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Oct 14

ColorMAE: Exploring data-independent masking strategies in Masked AutoEncoders

Masked AutoEncoders (MAE) have emerged as a robust self-supervised framework, offering remarkable performance across a wide range of downstream tasks. To increase the difficulty of the pretext task and learn richer visual representations, existing works have focused on replacing standard random masking with more sophisticated strategies, such as adversarial-guided and teacher-guided masking. However, these strategies depend on the input data thus commonly increasing the model complexity and requiring additional calculations to generate the mask patterns. This raises the question: Can we enhance MAE performance beyond random masking without relying on input data or incurring additional computational costs? In this work, we introduce a simple yet effective data-independent method, termed ColorMAE, which generates different binary mask patterns by filtering random noise. Drawing inspiration from color noise in image processing, we explore four types of filters to yield mask patterns with different spatial and semantic priors. ColorMAE requires no additional learnable parameters or computational overhead in the network, yet it significantly enhances the learned representations. We provide a comprehensive empirical evaluation, demonstrating our strategy's superiority in downstream tasks compared to random masking. Notably, we report an improvement of 2.72 in mIoU in semantic segmentation tasks relative to baseline MAE implementations.

  • 3 authors
·
Jul 17, 2024 2

MAR-3D: Progressive Masked Auto-regressor for High-Resolution 3D Generation

Recent advances in auto-regressive transformers have revolutionized generative modeling across different domains, from language processing to visual generation, demonstrating remarkable capabilities. However, applying these advances to 3D generation presents three key challenges: the unordered nature of 3D data conflicts with sequential next-token prediction paradigm, conventional vector quantization approaches incur substantial compression loss when applied to 3D meshes, and the lack of efficient scaling strategies for higher resolution latent prediction. To address these challenges, we introduce MAR-3D, which integrates a pyramid variational autoencoder with a cascaded masked auto-regressive transformer (Cascaded MAR) for progressive latent upscaling in the continuous space. Our architecture employs random masking during training and auto-regressive denoising in random order during inference, naturally accommodating the unordered property of 3D latent tokens. Additionally, we propose a cascaded training strategy with condition augmentation that enables efficiently up-scale the latent token resolution with fast convergence. Extensive experiments demonstrate that MAR-3D not only achieves superior performance and generalization capabilities compared to existing methods but also exhibits enhanced scaling capabilities compared to joint distribution modeling approaches (e.g., diffusion transformers).

  • 7 authors
·
Mar 26

Learning 3D Representations from 2D Pre-trained Models via Image-to-Point Masked Autoencoders

Pre-training by numerous image data has become de-facto for robust 2D representations. In contrast, due to the expensive data acquisition and annotation, a paucity of large-scale 3D datasets severely hinders the learning for high-quality 3D features. In this paper, we propose an alternative to obtain superior 3D representations from 2D pre-trained models via Image-to-Point Masked Autoencoders, named as I2P-MAE. By self-supervised pre-training, we leverage the well learned 2D knowledge to guide 3D masked autoencoding, which reconstructs the masked point tokens with an encoder-decoder architecture. Specifically, we first utilize off-the-shelf 2D models to extract the multi-view visual features of the input point cloud, and then conduct two types of image-to-point learning schemes on top. For one, we introduce a 2D-guided masking strategy that maintains semantically important point tokens to be visible for the encoder. Compared to random masking, the network can better concentrate on significant 3D structures and recover the masked tokens from key spatial cues. For another, we enforce these visible tokens to reconstruct the corresponding multi-view 2D features after the decoder. This enables the network to effectively inherit high-level 2D semantics learned from rich image data for discriminative 3D modeling. Aided by our image-to-point pre-training, the frozen I2P-MAE, without any fine-tuning, achieves 93.4% accuracy for linear SVM on ModelNet40, competitive to the fully trained results of existing methods. By further fine-tuning on on ScanObjectNN's hardest split, I2P-MAE attains the state-of-the-art 90.11% accuracy, +3.68% to the second-best, demonstrating superior transferable capacity. Code will be available at https://github.com/ZrrSkywalker/I2P-MAE.

