Overview

Multimodal classification studies how to combine different kinds of evidence—for example, medical images with clinical records, or meme images with text—to predict categories. Common approaches include feature or decision fusion, cross-attention and contrastive alignment, mixture-of-experts models, and large vision-language models; benchmarks range from medical diagnosis and sentiment analysis to document, time-series, and content moderation tasks. Current work also addresses missing or unreliable inputs through modality dropout, imputation, adaptive routing, and selective acquisition, while evaluating fairness, calibration, and interpretability. A central tension is that adding a modality can improve predictions when it contributes complementary information, but can also hurt when it is noisy, redundant, or unavailable at deployment.

Latest papers

200 papers24 papers in the last four weeks, down 4% on the four weeks before. 0.1% of all new papers.

Mar 3, 2026

On Discriminative vs. Generative classifiers: Rethinking MLLMs for Action Understanding

Multimodal Large Language Models (MLLMs) have advanced open-world action understanding and can be adapted as generative classifiers for closed-set settings by autoregressively generating action labels as text. However, this approach is inefficient, and shared subwords across action labels introduce semantic overlap, leading to ambiguity in generation. In contrast, discriminative classifiers learn task-specific representations with clear decision boundaries, enabling efficient one-step classification without autoregressive decoding. We first compare generative and discriminative classifiers with MLLMs for closed-set action understanding, revealing the superior accuracy and efficiency of the latter. To bridge the performance gap, we design strategies that elevate generative classifiers toward performance comparable with discriminative ones. Furthermore, we show that generative modeling can complement discriminative classifiers, leading to better performance while preserving efficiency. To this end, we propose Generation-Assisted Discriminative~(GAD) classifier for closed-set action understanding. GAD operates only during fine-tuning, preserving full compatibility with MLLM pretraining. Extensive experiments on temporal action understanding benchmarks demonstrate that GAD improves both accuracy and efficiency over generative methods, achieving state-of-the-art results on four tasks across five datasets, including an average 2.5% accuracy gain and 3x faster inference on our largest COIN benchmark.
Mar 3, 2026

LLM-MLFFN: Multi-Level Autonomous Driving Behavior Feature Fusion via Large Language Model

Accurate classification of autonomous vehicle (AV) driving behaviors is critical for safety validation, performance diagnosis, and traffic integration analysis. However, existing approaches primarily rely on numerical time-series modeling and often lack semantic abstraction, limiting interpretability and robustness in complex traffic environments. This paper presents LLM-MLFFN, a novel large language model (LLM)-enhanced multi-level feature fusion network designed to address the complexities of multi-dimensional driving data. The proposed LLM-MLFFN framework integrates priors from largescale pre-trained models and employs a multi-level approach to enhance classification accuracy. LLM-MLFFN comprises three core components: (1) a multi-level feature extraction module that extracts statistical, behavioral, and dynamic features to capture the quantitative aspects of driving behaviors; (2) a semantic description module that leverages LLMs to transform raw data into high-level semantic features; and (3) a dual-channel multi-level feature fusion network that combines numerical and semantic features using weighted attention mechanisms to improve robustness and prediction accuracy. Evaluation on the Waymo open trajectory dataset demonstrates the superior performance of the proposed LLM-MLFFN, achieving a classification accuracy of over 94%, surpassing existing machine learning models. Ablation studies further validate the critical contributions of multi-level fusion, feature extraction strategies, and LLM-derived semantic reasoning. These results suggest that integrating structured feature modeling with language-driven semantic abstraction provides a principled and interpretable pathway for robust autonomous driving behavior classification.
Mar 2, 2026

PathMoE: Interpretable Multimodal Interaction Experts for Pediatric Brain Tumor Classification

