Vision-Language Pretrained Models (VLPMs) offer a scalable path to open-vocabulary chest radiology understanding, yet two aspects remain underexplored: how structured clinical semantics extracted from medical reports can reduce in-batch noise during contrastive learning, and how cross-modal fusion can be designed to produce more faithful spatial grounding without added complexity. We introduce AlphaRAD, addressing these opportunities through two contributions. First, we construct a large-scale structured medical concept space from medical reports parsed by a Large Language Model for training, thereby mitigating in-batch learning noise and removing heuristic pair matching in contrastive learning, and thus naturally positioning AlphaRAD as a medical concept discriminator trained via $α$-Corrected Binary Cross-Entropy. Second, we propose FLaS (Factorized Latent Supervision), an extremely simple yet effective cross-modal feature fusion module that factorizes VLPM representations into independent subspaces, using dedicated alignment supervision to enhance the expressiveness of spatial grounding without introducing additional model parameters. Through extensive empirical validation, AlphaRAD shows strong zero-shot generalization across diverse chest radiology tasks. Notably, it establishes state-of-the-art average performance across 16 classification benchmarks, while achieving individual state-of-the-art results via distinct gains on 7 grounding/phrase grounding and 3 segmentation datasets.
Surgical phase recognition is key to context-aware computer-assisted feedback in vitreoretinal procedures, yet the scarcity of synchronized multimodal intraoperative data, particularly microscope views and intraoperative OCT, limits approaches that aim to replicate the multimodal integration surgeons perform naturally. Surgical narration, by contrast, is abundantly available online and offers rich semantic supervision. Prior work has mainly explored pairwise contrastive learning (e.g., intraoperative OCT-microscope or microscope-narration), leaving the joint modeling of all three modalities largely unexplored. We introduce a framework that uses microscope views as a shared anchor to bridge surgical narrations and intraoperative OCT (iOCT) without requiring a fully synchronized tri-modal dataset, leveraging real microscope-narration videos and a synthetic dataset of synchronized microscope video and tool-aligned iOCT pairs. Contrastive alignment transfers structural priors from the synthetic domain to real videos lacking iOCT, and a dual-head MS-TCN++ integrates the resulting embeddings for joint macro- and micro-phase prediction. Evaluated on real vitreoretinal surgeries, our framework improves macro-phase recognition over a zero-shot baseline (mean F1 0.38 to 0.53) and provides an exploratory route to estimating fine-grained instrument-tissue measurements that are not directly observable in real microscope video alone; these micro-phase estimates are validated quantitatively on synthetic data and shown only qualitatively on real surgery. To our knowledge, this is the first work to unify microscope view, iOCT B-scans, and surgical narrations in a shared latent space for surgical phase recognition.
Huseyin Umut Isik, Mehmet Alp Ozaydin, Sila Kurugol +1cs.CV cs.AI
Contrastive vision-language learning uses paired chest CT volumes and radiology reports to learn abnormality classifiers without manually annotated labels. However, two characteristics of chest CT challenge conventional global contrastive learning. First, many critical abnormalities are small or anatomically localized, and pooling an en- tire volume into a single embedding may dilute their visual evidence. Second, the standard contrastive objective treats every other scan in a batch as a negative. Because many chest CTs share abnormalities, this objective incorrectly pushes co-positive pairs apart. We propose Anatomy-Routed Contrastive Learning for 3D Chest CT (ARC-CT), a region-aware framework that addresses these limitations using only la- bels extracted from reports by an LLM, with no manual annotations or bounding boxes. ARC-CT combines three components: (1) an Anato- myQFormer localizing evidence via queries constrained by automatically generated organ masks; (2) a label-Jaccard soft InfoNCE objective in- tegrating the standard one-hot target with the label-set overlap of each pair, which reduces false-negative penalties between studies that share clinical findings; and (3) an organ-level alignment loss connecting mask- pooled visual features to organ-specific report text extracted offline with a large language model. ARC-CT achieves a 0.86 mask-free macro AUC across 18 abnormalities using a compact 3D ResNet-18 backbone. Over- all, ARC-CT outperforms both comparable efficient baselines and sev- eral larger transformer models. Our code and weights are available at https://github.com/arc-ct/arc-ct.