  • 5 authors
·
Dec 13, 2022

UNITER: UNiversal Image-TExt Representation Learning

Joint image-text embedding is the bedrock for most Vision-and-Language (V+L) tasks, where multimodality inputs are simultaneously processed for joint visual and textual understanding. In this paper, we introduce UNITER, a UNiversal Image-TExt Representation, learned through large-scale pre-training over four image-text datasets (COCO, Visual Genome, Conceptual Captions, and SBU Captions), which can power heterogeneous downstream V+L tasks with joint multimodal embeddings. We design four pre-training tasks: Masked Language Modeling (MLM), Masked Region Modeling (MRM, with three variants), Image-Text Matching (ITM), and Word-Region Alignment (WRA). Different from previous work that applies joint random masking to both modalities, we use conditional masking on pre-training tasks (i.e., masked language/region modeling is conditioned on full observation of image/text). In addition to ITM for global image-text alignment, we also propose WRA via the use of Optimal Transport (OT) to explicitly encourage fine-grained alignment between words and image regions during pre-training. Comprehensive analysis shows that both conditional masking and OT-based WRA contribute to better pre-training. We also conduct a thorough ablation study to find an optimal combination of pre-training tasks. Extensive experiments show that UNITER achieves new state of the art across six V+L tasks (over nine datasets), including Visual Question Answering, Image-Text Retrieval, Referring Expression Comprehension, Visual Commonsense Reasoning, Visual Entailment, and NLVR^2. Code is available at https://github.com/ChenRocks/UNITER.

  • 8 authors
·
Sep 25, 2019

Learning Occlusion-Robust Vision Transformers for Real-Time UAV Tracking

Single-stream architectures using Vision Transformer (ViT) backbones show great potential for real-time UAV tracking recently. However, frequent occlusions from obstacles like buildings and trees expose a major drawback: these models often lack strategies to handle occlusions effectively. New methods are needed to enhance the occlusion resilience of single-stream ViT models in aerial tracking. In this work, we propose to learn Occlusion-Robust Representations (ORR) based on ViTs for UAV tracking by enforcing an invariance of the feature representation of a target with respect to random masking operations modeled by a spatial Cox process. Hopefully, this random masking approximately simulates target occlusions, thereby enabling us to learn ViTs that are robust to target occlusion for UAV tracking. This framework is termed ORTrack. Additionally, to facilitate real-time applications, we propose an Adaptive Feature-Based Knowledge Distillation (AFKD) method to create a more compact tracker, which adaptively mimics the behavior of the teacher model ORTrack according to the task's difficulty. This student model, dubbed ORTrack-D, retains much of ORTrack's performance while offering higher efficiency. Extensive experiments on multiple benchmarks validate the effectiveness of our method, demonstrating its state-of-the-art performance. Codes is available at https://github.com/wuyou3474/ORTrack.

  • 7 authors
·
Apr 12 2

Attention Weighted Mixture of Experts with Contrastive Learning for Personalized Ranking in E-commerce

Ranking model plays an essential role in e-commerce search and recommendation. An effective ranking model should give a personalized ranking list for each user according to the user preference. Existing algorithms usually extract a user representation vector from the user behavior sequence, then feed the vector into a feed-forward network (FFN) together with other features for feature interactions, and finally produce a personalized ranking score. Despite tremendous progress in the past, there is still room for improvement. Firstly, the personalized patterns of feature interactions for different users are not explicitly modeled. Secondly, most of existing algorithms have poor personalized ranking results for long-tail users with few historical behaviors due to the data sparsity. To overcome the two challenges, we propose Attention Weighted Mixture of Experts (AW-MoE) with contrastive learning for personalized ranking. Firstly, AW-MoE leverages the MoE framework to capture personalized feature interactions for different users. To model the user preference, the user behavior sequence is simultaneously fed into expert networks and the gate network. Within the gate network, one gate unit and one activation unit are designed to adaptively learn the fine-grained activation vector for experts using an attention mechanism. Secondly, a random masking strategy is applied to the user behavior sequence to simulate long-tail users, and an auxiliary contrastive loss is imposed to the output of the gate network to improve the model generalization for these users. This is validated by a higher performance gain on the long-tail user test set. Experiment results on a JD real production dataset and a public dataset demonstrate the effectiveness of AW-MoE, which significantly outperforms state-of-art methods. Notably, AW-MoE has been successfully deployed in the JD e-commerce search engine, ...