Accurate classification of pediatric central nervous system tumors remains challenging due to histological complexity and limited training data. While pathology foundation models have advanced whole-slide image (WSI) analysis, they often fail to leverage the rich, complementary information found in clinical text and tissue microarchitecture. To this end, we propose PathMoE, an interpretable multimodal framework that integrates H&E slides, pathology reports, and nuclei-level cell graphs via an interaction-aware mixture-of-experts architecture built on state-of-the-art foundation models for each modality. By training specialized experts to capture modality uniqueness, redundancy, and synergy, PathMoE employs an input-dependent gating mechanism that dynamically weights these interactions, providing sample-level interpretability. We evaluate our framework on two dataset-specific classification tasks on an internal pediatric brain tumor dataset (PBT) and external TCGA datasets. PathMoE improves macro-F1 from 0.762 to 0.799 (+0.037) on PBT when integrating WSI, text, and graph modalities; on TCGA, augmenting WSI with graph knowledge improves macro-F1 from 0.668 to 0.709 (+0.041). These results demonstrate significant performance gains over state-of-the-art image-only baselines while revealing the specific modality interactions driving individual predictions. This interpretability is particularly critical for rare tumor subtypes, where transparent model reasoning is essential for clinical trust and diagnostic validation.
Feb 28, 2026

Multiple Inputs and Mixwd data for Alzheimer's Disease Classification Based on 3D Vision Transformer

The current methods for diagnosing Alzheimer Disease using Magnetic Resonance Imaging (MRI) have significant limitations. Many previous studies used 2D Transformers to analyze individual brain slices independently, potentially losing critical 3D contextual information. Region of interest-based models often focus on only a few brain regions despite Alzheimer's affecting multiple areas. Additionally, most classification models rely on a single test, whereas diagnosing Alzheimer's requires a multifaceted approach integrating diverse data sources for a more accurate assessment. This study introduces a novel methodology called the Multiple Inputs and Mixed Data 3D Vision Transformer (MIMD-3DVT). This method processes consecutive slices together to capture the feature dimensions and spatial information, fuses multiple 3D ROI imaging data inputs, and integrates mixed data from demographic factors, cognitive assessments, and brain imaging. The proposed methodology was experimentally evaluated using a combined dataset that included the Alzheimer's Disease Neuroimaging Initiative (ADNI), the Australian Imaging, Biomarker, and Lifestyle Flagship Study of Ageing (AIBL), and the Open Access Series of Imaging Studies (OASIS). Our MIMD-3DVT, utilizing single or multiple ROIs, achieved an accuracy of 97.14%, outperforming the state-of-the-art methods in distinguishing between Normal Cognition and Alzheimer's Disease.
Feb 27, 2026

Revisiting Integration of Image and Metadata for DICOM Series Classification: Cross-Attention and Dictionary Learning

Automated identification of DICOM image series is essential for large-scale medical image analysis, quality control, protocol harmonization, and reliable downstream processing. However, DICOM series classification remains challenging due to heterogeneous slice content, variable series length, and entirely missing, incomplete or inconsistent DICOM metadata. We propose an end-to-end multimodal framework for DICOM series classification that jointly models image content and acquisition metadata while explicitly accounting for all these challenges. (i) Images and metadata are encoded with modality-aware modules and fused using a bi-directional cross-modal attention mechanism. (ii) Metadata is processed by a sparse, missingness-aware encoder based on learnable feature dictionaries and value-conditioned modulation. By design, the approach does not require any form of imputation. (iii) Variability in series length and image data dimensions is handled via a 2.5D visual encoder and attention operating on equidistantly sampled slices. We evaluate the proposed approach on the publicly available Duke Liver MRI dataset and a large multi-institutional in-house cohort, assessing both in-domain performance and out-of-domain generalization. Across all evaluation settings, the proposed method consistently outperforms relevant image only, metadata-only and multimodal 2D/3D baselines. The results demonstrate that explicitly modeling metadata sparsity and cross-modal interactions improves robustness for DICOM series classification.
Feb 26, 2026