Human Activity Recognition (HAR) using inertial measurement units (IMUs) enables a wide range of applications, yet the field still lacks a unified model that can generalize across diverse subjects, devices, and activities. Training such a model is difficult due to two key challenges: sensing heterogeneity -- differences in sampling rates, channel configurations, and sensor placements -- and poor generalization to unseen activities and label vocabularies. We introduce HALO (Heterogeneity-Aware Language-aligned Open-set model), a domain-specific IMU foundation model that addresses both challenges through a two-stage training framework. Stage 1 pretrains the IMU encoder with heterogeneity-aware self-supervised learning, including adaptive-pooling tokenization, channel-independent feature extraction, and contextualized sensor conditioning that injects natural-language sensor descriptions into each channel embedding. Stage 2 aligns this IMU encoder with text embeddings via synonym-aware soft contrastive learning, enabling open-set recognition via cosine-similarity retrieval without per-dataset classifiers. Trained on 10 public HAR datasets and evaluated on 7 held-out datasets, HALO outperforms five state-of-the-art baselines on all 8 aggregate metrics, and still leads on 3 of 4 settings under baseline-matched inputs. Despite using only ~35M trainable parameters -- 10x fewer than the latest foundation model MOMENT (341.2M) -- HALO improves zero-shot open-set accuracy, measured over all 87 training labels, by 13.7 percentage points. On two further datasets with severe distribution shift, every model including HALO collapses zero-shot. A video demonstration of HALO's performance in real world is available at https://youtu.be/rooVKragtFU
12-lead electrocardiogram (ECG) is a standard, non-invasive examination widely used for diagnosing coronary artery disease, where clinical interpretation relies on comparing waveform patterns across multiple leads. However, most existing ECG analysis methods focus on single-lead signals or treat each lead independently, and typically process ECG signals as one-dimensional time-series data using CNNs or RNNs. While effective in modeling local waveform changes, such approaches have difficulty capturing inter-lead dependency and global waveform patterns essential for clinical diagnosis. To address this limitation, we propose a graph-based pseudo-multimodal contrastive learning framework called Graph-CMMC. ECG waveforms are transformed into Gramian Angular Difference Field (GADF) images to construct complementary representations of the same cardiac activity, enabling a pseudo-multimodal learning setting. Using all 12 leads, Graph-CMMC aligns waveform and GADF representations in a self-supervised manner, while a graph-based relational module is employed to model inter-lead dependency and enforce structural consistency across leads during contrastive learning. Experimental results on a multi-label coronary artery occlusion classification task demonstrate that the proposed framework achieves competitive performance compared to supervised learning methods. These results further suggest the effectiveness of using GADF as a complementary representation and incorporating explicit graph-based modeling of inter-lead dependency for learning robust 12-lead ECG representations.
Despite the growing number of public datasets, annotated medical images remain scarce. Supervised learning methods achieve strong performance on many benchmarks, however require large amounts of labeled data, which are costly and time-consuming to obtain in the medical domain. To address this limitation, contrastive self-supervised learning (SSL) has emerged as a promising alternative for learning useful representations from unlabeled data. In this work, we investigate two SSL frameworks, SimSiam and SimCLR, for retinal disease classification from fundus images. We focus on understanding how augmentation strategies and training parameters influence representation learning under resource-constrained settings. Given limited data and computational capacity, we explore the feasibility of training SSL models with small batch sizes incorporated with retinal-specific augmentation techniques. Through a series of experiments, we assess the quality of learned representations via linear evaluation and fine-tuning across downstream tasks, including multi-disease classification and diabetic retinopathy grading. Our results show that tailoring augmentation strategies to the characteristics of retinal images plays a critical role in improving performance. Even under constrained settings, lightweight SSL frameworks can learn transferable representations that reduce dependence on large annotated datasets and achieve competitive results.
Cell Painting microscopy captures how cells change after a chemical or genetic perturbation. Connecting these images to the perturbations that produced them could make large imaging screens easier to search and interpret, but the task remains difficult because biological effects are subtle and technical variation is substantial. We introduce MorphoCLIP, a contrastive model that links Cell Painting profiles with text descriptions of compounds, CRISPR knockouts, and ORF overexpressions. The model keeps its vision and language backbones frozen and trains only a compact cross-channel module and projection layers, so it can be trained on a single consumer GPU. On held-out CPJUMP1 data, MorphoCLIP searches in both directions: from a cell image to its perturbation description and from a description to matching cell images. In both cases, a correct match appears among the top ten results much more often than expected by chance. Adding a replicate-alignment loss makes profiles from repeated experiments more consistent, although this improvement does not yet translate into reliable gene-compound matching. Gene-aware labels and plate correction also show no consistent retrieval benefit. These findings suggest that text supervision can help organize chemical and genetic Cell Painting data. Matching compounds with genetic perturbations, however, remains an open problem.