  • 10 authors
·
Jun 8, 2023

Excision And Recovery: Visual Defect Obfuscation Based Self-Supervised Anomaly Detection Strategy

Due to scarcity of anomaly situations in the early manufacturing stage, an unsupervised anomaly detection (UAD) approach is widely adopted which only uses normal samples for training. This approach is based on the assumption that the trained UAD model will accurately reconstruct normal patterns but struggles with unseen anomalous patterns. To enhance the UAD performance, reconstruction-by-inpainting based methods have recently been investigated, especially on the masking strategy of suspected defective regions. However, there are still issues to overcome: 1) time-consuming inference due to multiple masking, 2) output inconsistency by random masking strategy, and 3) inaccurate reconstruction of normal patterns when the masked area is large. Motivated by this, we propose a novel reconstruction-by-inpainting method, dubbed Excision And Recovery (EAR), that features single deterministic masking based on the ImageNet pre-trained DINO-ViT and visual obfuscation for hint-providing. Experimental results on the MVTec AD dataset show that deterministic masking by pre-trained attention effectively cuts out suspected defective regions and resolve the aforementioned issues 1 and 2. Also, hint-providing by mosaicing proves to enhance the UAD performance than emptying those regions by binary masking, thereby overcomes issue 3. Our approach achieves a high UAD performance without any change of the neural network structure. Thus, we suggest that EAR be adopted in various manufacturing industries as a practically deployable solution.

  • 6 authors
·
Oct 6, 2023

Improving Synthetic Image Detection Towards Generalization: An Image Transformation Perspective

With recent generative models facilitating photo-realistic image synthesis, the proliferation of synthetic images has also engendered certain negative impacts on social platforms, thereby raising an urgent imperative to develop effective detectors. Current synthetic image detection (SID) pipelines are primarily dedicated to crafting universal artifact features, accompanied by an oversight about SID training paradigm. In this paper, we re-examine the SID problem and identify two prevalent biases in current training paradigms, i.e., weakened artifact features and overfitted artifact features. Meanwhile, we discover that the imaging mechanism of synthetic images contributes to heightened local correlations among pixels, suggesting that detectors should be equipped with local awareness. In this light, we propose SAFE, a lightweight and effective detector with three simple image transformations. Firstly, for weakened artifact features, we substitute the down-sampling operator with the crop operator in image pre-processing to help circumvent artifact distortion. Secondly, for overfitted artifact features, we include ColorJitter and RandomRotation as additional data augmentations, to help alleviate irrelevant biases from color discrepancies and semantic differences in limited training samples. Thirdly, for local awareness, we propose a patch-based random masking strategy tailored for SID, forcing the detector to focus on local regions at training. Comparative experiments are conducted on an open-world dataset, comprising synthetic images generated by 26 distinct generative models. Our pipeline achieves a new state-of-the-art performance, with remarkable improvements of 4.5% in accuracy and 2.9% in average precision against existing methods. Our code is available at: https://github.com/Ouxiang-Li/SAFE.

  • 6 authors
·
Aug 13, 2024

OneRef: Unified One-tower Expression Grounding and Segmentation with Mask Referring Modeling

Constrained by the separate encoding of vision and language, existing grounding and referring segmentation works heavily rely on bulky Transformer-based fusion en-/decoders and a variety of early-stage interaction technologies. Simultaneously, the current mask visual language modeling (MVLM) fails to capture the nuanced referential relationship between image-text in referring tasks. In this paper, we propose OneRef, a minimalist referring framework built on the modality-shared one-tower transformer that unifies the visual and linguistic feature spaces. To modeling the referential relationship, we introduce a novel MVLM paradigm called Mask Referring Modeling (MRefM), which encompasses both referring-aware mask image modeling and referring-aware mask language modeling. Both modules not only reconstruct modality-related content but also cross-modal referring content. Within MRefM, we propose a referring-aware dynamic image masking strategy that is aware of the referred region rather than relying on fixed ratios or generic random masking schemes. By leveraging the unified visual language feature space and incorporating MRefM's ability to model the referential relations, our approach enables direct regression of the referring results without resorting to various complex techniques. Our method consistently surpasses existing approaches and achieves SoTA performance on both grounding and segmentation tasks, providing valuable insights for future research. Our code and models are available at https://github.com/linhuixiao/OneRef.