Large Multimodal Models as General In-Context Classifiers

Which multimodal model should we use for classification? Previous studies suggest that the answer lies in CLIP-like contrastive Vision-Language Models (VLMs), due to their remarkable performance in zero-shot classification. In contrast, Large Multimodal Models (LMM) are more suitable for complex tasks. In this work, we argue that this answer overlooks an important capability of LMMs: in-context learning. We benchmark state-of-the-art LMMs on diverse datasets for closed-world classification and find that, although their zero-shot performance is lower than CLIP's, LMMs with a few in-context examples can match or even surpass contrastive VLMs with cache-based adapters, their "in-context" equivalent. We extend this analysis to the open-world setting, where the generative nature of LMMs makes them more suitable for the task. In this challenging scenario, LMMs struggle whenever provided with imperfect context information. To address this issue, we propose CIRCLE, a simple training-free method that assigns pseudo-labels to in-context examples, iteratively refining them with the available context itself. Through extensive experiments, we show that CIRCLE establishes a robust baseline for open-world classification, surpassing VLM counterparts and highlighting the potential of LMMs to serve as unified classifiers, and a flexible alternative to specialized models.
Feb 25, 2026

Detecting Hate and Inflammatory Content in Bengali Memes: A New Multimodal Dataset and Co-Attention Framework

Internet memes have become a dominant form of expression on social media, including within the Bengali speaking community. While often humorous, memes can also be exploited to spread offensive, harmful, and inflammatory content targeting individuals and groups. Detecting this type of content is exceptionally challenging due to its satirical, subtle, and culturally specific nature. This problem is magnified for low-resource languages like Bengali, as existing research predominantly focuses on high-resource languages. To address this critical research gap, we introduce Bn-HIB (Bangla Hate Inflammatory Benign), a novel dataset containing 3,247 manually annotated Bengali memes categorized as Benign, Hate, or Inflammatory. Significantly, Bn- HIB is the first dataset to distinguish inflammatory content from direct hate speech in Bengali memes. Furthermore, we propose the MCFM (Multi-Modal Co-Attention Fusion Model), a simple yet effective architecture that mutually analyses both the visual and textual elements of a meme. MCFM employs a co-attention mechanism to identify and fuse the most critical features from each modality, leading to a more accurate classification. Our experiments show that MCFM significantly outperforms several state-of-the-art models on the Bn-HIB dataset, demonstrating its effectiveness in this nuanced task. To facilitate reproducibility and future research, the Bn-HIB dataset has been made publicly available through Mendeley Data. Warning: This work contains material that may be disturbing to some audience members. Viewer discretion is advised
Feb 19, 2026

Characterizing the Predictive Impact of Modalities with Supervised Latent-Variable Modeling

Despite the recent success of Multimodal Large Language Models (MLLMs), existing approaches predominantly assume the availability of multiple modalities during training and inference. In practice, multimodal data is often incomplete because modalities may be missing, collected asynchronously, or available only for a subset of examples. In this work, we propose PRIMO, a supervised latent-variable imputation model that quantifies the predictive impact of any missing modality within the multimodal learning setting. PRIMO enables the use of all available training examples, whether modalities are complete or partial. Specifically, it models the missing modality through a latent variable that captures its relationship with the observed modality in the context of prediction. During inference, we draw many samples from the learned distribution over the missing modality to both obtain the marginal predictive distribution (for the purpose of prediction) and analyze the impact of the missing modalities on the prediction for each instance. We evaluate PRIMO on a synthetic XOR dataset, Audio-Vision MNIST, and MIMIC-III for mortality and ICD-9 prediction. Across all datasets, PRIMO obtains performance comparable to unimodal baselines when a modality is fully missing and to multimodal baselines when all modalities are available. PRIMO quantifies the predictive impact of a modality at the instance level using a variance-based metric computed from predictions across latent completions. We visually demonstrate how varying completions of the missing modality result in a set of plausible labels.
Feb 16, 2026

