Existing cell embedding methods predominantly rely on transcriptomic or proteomic measurements and represent each cell as a holistic entity, thereby overlooking the subcellular localization of individual molecules. Moreover, they rarely incorporate protein structural information, despite its fundamental role in determining molecular interactions and functions. In this work, we propose a multimodal framework for learning subcellularly resolved cell embeddings by jointly leveraging RNA expression profiles, protein sequence representations, and protein structural information. Specifically, we employ a cross-attention architecture to integrate transcriptomic, sequence, and structural modalities and model their interactions within distinct subcellular compartments. The resulting embeddings represent each cell through its fine-grained subcellular organization, capturing both molecular expression patterns and the functional properties of the associated proteins. By learning cell representations at subcellular resolution, our framework preserves spatially organized biological information while integrating complementary signals across multiple molecular levels. To the best of our knowledge, this is the first framework that produces subcellularly resolved cell embeddings by jointly incorporating transcriptomic information, protein sequence representations, and protein structural knowledge within a unified cross-modal learning paradigm.
Medical AI has demonstrated specialist-level diagnostic accuracy, yet these capabilities remain largely inaccessible in resource-constrained rural settings where bandwidth is scarce, compute is limited, and clinical decision-making requires integrating heterogeneous modalities. We introduce a cloud--edge collaborative architecture that addresses these constraints: lightweight, domain-specific models on the edge transform raw medical data into compact structured outputs, while a cloud LLM synthesizes these outputs into clinical summaries. An LLM-based orchestrator dynamically selects diagnostic tools based on patient context, promoting comprehensive modality coverage without processing irrelevant inputs. We evaluate on 20 multimodal clinical cases spanning cardiac, obstetric, trauma, and screening scenarios under three simulated network profiles (500,kbps--5,Mbps). The hybrid system achieves 98--99% diagnostic tool recall with 92--96% precision, matches or exceeds cloud-only baselines on clinical accuracy, and maintains bandwidth-invariant latency (25--35,s) at 4--15x lower token cost. These results highlight the role of architectural design in enabling efficient multimodal integration and improving factual grounding compared to cloud-only approaches under deployment constraints.
Spatially resolved omics studies increasingly combine transcriptomic and epigenomic assays, yet downstream analysis is often still performed using single-modality pipelines. We present LATTICE (Latent Alignment of Tissue-level and Transcriptomic Information for Cross-modal Embedding), a graph-based self-supervised framework that learns spot-level representations from harmonized multimodal features. LATTICE integrates five aligned modality blocks per Visium spot: Visium RNA, scMultiome RNA, scMultiome ATAC, spatial ATAC, and spatial CUT\&Tag. These modalities capture spatial transcriptomic measurements, single-cell inferred regulatory activity, and in situ chromatin and histone states within a unified lattice representation. LATTICE constructs a spatial neighborhood graph and trains a TransformerConv encoder using masked reconstruction, cross-modal alignment, and spatial smoothness objectives. On a private 11-sample melanoma cohort from an anonymized clinical collaborator comprising 54{,}912 total spots, LATTICE demonstrated stable optimization behavior, reproducible embeddings across analysis seeds, and complete multimodal integration across all samples. Adding scMultiome RNA to Visium RNA alone substantially improved concordance with Space Ranger clusters across 11 runs (adjusted Rand index [ARI] +0.157, normalized mutual information [NMI] +0.143, and spatial contiguity +0.174). Additional modalities further improved spatial contiguity and multimodal utility score (MUS), although they sometimes reduced agreement with RNA-derived reference labels, likely because the learned embeddings captured chromatin and regulatory structure beyond transcriptomic similarity alone. These results position LATTICE as a practical and empirically grounded framework for multimodal spatial omics integration, while also highlighting the need for stronger supervision and broader external benchmarking.