Decoding perceived speech from non-invasive brain recordings has garnered significant attention in recent years due to its wide range of potential applications. However, existing methods face considerable challenges in cross-subject decoding, primarily due to limited generalizability and the absence of explicit mechanisms for extracting subject-consistent information. These limitations result in high training costs and suboptimal decoding performance. To address these challenges, we propose an innovative Cross-Subject Perceived Speech Decoding (CPSD) framework, which comprises two training stages: source model pre-training and personal specialization. In the source model pre-training stage, contrastive learning is employed to capture shared representations across multiple source subjects. Subsequently, personal specialization initializes the model for the target subject by extracting consistent components from the source model and fine-tuning it using target subject data. Additionally, we introduce the Positional Encoding-based Spatial Attention (PESA) module, which remaps MEG/EEG data into a standardized reference space, thereby enhancing cross-subject consistency and facilitating model training. We evaluate the proposed CPSD framework on three perceived speech neural datasets encompassing different modalities and languages. The results demonstrate that our framework outperforms baseline methods by more than 6.8%, 15.4%, and 15.8% in Top-10 accuracy on the Armeni 2022, PKUEEG 2025, and Broderick 2018 datasets, respectively. Further analyses confirm the effectiveness, efficiency, and robustness of the proposed approach.
Non-invasive decoding of inner speech faces a fundamental data problem: a corpus pairing brain activity with a person's spontaneous inner monologue cannot be collected, and the available proxy paradigms (cued repetitive and retrospectively reported generative inner speech) are slow to acquire, poorly time-locked, and subject compliance is unverifiable. We therefore treat silent reading as a scalable proxy task and ask how much lexical and semantic information a contrastive decoder can extract from it. We report an open-vocabulary analysis of approximately 240,000 word presentations recorded from a single densely-sampled participant across 393 runs (ca. 49 h) of 19-channel dry-electrode EEG. Words from continuous narrative text were presented in rapid serial visual presentation, with typography randomised on every trial to partially decorrelate word identity from low-level visual form. A convolutional EEG encoder, optionally followed by a causal transformer, was trained with a CLIP-style contrastive objective to align short EEG windows with hidden-state embeddings of the presented word taken from a large language model. Decoding, evaluated as word-grouped top-10 retrieval against permutation baselines, was reliably above chance, extended to mid-frequency and rare words, and scaled log-linearly with training-data volume with no sign of saturation. Removing occipital and posterior-temporal electrodes reduced the word-level gain by roughly one third but left context tracking unchanged. Control analyses separate word-level decoding from narrative context tracking and from a non-neural positional prior introduced by the transformer's positional embedding. These results establish that open-vocabulary word-level information is recoverable from EEG during silent reading, and that decoding is data-limited rather than saturated.
Shenhav Nadir, Meir Yossef Levi, Eyal Gofer +1cs.CV
Despite the rapid progress of deep neural networks in visual recognition, their adoption in high-risk medical applications remains limited due to reliability and robustness concerns. Models may exploit spurious correlations, particularly in medical imaging, where devices or treatment artifacts often co-occur with pathology. In small or imbalanced datasets, such cues further reduce worst-group performance and undermine clinical trust. To solve these issues, two major challenges should be addressed: identifying dataset-specific spurious cues, which typically require domain knowledge, and mitigating reliance on them. To tackle both, we propose SpurCon, a lightweight framework based on a novel supervised contrastive loss formulation that leverages available metadata and predicted spurious labels to enhance robustness. We introduce a fast few-shot procedure, without network training, to estimate spurious labels using a small number of expert-annotated samples. We then propose a weighted supervised contrastive objective, WtSupCon, that reshapes the representation geometry by assigning sample-specific weights that depend on the [pathology, spurious, metadata] combination. For example, the highest weight is assigned to samples that differ only in their spurious label. This yields highly similar representations for images with the same metadata and pathology, differing only in the predicted spurious label. Our method operates on pretrained image encoders (such as BiomedCLIP) and trains only a lightweight projection head. We evaluate SpurCon on a synthetic setting and on Waterbirds, CheXpert, a chest X-ray classification dataset, and ISIC 2020, a skin cancer classification dataset. Our approach delivers the best spurious-mitigation performance, balancing well worst-group and overall accuracy on multiple datasets.
With the rapid advancement of large language models, brain-language decoding has achieved remarkable progress. However, it remains unclear whether decoded content genuinely reflects neural representations or is largely reconstructed by the language model itself. This ambiguity limits interpretability and hinders the investigation of intrinsic brain-language correspondence. To address this challenge, we propose MD-SigLIP. This margin-regularized structured semantic alignment framework directly aligns brain embeddings with text embeddings in a shared semantic space, enabling retrieval-based decoding. This formulation enables explicit modeling of the correspondence between neural representations and language semantics. Building upon duplicate-aware sigmoid contrastive learning, we introduce a listwise margin-regularized term that enforces structured ranking constraints between positive semantic clusters and negative samples. By modeling multi-positive semantic structure and margin-based ordering simultaneously, the method captures the manifold organization of language embeddings reflected in neural signals. Experiments demonstrate state-of-the-art retrieval performance under both full-vocabulary and subset evaluation settings.
