PC-MIL: Decoupling Feature Resolution from Supervision Scale in Whole-Slide Learning

Whole-slide image (WSI) classification in computational pathology is commonly formulated as slide-level Multiple Instance Learning (MIL) with a single global bag representation. However, slide-level MIL is fundamentally underconstrained: optimizing only global labels encourages models to aggregate features without learning anatomically meaningful localization. This creates a mismatch between the scale of supervision and the scale of clinical reasoning. Clinicians assess tumor burden, focal lesions, and architectural patterns within millimeter-scale regions, whereas standard MIL is trained only to predict whether "somewhere in the slide there is cancer." As a result, the model's inductive bias effectively erases anatomical structure. We propose Progressive-Context MIL (PC-MIL), a framework that treats the spatial extent of supervision as a first-class design dimension. Rather than altering magnification, patch size, or introducing pixel-level segmentation, we decouple feature resolution from supervision scale. Using fixed 20x features, we vary MIL bag extent in millimeter units and anchor supervision at a clinically motivated 2mm scale to preserve comparable tumor burden and avoid confounding scale with lesion density. PC-MIL progressively mixes slide- and region-level supervision in controlled proportions, enabling explicit train-context x test-context analysis. On 1,476 prostate WSIs from five public datasets for binary cancer detection, we show that anatomical context is an independent axis of generalization in MIL, orthogonal to feature resolution: modest regional supervision improves cross-context performance, and balanced multi-context training stabilizes accuracy across slide and regional evaluation without sacrificing global performance. These results demonstrate that supervision extent shapes MIL inductive bias and support anatomically grounded WSI generalization.

LoGo-MR: Screening Breast MRI for Cancer Risk Prediction by Efficient Omni-Slice Modeling

Efficient and explainable breast cancer (BC) risk prediction is critical for large-scale population-based screening. Breast MRI provides functional information for personalized risk assessment. Yet effective modeling remains challenging as fully 3D CNNs capture volumetric context at high computational cost, whereas lightweight 2D CNNs fail to model inter-slice continuity. Importantly, breast MRI modeling for shor- and long-term BC risk stratification remains underexplored. In this study, we propose LoGo-MR, a 2.5D local-global structural modeling framework for five-year BC risk prediction. Aligned with clinical interpretation, our framework first employs neighbor-slice encoding to capture subtle local cues linked to short-term risk. It then integrates transformer-enhanced multiple-instance learning (MIL) to model distributed global patterns related to long-term risk and provide interpretable slice importance. We further apply this framework across axial, sagittal, and coronal planes as LoGo3-MR to capture complementary volumetric information. This multi-plane formulation enables voxel-level risk saliency mapping, which may assist radiologists in localizing risk-relevant regions during breast MRI interpretation. Evaluated on a large breast MRI screening cohort (~7.5K), our method outperforms 2D/3D baselines and existing SOTA MIL methods, achieving AUCs of 0.77-0.69 for 1- to 5-year prediction and improving C-index by ~6% over 3D CNNs. LoGo3-MR further improves overall performance with interpretable localization across three planes, and validation across seven backbones shows consistent gains. These results highlight the clinical potential of efficient MRI-based BC risk stratification for large-scale screening. Code will be released publicly.

LDEPrompt: Layer-importance guided Dual Expandable Prompt Pool for Pre-trained Model-based Class-Incremental Learning

Prompt-based class-incremental learning methods typically construct a prompt pool consisting of multiple trainable key-prompts and perform instance-level matching to select the most suitable prompt embeddings, which has shown promising results. However, existing approaches face several limitations, including fixed prompt pools, manual selection of prompt embeddings, and strong reliance on the pretrained backbone for prompt selection. To address these issues, we propose a \textbf{L}ayer-importance guided \textbf{D}ual \textbf{E}xpandable \textbf{P}rompt Pool (\textbf{LDEPrompt}), which enables adaptive layer selection as well as dynamic freezing and expansion of the prompt pool. Extensive experiments on widely used class-incremental learning benchmarks demonstrate that LDEPrompt achieves state-of-the-art performance, validating its effectiveness and scalability.

