structures.
Deep learning has shown strong potential in medical image analysis, but most existing methods rely on large-scale annotations and a closed-world assumption that rarely holds in clinical practice. Although Generalized Category Discovery (GCD) has advanced rapidly on natural images, it remains underexplored in medical imaging. To address this issue, we propose MedXplore, a unified framework for reliable and unbiased medical GCD, optimizing from both perceptual and decision levels. Specifically, at the perceptual level, taking a frequency domain perspective, Frequency-SNR Adaptive Attention and Consistency (FAAC) performs learnable full-spectrum filtering and global-local energy contrast activation to not only highlight local abnormal signals relative to the global context, but also provide reliable semantic anchors for patch consistency learning. At the decision level, Adaptive Cosine-Angular Margin (ACAM) adjusts angular margins using semantic difficulty and feature confidence to balance intra-class compactness and inter-class separability. Together, the two modules improve lesion-sensitive representation learning and mitigate old-class bias. Experiments on multiple benchmarks show an average \textbf{8.5\%} gain in \textit{All} accuracy over the strongest competing methods. On Kvasir, MedXplore reduces false-old errors from 14.50\% to 0.80\%, demonstrating strong robustness under severe old-new ambiguity.
Wolff-Parkinson-White (WPW) syndrome is a congenital cardiac pre-excitation, clinically important and often missed on the resting 12-lead ECG. Detection is hard: the signature is subtle and the condition rare. We pool two public 12-lead corpora, PTB-XL and Chapman-Shaoxing-Ningbo: 66,951 recordings, 142 of them WPW, a prevalence of 0.21% (about 471:1). Under one pre-specified, leakage-controlled protocol, with a held-out fold contacted exactly once, we compare seven representations of the signal, holding the split and the evaluation fixed. Within these corpora and under a modest compute budget, added diversity and capacity do not raise the ceiling: the most orthogonal detector significantly hurts, a feature-union model matches a two-member vote, a convolutional network reaches the wavelet detector without exceeding it, and self-supervised pretraining fails a pre-specified gate. A leak-free learning curve, re-selecting features at every size, still rises at the full 115 positives for the strongest deployed detector (paired 90-to-100% difference +0.027, 95% CI [0.019, 0.033]), so it is not shown to have saturated. An error analysis tested against independent evidence finds that the missed cases have a narrower QRS, confirmed by an on-machine measurement outside our pipeline after we show the sign of this effect depends on which delineator measures it; that uncertain labels show no enrichment among the misses; and that some apparent false positives are recordings the corpus itself codes as pre-excited, placing part of the label problem in the negative class. We measure the optimism of non-nested selection at 0.11 to 0.13 average precision. The deployed output is a percentile rank in a frozen reference distribution, not a probability. On the held-out fold, on 14 positives, it reaches an average precision of 0.595 and an ROC area of 0.950. It is a screening pre-filter, not a diagnostic tool.
Cervical cytology classification models are typically evaluated on curated, class-balanced benchmarks, but real-world liquid-based cytology (LBC) collections are often small and class-imbalanced. This paper presents a class-imbalance-aware and calibration-aware ensemble classification study on the Mendeley LBC dataset, using its native four-class Bethesda taxonomy (NILM, LSIL, HSIL, SCC) rather than a collapsed binary formulation. Three lightweight architectures (Swin-Tiny, TinyViT-5M, DenseNet121) are trained directly on Mendeley LBC using weighted random sampling to counteract class imbalance, and compared against two soft-voting ensembles (Hybrid-2, Hybrid-3). Post-hoc temperature scaling is fit on a held-out calibration subset carved out of the training portion of each cross-validation fold, distinct from both the training data used to fit model weights and the evaluation fold used for final metrics, avoiding the optimistic calibration estimates that result when the same data is used for both purposes. Calibration substantially reduces expected calibration error, Brier score, and negative log-likelihood for every model and ensemble configuration tested, while discrimination metrics (accuracy, macro-F1, macro-AUROC) remain essentially unchanged. Ensemble size shows no consistent additional reliability benefit over the best individual model once all configurations are properly calibrated. Confusion matrices show that all classification errors, across every configuration, are confined to the boundary between high-grade lesions (HSIL) and carcinoma (SCC); no errors involve the negative (NILM) or low-grade (LSIL) categories. These results suggest that, for this dataset, calibration is the dominant lever for reliability, not ensemble size, though this conclusion should be read in light of the dataset's modest size.