Resp-Agent: An Agent-Based System for Multimodal Respiratory Sound Generation and Disease Diagnosis

Deep learning-based respiratory auscultation is currently hindered by two fundamental challenges: (i) inherent information loss, as converting signals into spectrograms discards transient acoustic events and clinical context; (ii) limited data availability, exacerbated by severe class imbalance. To bridge these gaps, we present Resp-Agent, an autonomous multimodal system orchestrated by a novel Active Adversarial Curriculum Agent (Thinker-A2^2CA). Unlike static pipelines, Thinker-A2^2CA serves as a central controller that actively identifies diagnostic weaknesses and schedules targeted synthesis in a closed loop. To address the representation gap, we introduce a modality-weaving Diagnoser that weaves clinical text with audio tokens via strategic global attention and sparse audio anchors, capturing both long-range clinical context and millisecond-level transients. To address the data gap, we design a flow matching Generator that adapts a text-only Large Language Model (LLM) via modality injection, decoupling pathological content from acoustic style to synthesize hard-to-diagnose samples. As a foundation for this work, we introduce Resp-229k, a benchmark corpus of 229k recordings paired with LLM-distilled clinical narratives. Extensive experiments demonstrate that Resp-Agent consistently outperforms prior approaches across diverse evaluation settings, improving diagnostic robustness under data scarcity and long-tailed class imbalance. Our code and data are available at https://github.com/zpforlove/Resp-Agent.
Feb 16, 2026

Feature Recalibration Based Olfactory-Visual Multimodal Model for Enhanced Rice Deterioration Detection

Multimodal methods are widely used in rice deterioration detection, but they exhibit limited capability in representing and extracting fine-grained abnormal features. Moreover, these methods rely on devices such as hyperspectral cameras and mass spectrometers, which increase detection costs and prolong data acquisition time. To address these issues, we propose a feature recalibration based olfactory-visual multimodal model for enhanced rice deterioration detection. A fine-grained deterioration embedding constructor (FDEC) is proposed to reconstruct the labeled multimodal embedded feature dataset, thereby enhancing sample representation. A fine-grained deterioration recalibration attention network (FDRA-Net) is proposed to emphasize signal variations and improve sensitivity to fine-grained deterioration on the rice surface. Compared with SS-Net, the proposed method improves classification accuracy by 8.67%, with an average improvement of 11.51% over other traditional baseline models, while simultaneously simplifying the detection procedure. Furthermore, field detection results demonstrate advantages in both accuracy and operational simplicity. The proposed method can also be extended to other agrifood applications in agriculture and the food industry.
Oct 17, 2025

Theoretical Refinement of CLIP by Utilizing Linear Structure of Optimal Similarity

In this study, we propose an enhancement to the similarity computation mechanism in multimodal contrastive pretraining frameworks such as CLIP. Prior theoretical research has demonstrated that the optimal similarity metrics between paired modalities should correspond to the pointwise mutual information (PMI) between the two modalities. However, the current implementations of CLIP and its variants fail to fully utilize the underlying linear structure of PMI. We therefore propose KME-CLIP, which leverages this structure through the inner product in a reproducing kernel Hilbert space (RKHS). We theoretically prove that, under our assumptions, the KME-CLIP similarity can bring the contrastive loss arbitrarily close to its optimal value, which is attained by PMI, as the size of the point set grows, and we empirically evaluate KME-CLIP against CLIP and its kernel-based variants across several retrieval and classification tasks.
Sep 30, 2025

MultiFair: Multimodal Balanced Fairness-Aware Medical Classification with Dual-Level Gradient Modulation