Ultrasound is the primary imaging modality for assessing thyroid nodules, and the ACR TI-RADS framework standardizes diagnosis through five ultrasound feature categories that are aggregated into five risk levels (TR1-TR5). Although widely adopted in clinical practice, most deep learning approaches focus on binary malignancy classification, while multi-class prediction and explicit utilization of feature-level supervision remain underexplored, largely due to limited annotated data. In this study, we introduce the STN dataset of 600 thyroid nodules with paired transverse and longitudinal ultrasound images, bounding box annotations, and complete labels for all five TI-RADS feature categories. Following the clinical decision process, we investigate how structured feature information can guide representation learning during training while requiring only images at inference. We demonstrate that text embeddings derived from standardized feature descriptions form a stable surrogate representation for TI-RADS risk levels. Based on this observation, we propose CMCNet, which aligns image embeddings to fixed textual embeddings via a Center-Margin Contrastive Loss that simultaneously promotes intra-class compactness and inter-class separation. Experimental results show that this embedding alignment strategy is more data-efficient and robust than direct multitask learning, and consistently outperforms InfoNCE, center loss, a strong multitask baseline, and a VQA-style multimodal model, particularly in imbalanced settings. The dataset is freely available at doi: 10.5281/zenodo.19125693 and the source code is available at: https://www.healthinformaticslab.org/supp/.
Fenosoa Randrianjatovo, Maya Saleh, Simon Girard +1q-bio.GN cs.LG stat.CO stat.ME
Omics datasets, particularly single-cell RNA sequencing data, are high-dimensional, sparse, noisy, and dominated by zero values, making faithful low-dimensional representation challenging. Existing dimensionality-reduction methods may distort local neighbourhoods, global organization, or the cohesion of meaningful populations, with similar limitations arising in genealogical data. We introduce Contrastive Manifold Approximation and Projection (CosMAP), a graph-based unsupervised dimensionality-reduction method for producing faithful and interpretable embeddings. CosMAP extends the graph-based framework of UMAP by combining cosine-similarity neighbourhoods with temperature-normalized contrastive affinities, which are optimized in the embedding space using an attractive--repulsive objective. It further employs a two-phase refinement strategy: an intermediate higher-dimensional representation is first learned and then used to reconstruct the neighbourhood graph and initialize the final low-dimensional embedding. We evaluate CosMAP on MNIST and USPS handwritten-digit datasets, mouse retina and cortex single-cell RNA-sequencing datasets, and a large genealogical kinship dataset derived from BALSAC-CARTaGENE. Compared with state-of-the-art dimensionality-reduction methods, CosMAP produces more coherent visual representations, improves neighbourhood preservation, and provides clearer global organization of digit classes, biological cell populations, and regional genealogical patterns. These results indicate that CosMAP offers a robust framework for exploratory analysis of complex, sparse, high-dimensional data. The implementation is publicly available at https://github.com/FenosoaRandrianjatovo/CosMAP-dr.
Cross-subject electroencephalogram (EEG)-based emotion recognition remains challenging due to substantial inter-individual variability and discrete formulation that overlooks affective continuity. Existing methods operate in Euclidean space and focus on marginal distribution alignment, failing to preserve the semantic structure of emotions across subjects. This article proposes MGMCL, reconceptualizing emotion recognition as learning continuous representations on symmetric positive definite (SPD) Riemannian manifolds. The frame?work introduces multi-granularity manifold contrastive learning at instance, emotion, and trajectory levels while preserving semantic ordering. Neural ordinary differential equations on manifolds model continuous emotion dynamics. Cross-subject generalization employs Gromov-Wasserstein manifold alignment. Weakly-supervised learning enables continuous valence-arousal-dominance prediction from discrete labels. Extensive experiments on three public datasets demonstrate state-of-the-art performance: 91.23% accuracy on SEED, 73.82% on SEED-IV, and 76.38% on DEAP, achieving consistent improvements of 1.89%, 1.66%, and 1.28% over previous best methods, respectively.
Spatial transcriptomics can resolve gene expression at single-cell resolution, but it is costly, limited to targeted panels of a few hundred to a few thousand genes, and applicable to only a small number of samples. H&E imaging, by contrast, is cheap and collected routinely at scale. This makes predicting single-cell expression directly from morphology a practical way to bring molecular analysis to large tissue archives. We therefore present VOICE, a multimodal foundation model that predicts single-cell gene expression from H&E images using paired Xenium data. VOICE first aligns cell centered H&E morphology from a pathology foundation model with single-cell expression embeddings from a transcriptome foundation model, trained using contrastive learning over 23 million cells. Next it predicts expression through two branches. One branch directly regresses expression from morphology. The other branch retrieves measured expression from similar reference cells, recovering genes that do not have morphological signal. Because genes vary in morphological predictability, VOICE fuses the two branches with a per-gene weight. After training, VOICE generalizes to heldout patients, slides, and partially overlapping gene panels from Xenium, and it consistently outperforms prior single-cell expression prediction methods on seven metrics.