CoRe-ECG: Advancing Self-Supervised Representation Learning for 12-Lead ECG via Contrastive and Reconstructive Synergy

Accurate interpretation of electrocardiogram (ECG) remains challenging due to the scarcity of labeled data and the high cost of expert annotation. Self-supervised learning (SSL) offers a promising solution by enabling models to learn expressive representations from unlabeled signals. Existing ECG SSL methods typically rely on either contrastive learning or reconstructive learning. However, each approach in isolation provides limited supervisory signals and suffers from additional limitations, including non-physiological distortions introduced by naive augmentations and trivial correlations across multiple leads that models may exploit as shortcuts. In this work, we propose CoRe-ECG, a unified contrastive and reconstructive pretraining paradigm that establishes a synergistic interaction between global semantic modeling and local structural learning. CoRe-ECG aligns global representations during reconstruction, enabling instance-level discriminative signals to guide local waveform recovery. To further enhance pretraining, we introduce Frequency Dynamic Augmentation (FDA) to adaptively perturb ECG signals based on their frequency-domain importance, and Spatio-Temporal Dual Masking (STDM) to break linear dependencies across leads, increasing the difficulty of reconstructive tasks. Our method achieves state-of-the-art performance across multiple downstream ECG datasets. Ablation studies further demonstrate the necessity and complementarity of each component. This approach provides a robust and physiologically meaningful representation learning framework for ECG analysis.

Do Instance Priors Help Weakly Supervised Semantic Segmentation?

Semantic segmentation requires dense pixel-level annotations, which are costly and time-consuming to acquire. To address this, we present SeSAM, a framework that uses a foundational segmentation model, i.e. Segment Anything Model (SAM), with weak labels, including coarse masks, scribbles, and points. SAM, originally designed for instance-based segmentation, cannot be directly used for semantic segmentation tasks. In this work, we identify specific challenges faced by SAM and determine appropriate components to adapt it for class-based segmentation using weak labels. Specifically, SeSAM decomposes class masks into connected components, samples point prompts along object skeletons, selects SAM masks using weak-label coverage, and iteratively refines labels using pseudo-labels, enabling SAM-generated masks to be effectively used for semantic segmentation. Integrated with a semi-supervised learning framework, SeSAM balances ground-truth labels, SAM-based pseudo-labels, and high-confidence pseudo-labels, significantly improving segmentation quality. Extensive experiments across multiple benchmarks and weak annotation types show that SeSAM consistently outperforms weakly supervised baselines while substantially reducing annotation cost relative to fine supervision.

AC-MIL: Weakly Supervised Atrial LGE-MRI Quality Assessment via Adversarial Concept Disentanglement

High-quality Late Gadolinium Enhancement (LGE) MRI can be helpful for atrial fibrillation management, yet scan quality is frequently compromised by patient motion, irregular breathing, and suboptimal image acquisition timing. While Multiple Instance Learning (MIL) has emerged as a powerful tool for automated quality assessment under weak supervision, current state-of-the-art methods map localized visual evidence to a single, opaque global feature vector. This black box approach fails to provide actionable feedback on specific failure modes, obscuring whether a scan degrades due to motion blur, inadequate contrast, or a lack of anatomical context. In this paper, we propose Adversarial Concept-MIL (AC-MIL), a weakly supervised framework that decomposes global image quality into clinically defined radiological concepts using only volume-level supervision. To capture latent quality variations without entangling predefined concepts, our framework incorporates an unsupervised residual branch guided by an adversarial erasure mechanism to strictly prevent information leakage. Furthermore, we introduce a spatial diversity constraint that penalizes overlap between distinct concept attention maps, ensuring localized and interpretable feature extraction. Extensive experiments on a clinical dataset of atrial LGE-MRI volumes demonstrate that AC-MIL successfully opens the MIL black box, providing highly localized spatial concept maps that allow clinicians to pinpoint the specific causes of non-diagnostic scans. Crucially, our framework achieves this deep clinical transparency while maintaining highly competitive ordinal grading performance against existing baselines. Code to be released on acceptance.

SIMPLER: H&E-Informed Representation Learning for Structured Illumination Microscopy

Structured Illumination Microscopy (SIM) enables rapid, high-contrast optical sectioning of fresh tissue without staining or physical sectioning, making it promising for intraoperative and point-of-care diagnostics. Recent foundation and large-scale self-supervised models in digital pathology have demonstrated strong performance on section-based modalities such as Hematoxylin and Eosin (H&E) and immunohistochemistry (IHC). However, these approaches are predominantly trained on thin tissue sections and do not explicitly address thick-tissue fluorescence modalities such as SIM. When transferred directly to SIM, performance is constrained by substantial modality shift, and naive fine-tuning often overfits to modality-specific appearance rather than underlying histological structure. We introduce SIMPLER (Structured Illumination Microscopy-Powered Learning for Embedding Representations), a cross-modality self-supervised pretraining framework that leverages H&E as a semantic anchor to learn reusable SIM representations. H&E encodes rich cellular and glandular structure aligned with established clinical annotations, while SIM provides rapid, nondestructive imaging of fresh tissue. During pretraining, SIM and H&E are progressively aligned through adversarial, contrastive, and reconstruction-based objectives, encouraging SIM embeddings to internalize histological structure from H&E without collapsing modality-specific characteristics. A single pretrained SIMPLER encoder transfers across multiple downstream tasks, including multiple instance learning and morphological clustering, consistently outperforming SIM models trained from scratch or H&E-only pretraining. Importantly, joint alignment enhances SIM performance without degrading H&E representations, demonstrating asymmetric enrichment rather