Medical decision systems increasingly rely on data from multiple sources to ensure reliable and unbiased diagnosis. However, existing multimodal learning models fail to achieve this goal because they often overlook two critical challenges. First, various data modalities may learn unevenly, thereby converging to a model biased towards certain modalities. Second, the model may emphasize learning on certain demographic groups causing unfair performances. The two aspects can influence each other, as different data modalities may favor respective groups during optimization, leading to both imbalanced and unfair multimodal learning. This paper proposes a novel approach called MultiFair for multimodal medical classification, which addresses these challenges with a dual-level gradient modulation process. MultiFair dynamically modulates training gradients regarding the optimization direction and magnitude at both data modality and group levels. We evaluate MultiFair on three real-world medical classification datasets with diverse demographic attributes,including multiclass classification and missing-modality settings. Experimental results demonstrate its effectiveness.
Sep 19, 2025

Diff-Feat: Diffusion-Based Cross-Modal Feature Extraction for Multi-Label Classification

Multi-label classification has broad applications and depends on powerful representations capable of capturing multiple interactions. We introduce Diff-Feat, a simple yet effective framework that extracts intermediate features from pre-trained diffusion-Transformer models for both images and text, and fuses them for downstream tasks. We observe distinct patterns in optimal feature selection: for vision tasks, the most discriminative intermediate feature along the diffusion process occurs at the middle step and is located at the middle block in Transformer. In contrast, for language tasks, the best feature occurs at the noise-free step and is located at the deepest block. Notably, a consistent phenomenon across diverse datasets: a fixed "Middle Layer" yields the best performance on various downstream classification tasks for images (under DiT-XL/2-256×\times256 and various U-ViT architectures). We further analyze the underlying mechanism and its scaling behavior across model scales. To efficiently select representations, we devise a heuristic local-search algorithm that pinpoints the locally optimal "image-text"×\times"block-timestep" pair among a few candidates, avoiding an exhaustive grid search. A simple fusion-linear projection followed by addition-of the selected representations achieves 46.1% mAP on Visual Genome 500 (with 500 categories) and 80.2% mAP on Pix2Cap-COCO (with 80 categories), consistently outperforming strong baseline methods. Code is available at https://github.com/lt-0123/Diff-Feat.
Sep 15, 2025

Scaling to Multimodal and Multichannel Heart Sound Classification with Synthetic and Augmented Biosignals

Cardiovascular diseases (CVDs) are the leading cause of death worldwide, accounting for approximately 17.9 million deaths each year. Early detection is critical, creating a demand for accurate and inexpensive pre-screening methods. Deep learning has recently been applied to classify abnormal heart sounds indicative of CVDs using synchronised phonocardiogram (PCG) and electrocardiogram (ECG) signals, as well as multichannel PCG (mPCG). However, state-of-the-art architectures remain underutilised due to the limited availability of synchronised and multichannel datasets. Augmented datasets and pre-trained models provide a pathway to overcome these limitations, enabling transformer-based architectures to be trained effectively. This work combines traditional signal processing with denoising diffusion models, WaveGrad and DiffWave, to create an augmented dataset to fine-tune a Wav2Vec 2.0-based classifier on multimodal and multichannel heart sound datasets. The approach achieves state-of-the-art performance. On the Computing in Cardiology (CinC) 2016 dataset of single channel PCG, accuracy, unweighted average recall (UAR), sensitivity, specificity and Matthew's correlation coefficient (MCC) reach 92.48%, 93.05%, 93.63%, 92.48%, 94.93% and 0.8283, respectively. Using the synchronised PCG and ECG signals of the training-a dataset from CinC, 93.14%, 92.21%, 94.35%, 90.10%, 95.12% and 0.8380 are achieved for accuracy, UAR, sensitivity, specificity and MCC, respectively. Using a wearable vest dataset consisting of mPCG data, the model achieves 77.13% accuracy, 74.25% UAR, 86.47% sensitivity, 62.04% specificity, and 0.5082 MCC. These results demonstrate the effectiveness of transformer-based models for CVD detection when supported by augmented datasets, highlighting their potential to advance multimodal and multichannel heart sound classification.
Aug 30, 2025