Predicting 30-day hospital readmission is essential for assessing patient stability and optimizing healthcare resources. As clinical risk evolves with the accumulation of evidence during hospitalization, capturing these dynamic trajectories is essential. However, many existing approaches compress the complex longitudinal history into fixed representations, often losing the granular, day-level clinical signals that reflect a patient's evolving physiological state. To address this, we propose Mr.Dec (Multimodal Readmission-risk prediction Decoder), which models each admission as a natural chronological sequence of daily multimodal events. By leveraging a Transformer Decoder, Mr.Dec integrates daily Electronic Health Record(EHR) updates and intermittent Chest X-ray(CXR) findings in a time-aligned stream, reflecting the actual clinical workflow. To ensure robustness, we utilize Disease-Specific Supervised Contrastive Learning as an auxiliary regularization to induce a diagnosis-aware structure in the latent space. Evaluations on the MIMIC-IV and MIMIC-CXR datasets show that Mr.Dec achieves state-of-the-art performance by preserving the integrity of the clinical sequence. Furthermore, our model identifies "Critical Days" within an admission, providing actionable and clinically grounded interpretations for real-time risk stratification. Code is available at: https://github.com/yejix-ai/MR.DEC
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.
Decoding visual experience from non-invasive brain activity is central to neuroscience and brain-computer interfaces. Functional magnetic resonance imaging (fMRI) offers fine spatial detail, but its slow hemodynamics and burdensome acquisition limit temporally resolved decoding. Electroencephalography (EEG) and magnetoencephalography (MEG) provide millisecond resolution, making image retrieval compelling: identify the viewed image from one neural response and a fixed candidate bank. Contrastive alignment to pretrained visual representations enables zero-shot retrieval from EEG and MEG, but most systems collapse heterogeneous visual supervision into a single embedding before ranking. This early consolidation imposes one similarity geometry on every candidate order and removes encoder-specific disagreements from the final ranking. We propose CORTIVA, a candidate-score fusion framework that preserves this complementary evidence. Three decoding routes are aligned to heterogeneous visual targets, score the same indexed candidates independently, and combine only their temperature-scaled score vectors before ranking. On the 200-way THINGS-EEG2 benchmark, CORTIVA reaches 73.5% Top-1 and 95.3% Top-5 across ten participants, exceeding the strongest reported baseline by 10.3 and 5.4 percentage points. With a modality-specific neural encoder, the same fusion principle reaches 42.4% Top-1 on THINGS-MEG. Matched route-removal retraining and four weight controls demonstrate that CORTIVA's gain arises from integrating complementary route scores and persists with uniform weighting, without requiring a specialized weighting rule. Independent DINOv2 analyses further reproduce the local error neighborhoods and posterior neural-visual correspondence. These results establish candidate-score fusion as a simple and testable alternative to embedding-level consolidation for neural image retrieval.
Vision-language pre-training (VLP) serves as a cornerstone for medical multimodal representation learning. However, existing medical VLP frameworks are often constrained by the limited context windows and shallow representational capacities of lightweight text encoders when processing lengthy, terminology-dense clinical reports. While integrating medical large language models (LLMs) offers unprecedented clinical reasoning capabilities, it introduces three major bottlenecks: (i) the anisotropic representational collapse of generative LLMs under standard contrastive objectives, (ii) the prohibitive memory overhead of joint end-to-end training with large batch sizes, and (iii) the medical hallucinations induced by vanilla contrastive losses that ignore fine-grained anatomical laterality and negation modifiers. To address these challenges, we propose \textbf{SCALPEL}, a \textbf{S}emantic \textbf{C}ross-modal \textbf{A}lignment framework via \textbf{L}LM-\textbf{P}owered \textbf{E}ncoder \textbf{L}earning. First, Clinical Report Contrastive fine-tuning converts a generative LLM into an isotropic encoder via domain-specific clinical text adaptation. Second, an asymmetric alignment strategy leverages offline feature caching to enable efficient training. Critically, we formulate an Anatomy-Negation Aware Objective that explicitly penalizes mismatched image-text pairs involving laterality confusion or false negations. Extensive experiments across MIMIC-CXR, CheXpert, and IU X-Ray benchmarks demonstrate that SCALPEL achieves state-of-the-art performance in cross-modal retrieval, zero-shot disease classification and medical visual question answering.