  • 5 authors
·
Oct 10, 2024

Multiple Instance Learning Framework with Masked Hard Instance Mining for Gigapixel Histopathology Image Analysis

Digitizing pathological images into gigapixel Whole Slide Images (WSIs) has opened new avenues for Computational Pathology (CPath). As positive tissue comprises only a small fraction of gigapixel WSIs, existing Multiple Instance Learning (MIL) methods typically focus on identifying salient instances via attention mechanisms. However, this leads to a bias towards easy-to-classify instances while neglecting challenging ones. Recent studies have shown that hard examples are crucial for accurately modeling discriminative boundaries. Applying such an idea at the instance level, we elaborate a novel MIL framework with masked hard instance mining (MHIM-MIL), which utilizes a Siamese structure with a consistency constraint to explore the hard instances. Using a class-aware instance probability, MHIM-MIL employs a momentum teacher to mask salient instances and implicitly mine hard instances for training the student model. To obtain diverse, non-redundant hard instances, we adopt large-scale random masking while utilizing a global recycle network to mitigate the risk of losing key features. Furthermore, the student updates the teacher using an exponential moving average, which identifies new hard instances for subsequent training iterations and stabilizes optimization. Experimental results on cancer diagnosis, subtyping, survival analysis tasks, and 12 benchmarks demonstrate that MHIM-MIL outperforms the latest methods in both performance and efficiency. The code is available at: https://github.com/DearCaat/MHIM-MIL.

  • 6 authors
·
Sep 14 2

SimMIM: A Simple Framework for Masked Image Modeling

This paper presents SimMIM, a simple framework for masked image modeling. We simplify recently proposed related approaches without special designs such as block-wise masking and tokenization via discrete VAE or clustering. To study what let the masked image modeling task learn good representations, we systematically study the major components in our framework, and find that simple designs of each component have revealed very strong representation learning performance: 1) random masking of the input image with a moderately large masked patch size (e.g., 32) makes a strong pre-text task; 2) predicting raw pixels of RGB values by direct regression performs no worse than the patch classification approaches with complex designs; 3) the prediction head can be as light as a linear layer, with no worse performance than heavier ones. Using ViT-B, our approach achieves 83.8% top-1 fine-tuning accuracy on ImageNet-1K by pre-training also on this dataset, surpassing previous best approach by +0.6%. When applied on a larger model of about 650 million parameters, SwinV2-H, it achieves 87.1% top-1 accuracy on ImageNet-1K using only ImageNet-1K data. We also leverage this approach to facilitate the training of a 3B model (SwinV2-G), that by 40times less data than that in previous practice, we achieve the state-of-the-art on four representative vision benchmarks. The code and models will be publicly available at https://github.com/microsoft/SimMIM.

  • 8 authors
·
Nov 18, 2021

DeFacto: Counterfactual Thinking with Images for Enforcing Evidence-Grounded and Faithful Reasoning

Recent advances in multimodal language models (MLLMs) have achieved remarkable progress in vision-language reasoning, especially with the emergence of "thinking with images," which integrates explicit visual steps into the reasoning process. While this paradigm strengthens image-based reasoning, a significant challenge remains: models may arrive at correct answers by relying on irrelevant or spurious regions, driven by prior knowledge or dataset biases. Even when the answer is correct, flawed reasoning indicates that the model has not truly understood the image, highlighting the critical importance of reasoning fidelity in multimodal tasks. To address this issue, we propose DeFacto, a counterfactual reasoning framework that jointly enforces accurate answering and faithful reasoning. A key component of our approach is the design of three complementary training paradigms: (i) positive, (ii) counterfactual, and (iii) random-masking. To enable these paradigms, we develop a pipeline that automatically localizes question-relevant evidence and constructs positive, counterfactual, and random variants, resulting in a dataset of about 100k images. Building on this framework, we train multimodal language models with GRPO-based reinforcement learning, where we design three complementary rewards to guide the model toward accurate answering and evidence-grounded reasoning. Experiments on diverse benchmarks demonstrate that DeFacto substantially improves both answer accuracy and reasoning faithfulness, establishing a stronger foundation for interpretable multimodal reasoning. The code is available on GitHub and the dataset is released on HuggingFace.