Why Supervised Fine-Tuning Fails to Learn: A Systematic Study of Incomplete Learning in Large Language Models

Supervised Fine-Tuning (SFT) is the standard approach for adapting large language models (LLMs) to downstream tasks. However, we observe a persistent failure mode: even after convergence, models often fail to correctly reproduce a subset of their own supervised training data. We refer to this behavior as the Incomplete Learning Phenomenon(ILP). This paper presents the first systematic study of ILP in LLM fine-tuning. We formalize ILP as post-training failure to internalize supervised instances and demonstrate its prevalence across multiple model families, domains, and datasets. Through controlled analyses, we identify five recurrent sources of incomplete learning: (1) missing prerequisite knowledge in the pre-trained model, (2) conflicts between SFT supervision and pre-training knowledge, (3) internal inconsistencies within SFT data, (4) left-side forgetting during sequential fine-tuning, and (5) insufficient optimization for rare or complex patterns. We introduce a diagnostic-first framework that maps unlearned samples to these causes using observable training and inference signals, and study several targeted mitigation strategies as causal interventions. Experiments on Qwen, LLaMA, and OLMo2 show that incomplete learning is widespread and heterogeneous, and that improvements in aggregate metrics can mask persistent unlearned subsets. The findings highlight the need for fine-grained diagnosis of what supervised fine-tuning fails to learn, and why.

Component-Adaptive and Lesion-Level Supervision for Improved Small Structure Segmentation in Brain MRI

We propose a unified objective function, termed CATMIL, that augments the base segmentation loss with two auxiliary supervision terms operating at different levels. The first term, Component-Adaptive Tversky, reweights voxel contributions based on connected components to balance the influence of lesions of different sizes. The second term, based on Multiple Instance Learning, introduces lesion-level supervision by encouraging the detection of each lesion instance. These terms are combined with the standard nnU-Net loss to jointly optimize voxel-level segmentation accuracy and lesion-level detection. We evaluate the proposed objective on the MSLesSeg dataset using a consistent nnU-Net framework and 5-fold cross-validation. The results show that CATMIL achieves the most balanced performance across segmentation accuracy, lesion detection, and error control. It improves Dice score (0.7834) and reduces boundary error compared to standard losses. More importantly, it substantially increases small lesion recall and reduces false negatives, while maintaining the lowest false positive volume among compared methods. These findings demonstrate that integrating component-level and lesion-level supervision within a unified objective provides an effective and practical approach for improving small lesion segmentation in highly imbalanced settings. All code and pretrained models are available at \href{https://github.com/luumsk/SmallLesionMRI}{this url}.

Needle in a Haystack -- One-Class Representation Learning for Detecting Rare Malignant Cells in Computational Cytology

In computational cytology, detecting malignancy on whole-slide images is difficult because malignant cells are morphologically diverse yet vanishingly rare amid a vast background of normal cells. Accurate detection of these extremely rare malignant cells remains challenging due to large class imbalance and limited annotations. Conventional weakly supervised approaches, such as multiple instance learning (MIL), often fail to generalize at the instance level, especially when the fraction of malignant cells (witness rate) is exceedingly low. In this study, we explore the use of one-class representation learning techniques for detecting malignant cells in low-witness-rate scenarios. These methods are trained exclusively on slide-negative patches, without requiring any instance-level supervision. Specifically, we evaluate two OCC approaches, DSVDD and DROC, and compare them with FS-SIL, WS-SIL, and the recent ItS2CLR method. The one-class methods learn compact representations of normality and detect deviations at test time. Experiments on a publicly available bone marrow cytomorphology dataset (TCIA) and an in-house oral cancer cytology dataset show that DSVDD achieves state-of-the-art performance in instance-level abnormality ranking, particularly in ultra-low witness-rate regimes ($\leq 1\%$) and, in some cases, even outperforming fully supervised learning, which is typically not a practical option in whole-slide cytology due to the infeasibility of exhaustive instance-level annotations. DROC is also competitive under extreme rarity, benefiting from distribution-augmented contrastive learning. These findings highlight one-class representation learning as a robust and interpretable superior choice to MIL for malignant cell detection under extreme rarity.