Decoding speech information directly from scalp electroencephalography (EEG) into text provides a potential non-invasive neural communication pathway for individuals with severe speech and motor impairments. Compared with invasive approaches such as electrocorticography, EEG is safer and more widely deployable, yet substantially more challenging to decode.This challenge is exacerbated for Chinese sentence decoding, which must handle a high-dimensional output space with thousands of characters, severe inter-subject variability, and low signal-to-noise ratios for text alignment.Existing methods commit to a single supervisory axis---either text semantics or audio acoustic features---yet neither can simultaneously satisfy the demands of sentence-level discriminability and fine-grained temporal resolution required for large-vocabulary Chinese decoding. We introduce EEGAlign, a novel parameter-efficient framework that jointly aligns EEG with two axes---text alignment with BGE-M3 text embeddings and audio alignment with wav2vec~2.0 speech features via contrastive learning followed by CTC character-sequence decoding. On ChineseEEG-2 data, EEGAlign yields state-of-the-art closed-set sentence classification performance, reaching up to 82.37% Top-1 accuracy on Reading Aloud EEG and 41.43% on Passive Listening EEG out of 101 candidates. Ablation studies show that the two alignment axes are highly complementary: combining them yields consistently better performance than either alone. To the best of our knowledge, this is the first study on decoding large-vocabulary Chinese sentences from non-invasive EEG during overt speech production, and achieving strong classification performance with relatively large closed-set candidate-sentence setting.
Predicting the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of small molecules remains a major challenge in drug discovery. Here, we present MEGA-CL, a foundation graph neural network framework for universal molecular ADMET prediction. MEGA-CL integrates self-supervised contrastive learning with a multi-head external attention mechanism and an enhanced message-passing architecture, enabling simultaneous modeling of local chemical substructures and global inter-graph relationships while mitigating over-smoothing effects commonly observed in deep graph networks. Across 13 benchmark datasets and 21 downstream ADMET tasks, MEGA-CL consistently outperforms state-of-the-art baseline models. In particular, the framework demonstrates robust performance on challenging regression tasks, including clearance (CL) and steady-state volume of distribution (VDss), while maintaining strong generalization ability in independent external validation. Clinically relevant predictive accuracy was achieved, with more than 75% of predictions falling within a 3-fold error range. In an external evaluation on 18 novel compounds derived from recently approved FDA drugs, over 50% of human liver microsome clearance (HLMC) predictions were within a 2-fold error range. To further assess its practical applicability, MEGA-CL was prospectively evaluated on three preclinical drug candidates using in vitro hepatic microsomal metabolism assays and CYP450 inhibition assays guided by model predictions. The predicted HLMC values for all candidates were within 2.5-fold of the experimentally measured values, and 73.3% of CYP450 inhibition endpoints (11/15) were correctly classified. These results demonstrate the potential of MEGA-CL as a generalizable framework for accelerating in silico ADMET evaluation and early-stage drug candidate optimization.
Tracking residual tumor after surgery is essential for catching recurrence early, but automating post-operative glioma segmentation remains a difficult task. Although transformer-based architectures, such as SwinUNETR, achieved impressive results, few studies test how well they generalize across clinical protocols. In this paper, we conduct an ablation study on the MU-GLIOMA-POST and UCSF-ALPTDG datasets and show that the standard Generalized Dice Loss (GDL) is unstable under domain shift: the Whole Lesion (WL) Dice drops from 0.88 on the internal validation set to 0.73 on the external UCSF test set. To address this, we pair brain-masked percentile normalization with voxel-level contrastive learning. We also propose a Subspace-Aware Class Attention (SACA) module that re-calibrates the bottleneck features and raises Enhancing Tumor (ET) sensitivity by 8% (9.1% relative improvement) on internal validation. Ensembling these refinements with nnU-Net brings every stable configuration to a WL Dice of 0.94, and the SACA variant ensemble achieves the best boundary error (HD95) of 2.92 mm on MU-GLIOMA-POST.
Vision-language models trained with contrastive objectives have shown promise in medical image analysis. However, conventional global image-text alignment is ill-suited for mammography, where diagnostically relevant lesions are spatially localized and occupy only a small fraction of the image. Subtle morphological cues critical for malignancy assessment can be diluted when representations are learned at the whole-image level. In this work, we propose a novel region-grounded vision-language learning method for detection-guided mammographic lesion classification. The method mirrors radiologists' diagnostic paradigm. First, a region-text contrastive pretraining stage aligns lesion-specific features with structured clinical descriptors derived from radiology metadata. To mitigate semantic collapse and background bias in low-vocabulary settings, we introduce a multi-component objective incorporating positive alignment, fine-grained semantic hard negatives, and background suppression. Second, an auxiliary lesion detection head is jointly optimized with contrastive classification to preserve spatial sensitivity and enable localization-aware malignancy classification. Extensive experiments on two independent datasets, CBIS-DDSM and VinDr-Mammo, show superior performance of our method compared to related methods under in-domain, cross-dataset, and transfer learning settings.