Integrated Multivariate Segmentation Tree for Heterogeneous Credit Data Analysis in Small- and Medium-Sized Enterprises

Traditional decision tree models, which rely exclusively on numerical variables, often face challenges in handling high-dimensional data and are limited in their ability to incorporate textual information effectively. To address these limitations, we propose the integrated multivariate segmentation tree (IMST), a comprehensive framework designed to improve credit evaluation for small- and medium-sized enterprises (SMEs) by integrating financial data with textual sources. This method comprises three core stages: (1) transforming textual data into numerical matrices through matrix factorization, (2) selecting salient financial features using Lasso regression, and (3) constructing a multivariate segmentation tree based on either the Gini index or entropy, with weakest-link pruning applied to control model complexity. Experimental results based on a dataset of 1,428 Chinese SMEs demonstrated that IMST achieved an accuracy rate of 88.9%, surpassing both baseline decision trees (87.4%) and conventional models such as support vector machines and neural networks. Furthermore, the proposed model demonstrated superior interpretability and computational efficiency, featuring a more streamlined architecture and improved risk detection capabilities.
Aug 11, 2025

VGGSounder: Audio-Visual Evaluations for Foundation Models

The emergence of audio-visual foundation models underscores the importance of reliably assessing their multi-modal understanding. The VGGSound dataset is commonly used as a benchmark for evaluation audio-visual classification. However, our analysis identifies several limitations of VGGSound, including incomplete labelling, partially overlapping classes, and misaligned modalities. These lead to distorted evaluations of auditory and visual capabilities. To address these limitations, we introduce VGGSounder, a comprehensively re-annotated, multi-label test set that extends VGGSound and is specifically designed to evaluate audio-visual foundation models. VGGSounder features detailed modality annotations, enabling precise analyses of modality-specific performance. Furthermore, we reveal model limitations by analysing performance degradation when adding another input modality with our new modality confusion metric.
Aug 7, 2025

Disentangling Bias by Modeling Intra- and Inter-modal Causal Attention for Multimodal Sentiment Analysis

Multimodal sentiment analysis (MSA) aims to understand human emotions by integrating information from multiple modalities, such as text, audio, and visual data. However, existing methods often suffer from spurious correlations both within and across modalities, leading models to rely on statistical shortcuts rather than true causal relationships, thereby undermining generalization. To mitigate this issue, we propose a Multi-relational Multimodal Causal Intervention (MMCI) framework, which leverages the backdoor adjustment from causal theory to address the confounding effects of such shortcuts. Specifically, we first model the multimodal inputs as a multi-relational graph to explicitly capture intra- and inter-modal dependencies. Then, we apply an attention mechanism to separately estimate and disentangle the causal features and shortcut features corresponding to these intra- and inter-modal relations. Finally, by approximating backdoor adjustment, we stratify the shortcut features and dynamically combine them with the causal features to encourage MMCI to produce stable predictions under distribution shifts. Extensive experiments on several standard MSA datasets and out-of-distribution (OOD) settings demonstrate that our method effectively suppresses biases and improves performance.
Jul 29, 2025

ArtSeek: Deep artwork understanding via multimodal in-context reasoning and late interaction retrieval