Yue Zhang, Nandini Amit Gadhia, Georgios Karagiannis +1q-bio.QM cs.LG
Classifying heterogeneous omics data remains a fundamental challenge in computational biology, particularly in high-dimensional, small-sample settings where nonlinear interactions dominate and class imbalance further complicates reliable prediction of minority phenotypes. While traditional kernel methods rely on feature abundance, they fail to leverage the known interaction landscapes of biological systems. In this work, we propose a structured Gaussian process classification framework that integrates graph-encoded biological pathways directly into the kernel construction. By propagating information along known interaction networks and combining this with abundance-derived features, the resulting classifier captures both quantitative measurements and topological context. We benchmark our proposed methodology on three publicly available gut and fecal microbiome datasets. To address severe class imbalance, we evaluate complementary strategies, including data-level resampling, threshold calibration, and confusion-matrix-based adjustments, and report minority-class performance alongside accuracy. The hybrid approach yields a performance gain over unstructured baselines and matches the performance of established benchmarks for similar datasets. Furthermore, the probabilistic nature of the framework naturally provides calibrated predictive uncertainty, enabling robust differentiation between confident predictions and ambiguous samples.
Okba Bekhelifi, Naoual El Djouher Mebtouchecs.LG eess.SP
For predictive models, the often-reported performance metrics are the loss and accuracy. In synchronous Brain- Computer Interface (BCI) systems, these metrics are informative for most BCI paradigms; however, for Event-Related Potential (ERP) applications the spelling rate, which measures the number of characters correctly selected is more important as it influences the estimation of information transfer rate (ITR) and any related metric measuring spelling performance. Moreover, ERP-based BCIs hold imbalanced data class distributions, which require reporting metrics that can handle the imbalance, such as the area under the receiver operating characteristic curve (ROC AUC). In this work, we study the correlation of the spelling rate with 13 metrics to identify which among them best reflect user spelling performance and how they are affected by trial repetition. The Results of two datasets (a private LARESI ERP dataset and the public OpenBMI ERP dataset) favor the Brier score, Matthews Correlation Coefficient (MCC), and the metrics that account for class imbalance in binary classification: ROC AUC, area under the Precision-Recall curve (PR AUC), Average Precision (AP), and partial AUC (pAUC). These findings encourage researchers and practitioners to report those metrics in ERP-based BCI experiments.
Cardiac discharge phenotyping informs post-discharge treatment and follow-up, but real-world records are often incomplete and class-imbalanced, increasing the risk of missed high-risk phenotypes. We propose CW-B, a clinical risk-aligned class-weighted XGBoost pipeline for five-class cardiac discharge phenotyping under real-world class imbalance and missingness. CW-B combines fold-specific class-balanced instance weighting, missingness-indicator augmentation, and classwise error auditing to improve recognition of clinically prioritized phenotypes while preserving interpretable and auditable decision logic. In five-fold stratified cross-validation, CW-B achieves the best Accuracy, Macro-F1, Balanced Accuracy, and Prioritized F1 among tree-based, ensemble, and neural baselines. Overall, CW-B provides a practical and deployment-oriented approach for more reliable cardiac discharge phenotyping in real-world clinical settings.
Nataliya Shakhovska, Valentyna Chopyak, Ivan Izonin +1cs.LG cs.AI
Cryopathy syndromes are difficult to classify because laboratory patterns often overlap across diagnostic categories, while some diagnoses are rare. This makes routine interpretation of cryoglobulin-related tests challenging and increases dependence on expert judgment. The aim of this study was to develop and compare machine learning approaches for automated classification of cryopathy syndromes from laboratory data and to identify a practical strategy for clinical decision support. Methods: We analysed laboratory records from 2,686 patients assigned to 14 diagnostic categories. The dataset included demographic variables, cryoglobulin measurements, precipitation tests, and hemagglutinin and hemolysin titers. Data preprocessing included cleaning, encoding, imputation, normalization, and construction of clinically informed interaction features. We evaluated 12 modelling strategies, including Random Forest, Gradient Boosted Trees, Multi-Layer Perceptron, soft-voting ensembles, class balancing with Synthetic Minority Over-sampling Technique, hierarchical classification, period-aware models, targeted binary classifiers, and probability calibration. Performance was assessed using stratified train-test evaluation and stratified 5-fold cross-validation. The main metrics were macro-averaged F1 score, accuracy, Top-3 accuracy, and expected calibration error. The overall task proved difficult because of marked class imbalance and clinical overlap between diagnoses. The best multiclass performance was achieved by a soft-voting ensemble of Random Forest and Gradient Boosted Trees. Cross-validation confirmed stable performance for the balanced Random Forest model. Tree-based methods consistently outperformed the neural network model. Feature engineering improved discrimination, and the most informative predictors were derived cryoglobulin-based interaction features.