Jingteng Li, Alexander Capstick, Louise Rigny +3cs.LG
Recent research in clinical machine learning, focusing on outcome predictions in intensive care unit (ICU), has shifted from bespoke supervised models to foundation models, utilising modern representation learning methods. Here, foundation models are pre-trained on mixtures of complex clinical data modalities, useful for various downstream tasks. Existing works often utilise Electronic Health Records (EHR) to provide rich and diverse patient observations to train clinical foundation models. However, existing methods do not sufficiently explore the shared temporal structures between clinical events and time series (TS) observations recorded in EHRs. This limitation potentially leads to less robust and adaptive clinical foundation models, resulting in reduced performance on downstream tasks. To fully exploit this temporal structure, we propose LLM4EHR, a new clinical foundation model trained on ICU EHR data. Combining domain adapted large language models with a transformer TS encoder, we pre-trained LLM4EHR by temporally aligning the EHR events and TS. For this, we propose a regularised contrastive objective to learn robust EHR TS representations conditioned on EHR event embeddings produced by the domain adapted LLM. Supported by an ablation study, we find that learnt EHR TS embeddings from LLM4EHR improve performance on various downstream clinical tasks with competitive performance. Further, we empirically demonstrate that LLM4EHR learns transferable clinical TS embeddings that can be deployed to new cohorts via k-shot adaptation. These findings provide a step towards building more generalisable and performant clinical foundation models.
Long-tailed label distributions reduce the reliability of deep learning for electrocardiogram (ECG) arrhythmia diagnosis, particularly for clinically important but rare abnormalities. Existing rebalancing and logit adjustment methods mainly address class frequency while overlooking direction-dependent morphological variability across ECG classes. This study proposes Angular Gaussian Supervised Contrastive Learning (AG-SCL) for long-tailed multi-label ECG diagnosis. AG-SCL integrates three components into a unified framework: an Angular Gaussian contrastive branch that models full-covariance class uncertainty on unit-normalized embeddings, Adaptive Logit Adjustment that learns bounded label-state-specific prior corrections instead of fixed frequency-based margins, and tail-aware augmentation that generates morphology-preserving views while protecting the 7-25 Hz QRS-dominant band. The method was evaluated on the public PTB-XL benchmark and a nocturnal ECG dataset comprising 1317 hours of recordings from 141 subjects. AG-SCL achieved the best macro-level performance on both datasets. On PTB-XL, it obtained a balanced accuracy of 0.838, sensitivity of 0.709, specificity of 0.968, mean average precision of 0.495, and TPR at 5% FPR of 0.778. On Noc-ECG, the corresponding values were 0.918, 0.889, 0.947, 0.488, and 0.900. The largest gains occurred in rare or morphologically unstable rhythm classes, while ablation studies confirmed the contributions of full-covariance modelling, Adaptive Logit Adjustment, and tail-aware augmentation. AG-SCL improves long-tailed ECG diagnosis by combining prior calibration with anisotropic representation learning, enhancing sensitivity to rare arrhythmias while maintaining clinically relevant specificity. Our code is available at: https://github.com/Open-EXG/AG-SCL-for-Long-Tailed-ECG.
Gabriel Mahuas, Victoria Shevchenko, Ugo Tanielian +2cs.LG q-bio.NC
Self-supervised pretrained foundation models (FM) have shown early promise for non-invasive electroencephalogram (EEG) decoding applications. Many recent large-scale models converged on the approach of tokenizing raw EEG followed by masked reconstruction pretraining. However, this recipe has been shown to be suboptimal for data, like EEG, with high noise amplitude and information confined to limited dimensions such as narrow frequency bands. Building on this insight, we develop a novel contrastive-pretrained EEG model with multiscale temporal convolution input layers and Transformer encoder blocks (CoCoT). CoCoT matches or beats state-of-the-art reconstruction-pretrained EEG models on extensive benchmark decoding tasks with heterogeneous electrode configurations. Furthermore, CoCoT trained from scratch outperforms previous single-task decoding models and even rivals pretrained models, showcasing the architecture's flexibility and data efficiency. Through systematic ablations, including model architecture and pretraining objective, we demonstrate the viability of contrastive learning for building EEG FMs while suggesting key architectural design considerations, prompting further investigations in alternative large-scale pretraining strategies.