Analyzing digitized artworks requires both visual interpretation and deep artistic, contextual, and historical knowledge. We introduce ArtSeek, a multimodal framework for art analysis that combines multimodal large language models with retrieval-augmented generation. Unlike prior work, our pipeline relies only on image input, so it applies to artworks without links to Wikidata or Wikipedia, common in most digitized collections. ArtSeek integrates three components: a late-interaction multimodal retrieval module, a contrastive multitask network predicting artist, genre, style, media, and tags, and an agentic reasoning strategy enabled through in-context examples. Central to this approach is WikiFragments, a dataset of image-text fragments extracted from the entire English Wikipedia to support knowledge-grounded multimodal reasoning. Our multimodal query encoding raises retrieval NDCG@5 from 33.9 to 44.9 over encoding the full image-text query, and fixed-budget token pooling keeps late-interaction search practical over millions of fragments at under 7% of the cost of full multi-vector retrieval. ArtSeek sets a new state of the art in artwork attribute classification, with +8.4% F1 in style classification over GraphCLIP, and gains +7.1 BLEU@1 on ArtPedia captioning. On five knowledge-grounded question answering benchmarks graded by an LLM judge from a different model family, retrieval helps where the answer is documented in our index or lies inside the classifier's label space (+0.19 mean correctness on two of them) and is neutral where it is not; what separates the two regimes is how much of a benchmark our knowledge base covers. The gain transfers to two non-Qwen backbones (+0.22 to +0.28). A blind human study and a qualitative analysis of successes and failures corroborate this picture and expose where retrieval still misleads. Data and code: https://cilab.di.uniba.it/artseek/
May 10, 2025

Batch Augmentation with Unimodal Fine-tuning for Multimodal Fusion of Large Language Models

In this paper, we propose batch augmentation with unimodal fine-tuning for multimodal learning. We start with pre-trained unimodal models. We fine-tune the unimodal models with the application data. After that, we form a Multi-Layer Perceptron (MLP) head that takes information from unimodal models and provides output. Finally, we train the MLP layer and unimodal parts with batch augmentation. Depending on the data, some unimodal models can be replaced by hard-coded scripts or AI agents. The unimodal training can also follow batch augmentation when the data is augmentable. We write a multimodal batch augmentation dataloader script that implements the batch augmentation for the multimodal data. We investigate the proposed method on the FPU23 ultrasound and UPMC Food-101 multimodal datasets. The multimodal large language model (LLM) with the proposed training achieves the best average result among the investigated methods across both datasets. According to our literature search, the proposed method achieves state-of-the-art (SOTA) accuracy of 93.29% on the UPMC Food-101 dataset, while we apply the ViT-L/16 model for vision and the GPT-2 model for text. We share the scripts of the proposed method with traditional counterparts at the following repository: github.com/dipuk0506/multimodal
Dec 23, 2023

GestaltMML: Enhancing Rare Genetic Disease Diagnosis through Multimodal Machine Learning Combining Facial Images and Clinical Text

Individuals with suspected rare genetic disorders often undergo multiple clinical evaluations, imaging studies, laboratory tests, and genetic tests over a prolonged period of time, a process commonly described as the diagnostic odyssey. Addressing this odyssey has substantial clinical, psychosocial, and economic benefits. Many rare genetic diseases have distinctive facial features that artificial intelligence algorithms can use to facilitate clinical diagnosis, to prioritize candidate diseases for further laboratory or genetic testing, and to support the phenotype-driven reinterpretation of genome or exome sequencing data. Existing methods that use frontal facial photographs were built on conventional convolutional neural networks, rely exclusively on facial images, and cannot capture non-facial phenotypic traits or demographic information that are essential for accurate diagnosis. Here we introduce GestaltMML, a multimodal machine learning approach based solely on the Transformer architecture. It integrates facial images, demographic information (age, sex, ethnicity), and clinical notes (optionally a list of Human Phenotype Ontology terms) to improve prediction accuracy. We evaluate GestaltMML on 528 diseases from the GestaltMatcher Database and on several in-house and published cohorts, including Beckwith-Wiedemann syndrome, Sotos syndrome, NAA10-related neurodevelopmental syndrome, Cornelia de Lange syndrome, and KBG syndrome. GestaltMML improves on the state-of-the-art image-only ensembled model, narrows the diagnostic accuracy gap for patients from under-represented ancestries, and clarifies when multimodal fusion is beneficial and when image-only inference is preferable. The results suggest that GestaltMML can greatly narrow the candidate diagnoses of rare diseases and may facilitate the reinterpretation of sequencing data.