Diana Shadibaeva, Rochak Dhakal, Kui Zhang +3physics.med-ph cs.LG
Cardiac amyloidosis (CA) is increasingly recognized but remains substantially underdiagnosed, because its clinical and imaging phenotype overlaps with more common cardiomyopathies. Definitive subtype assignment and management further require integration of multimodal evidence to distinguish transthyretin from light chain disease. Machine learning and deep learning have been applied across the diagnostic and management pathway. These applications span ECG, echocardiography, and health record-based case finding, as well as CMR and nuclear interpretation, including SPECT/CT biomarker quantification, prognostic modeling, and treatment response assessment. This narrative review synthesizes these studies by clinical tasks, namely screening, detection, quantification, prognosis, and treatment response monitoring, rather than by input modality. This task-based organization clarifies why apparently similar AI models require different cohorts, reference standards, evaluation metrics, and implementation thresholds. The evidence reveals a maturity gradient. Binary detection and AI assisted quantification on bone scintigraphy and SPECT/CT are closest to clinical translation. Detection is supported by large externally validated cohorts, and quantification by interpretable, outcome linked measurement of myocardial tracer burden. By contrast, subtype aware classification, prognostic risk stratification, and treatment response monitoring remain at an early stage. These tasks are limited by small cohorts, enriched retrospective designs, heterogeneous labels, incomplete external validation, and uncertain calibration in realistic prevalence settings. Across tasks, high discrimination alone is insufficient.
Haitao Wu, Qirui Zhang, Zhouheng Yao +8cs.CV cs.LG
Modeling the bidirectional correspondence between external sensory stimuli and internal neural activity has emerged as a critical frontier in neuroscience. However, existing approaches predominantly treat brain encoding and decoding as isolated tasks, relying heavily on unimodal alignment and external priors while overlooking the brain's intrinsic nature as a multimodal integration system. To address these limitations, we propose BrainJanus, the first unified brain model that integrates brain, vision, and language within a single framework. Specifically, we introduce a Unified Brain Tokenizer to quantize continuous neural dynamics into discrete tokens aligned with visual and linguistic representations in a shared Omni space. Building on this, we utilize an All-in-One autoregressive architecture that leverages next-token prediction to enable seamless any-to-any generation, which encompasses image-to-brain and text-to-brain encoding, and brain-to-image and brain-to-text decoding. Extensive experiments demonstrate that BrainJanus achieves superior performance across diverse benchmarks. Furthermore, our framework exhibits zero-shot generalization and preserves interpretable biological topography, highlighting its potential as a general-purpose brain modeling paradigm. The code is available at \href{https://github.com/HaitaoWuTJU/BrainJanus}{GitHub}.
Predicting immune biomarkers associated with the tumor immune microenvironment (TIME) is critical for advancing precision oncology, yet existing approaches are largely limited to single image modalities and suffer from insufficient resolution and incomplete utilization of complementary clinical and biological information. Here we introduce MixTIME, a multimodal foundation model that leverages a mixture-of-experts (MoE) architecture to integrate pathology foundation models trained across distinct modalities: image only (UNIv2), image text (CONCHv1.5), and image transcriptomic (STPath) representations for pixel-level and slide-level prediction of multiplex immunofluorescence (mIF) protein expression from hematoxylin and eosin (HE) whole-slide images. MixTIME employs a learnable router to dynamically weight expert contributions and is trained with a distribution- and tendency-aware loss function. Benchmarked on two datasets of different scales, MixTIME achieves state-of-the-art performance across 17 protein markers as measured by correlation metrics. The predicted mIF profiles substantially enhance downstream tasks, including spatial domain identification, survival prediction, and AI-assisted pathology report generation validated by expert pathologists from multiple institutes across the world. Furthermore, MixTIME enables longitudinal tracking of protein expression dynamics across clinical time points and reveals protein gene interaction patterns linked to drug resistance and immune suppression in tumor microenvironments. Collectively, MixTIME provides a scalable framework for multimodal biomarker discovery and clinical translation in computational pathology.
Despite increasing adoption of multimodal approaches in Alzheimer's Disease (AD) research -- aimed at integrating molecular, structural, clinical, and genetic biomarkers to enhance disease characterization -- the relationships among these modalities remain poorly understood. A systematic analysis of their dynamic interaction is essential for improving disease modeling, identifying redundant assessments, and reducing patient burden and acquisition costs. In this paper, we present a quantitative analysis of multimodal AD biomarkers by integrating tau-PET, structural MRI, cognitive scores (MMSE and CDR), and APOE4 data from 789 subjects drawn from the ADNI dataset. In our analyses, we (A) quantify cross-modal mutual information and explained variance to assess redundancy and predictive dependencies; (B) examine associations between tau topologies and structural atrophy across brain regions to select informative ROIs; (C) perform a statistical decomposition of the tau-cognition association into atrophy-related and atrophy-independent components; (D) and identify a dominant neurodegenerative trajectory that aligns with cognitive decline. This study provides a systematic characterization of cross-modal relationships, improving the interpretability and selection of biomarkers in AD. Code is publicly available at: https://github.com/antonioscardace/Multimodal-AD.