Myocardial substrate abnormalities, such as myocardial scar and myocardial infarction (MI), are associated with adverse cardiovascular outcomes. Electrocardiography (ECG) provides a low-cost and widely available tool for detecting these abnormalities, but ECG-based detection remains challenging due to heterogeneous lead-dependent manifestations, high-dimensional multi-lead signals, class imbalance, and the limited interpretability of deep learning models. We propose a multi-scale attention-enhanced convolutional network (MSAIC-Net) for ECG-based myocardial substrate abnormality detection. MSAIC-Net employs parallel atrous convolutional branches to extract ECG features across multiple temporal receptive fields. %, enabling the model to capture both local and longer-range temporal patterns. Channel attention is then used to adaptively reweight informative lead-wise and feature-channel representations. To address class imbalance and improve feature separability, we introduce a novel imbalance-aware supervised contrastive learning strategy that encourages samples from the same class to form compact representations while increasing separation between abnormal and normal samples. Lead-wise permutation importance is further incorporated to quantify the contribution of each ECG lead and improve model interpretability. The proposed method was evaluated on two complementary datasets: a low-data institutional cohort from the University of Virginia (UVA) Health System for myocardial scar classification and the large-scale public PTB-XL dataset from PhysioNet for MI identification. Experimental results show that MSAIC-Net outperforms baseline models, with particularly pronounced improvements in the low-data UVA cohort. Overall, the proposed framework provides an effective and interpretable approach for ECG-based detection of myocardial substrate abnormalities.
Chest radiography is a widely used imaging modality for thoracic disease diagnosis, yet its conventional interpretation remains time-consuming and heavily dependent on expert knowledge. While deep learning has improved diagnostic efficiency through automated feature extraction, challenges such as class imbalance and the localization of multiple co-existing pathologies remain unsolved. In this paper, inspired by the strength of Convolutional Block Attention Module (CBAM) in feature refinement and the capability of CNN blocks in feature extraction, we propose a strategy to integrate CBAM into traditional CNN blocks to enhance performance in multi-label classification tasks. Our method achieves a mean AUC of 0.8695 on ChestXray14 dataset, outperforming several state-of-the-art baselines.Our source code is available at: https://github.com/NNNguyenDuyyy/FETC_CBAM_Enhanced_CNN.git
Chest X-ray classification suffers from severe class imbalance where gradient updates bias toward majority classes, causing feature drift and poor performance on rare but critical pathologies. We propose a Momentum-Anchored Multi-Scale Fusion Network that uses exponential moving averages (EMA) as a temporal anchoring mechanism to stabilize feature representations under long-tailed distributions. Our approach applies selective momentum updates to the final expansion block of an EfficientNet backbone, creating a slowly-evolving reference branch that resists gradient-induced drift while preserving discriminative patterns for minority classes. Combined with multi-scale spatial fusion ($1\times 1$, $3 \times 3$, $5 \times 5$ convolutions), this anchoring strategy maintains representational stability throughout training. On ChestX-ray14, our method achieves 0.8682 average AUC, outperforming state-of-the-art approaches and showing particular improvements on rare pathologies like Hernia (0.9470) and Pneumonia (0.8165). The results demonstrate that momentum anchoring effectively counters feature instability in long-tailed medical image classification.
Martina Pavan, Matteo Caligiuri, Francesco Barbato +1cs.CV
Exploiting deep learning in medical imaging faces critical challenges, including strict privacy constraints, heterogeneous imaging devices with varying acquisition properties, and class imbalance due to the uneven prevalence of pathologies. In this work, we propose FedSSG, a novel Federated Learning framework that addresses domain shifts caused by diverse imaging devices while mitigating the under-representation of rare pathologies. The key contribution is a strategy for generating synthetic samples and distributing them across clients to improve coverage of both underrepresented pathologies and imaging devices. Experimental results demonstrate that our approach significantly enhances model performance and generalization across heterogeneous institutions, with minimal computational overhead at the client side.