Sai Spandana Chintapalli, Pratik Chaudhari, Christos Davatzikoscs.LG
Quantifying variability in a target population relative to a reference population is central to many scientific and clinical problems (e.g., diseased vs. healthy). Yet, without paired data and in the presence of heterogeneous target variation, existing methods struggle to separate multiple modes of target-specific variation. We propose \textit{CASL-VAE}, a deep contrastive latent variable model that learns structured latent generative factors from unpaired data. CASL-VAE factorizes variation into continuous common latent factors shared across populations and hierarchical salient latent factors that model target-specific heterogeneity as discrete subtypes and continuous within-subtype variation. Using variational inference, we show how approximate joint likelihood optimization over reference and target domains can be performed using unpaired data, providing a principled basis for paired-sample generation and cross-domain analysis. We validate CASL-VAE on semi-synthetic neuroimaging data, demonstrating improved subtype recovery and paired-sample generation compared to baseline clustering and generative models. We also validate its ability to reveal biologically plausible heterogeneity in Alzheimer's disease.
Recent advancements in multimodal learning for medical time series (MedTS) classification highlight the benefits of integrating complementary modalities for clinical decision. However, existing methods typically focus on bi-modal interactions (e.g., time series and text), leaving the tri-modal synergy between time series, vision, and language largely unexplored. Inspired by diagnostic practice synergizing numerical assessment, visual inspection and clinical context, we introduce MedTVL, a text-guided dual-pathway architecture tailored for MedTS classification. Specifically, it synergizes a convolution-based temporal pathway for fine-grained temporal dynamics from raw numerical sequences and a transformer-based visual pathway for holistic morphological structures from time-series-derived images. Such combination of cross-modal and architectural heterogeneity provides a comprehensive diagnostic perspective. To further resolve potential diagnostic ambiguity, both pathways are guided by adaptive medical textual semantics. Finally, a Mixture-of-Experts mechanism dynamically routes each instance to specialized fusion experts, capturing instance-specific reliance on the temporal and visual pathway outputs. In addition, MedTVL supports multimodal contrastive learning to mitigate the clinical label scarcity challenge. Extensive experiments across multiple medical datasets and tasks, spanning supervised, few-shot, and contrastive learning settings, demonstrate the superiority and transferability of MedTVL, highlighting its potential for robust clinical decision support.
Automatic sleep staging is a key technology for precise diagnosis and treatment of sleep disorders as well as long-term home sleep monitoring. Portable electroencephalogram (EEG) devices have become the focus of research due to their convenience in data collection. However, current methods still face three major challenges: large parameter sizes that easily lead to overfitting on small datasets, low accuracy in classifying difficult stages such as N1 and REM, unclear optimal training dataset size, and difficulty in deployment. This paper proposes GamSleepNet, a lightweight and low-latency automatic sleep staging framework for single-channel EEG. The framework features the FEB module, which combines improved Gabor kernels with learnable filters for feature extraction, uses the Mamba architecture to build a temporal classification network, introduces a novel contrastive loss and a two-stage training strategy, and experimentally validates the optimal dataset size for single-channel EEG sleep staging models. On the Sleepedf dataset, this model achieves an overall accuracy of 87.86 percent with only 30.86 thousand parameters, with all metrics reaching SOTA levels and significantly improving the identification accuracy of challenging sleep stages.
Dongmin Bang, Sugyun An, Inyoung Sung +3cs.LG cs.AI q-bio.QM
Accurate prediction of patient-specific therapeutic response from pre-treatment transcriptomes is hindered by the scarcity of matched clinical response labels and post-treatment molecular profiles. Preclinical transfer-learning models can simulate drug-induced expression changes but are often hard to interpret and unstable, whereas knowledge-graph methods provide mechanistic context yet remain static and fail to capture drug-induced transcriptomic perturbation dynamics. We propose PREDIKTOR, a patient-centered multi-view framework that aligns a personalized network view with a transferable transcriptomic perturbation view to predict clinical drug response. For each patient, we construct an individualized gene regulatory network from tumor expression using DysRegNet and augment it with drug-target links from DrugBank; a graph neural encoder yields a drug-centric, mechanistically grounded embedding. In parallel, a frozen condition-specific gene-gene attention model pretrained on LINCS L1000 generates a simulated post-perturbation transcriptomic profile for the same patient-drug pair. We align the two views in a shared latent space via a CLIP-style contrastive objective with drug-context hard negatives, then concatenate the representations for end-to-end response classification. On TCGA, PREDIKTOR consistently outperforms state-of-the-art baselines under patient-, drug-, and tissue-split evaluations, and transfers zero-shot to the I-SPY2 trial, improving AUROC by 5.6% over competing methods. The aligned embeddings yield stable gene and pathway attributions that recover known mechanisms, supporting actionable and interpretable precision oncology.