  • 9 authors
·
Sep 25

Feature Attenuation of Defective Representation Can Resolve Incomplete Masking on Anomaly Detection

In unsupervised anomaly detection (UAD) research, while state-of-the-art models have reached a saturation point with extensive studies on public benchmark datasets, they adopt large-scale tailor-made neural networks (NN) for detection performance or pursued unified models for various tasks. Towards edge computing, it is necessary to develop a computationally efficient and scalable solution that avoids large-scale complex NNs. Motivated by this, we aim to optimize the UAD performance with minimal changes to NN settings. Thus, we revisit the reconstruction-by-inpainting approach and rethink to improve it by analyzing strengths and weaknesses. The strength of the SOTA methods is a single deterministic masking approach that addresses the challenges of random multiple masking that is inference latency and output inconsistency. Nevertheless, the issue of failure to provide a mask to completely cover anomalous regions is a remaining weakness. To mitigate this issue, we propose Feature Attenuation of Defective Representation (FADeR) that only employs two MLP layers which attenuates feature information of anomaly reconstruction during decoding. By leveraging FADeR, features of unseen anomaly patterns are reconstructed into seen normal patterns, reducing false alarms. Experimental results demonstrate that FADeR achieves enhanced performance compared to similar-scale NNs. Furthermore, our approach exhibits scalability in performance enhancement when integrated with other single deterministic masking methods in a plug-and-play manner.

  • 5 authors
·
Jul 5, 2024

MimicDroid: In-Context Learning for Humanoid Robot Manipulation from Human Play Videos

We aim to enable humanoid robots to efficiently solve new manipulation tasks from a few video examples. In-context learning (ICL) is a promising framework for achieving this goal due to its test-time data efficiency and rapid adaptability. However, current ICL methods rely on labor-intensive teleoperated data for training, which restricts scalability. We propose using human play videos -- continuous, unlabeled videos of people interacting freely with their environment -- as a scalable and diverse training data source. We introduce MimicDroid, which enables humanoids to perform ICL using human play videos as the only training data. MimicDroid extracts trajectory pairs with similar manipulation behaviors and trains the policy to predict the actions of one trajectory conditioned on the other. Through this process, the model acquired ICL capabilities for adapting to novel objects and environments at test time. To bridge the embodiment gap, MimicDroid first retargets human wrist poses estimated from RGB videos to the humanoid, leveraging kinematic similarity. It also applies random patch masking during training to reduce overfitting to human-specific cues and improve robustness to visual differences. To evaluate few-shot learning for humanoids, we introduce an open-source simulation benchmark with increasing levels of generalization difficulty. MimicDroid outperformed state-of-the-art methods and achieved nearly twofold higher success rates in the real world. Additional materials can be found on: ut-austin-rpl.github.io/MimicDroid

  • 8 authors
·
Sep 11

NeRF-MAE: Masked AutoEncoders for Self-Supervised 3D Representation Learning for Neural Radiance Fields

Neural fields excel in computer vision and robotics due to their ability to understand the 3D visual world such as inferring semantics, geometry, and dynamics. Given the capabilities of neural fields in densely representing a 3D scene from 2D images, we ask the question: Can we scale their self-supervised pretraining, specifically using masked autoencoders, to generate effective 3D representations from posed RGB images. Owing to the astounding success of extending transformers to novel data modalities, we employ standard 3D Vision Transformers to suit the unique formulation of NeRFs. We leverage NeRF's volumetric grid as a dense input to the transformer, contrasting it with other 3D representations such as pointclouds where the information density can be uneven, and the representation is irregular. Due to the difficulty of applying masked autoencoders to an implicit representation, such as NeRF, we opt for extracting an explicit representation that canonicalizes scenes across domains by employing the camera trajectory for sampling. Our goal is made possible by masking random patches from NeRF's radiance and density grid and employing a standard 3D Swin Transformer to reconstruct the masked patches. In doing so, the model can learn the semantic and spatial structure of complete scenes. We pretrain this representation at scale on our proposed curated posed-RGB data, totaling over 1.8 million images. Once pretrained, the encoder is used for effective 3D transfer learning. Our novel self-supervised pretraining for NeRFs, NeRF-MAE, scales remarkably well and improves performance on various challenging 3D tasks. Utilizing unlabeled posed 2D data for pretraining, NeRF-MAE significantly outperforms self-supervised 3D pretraining and NeRF scene understanding baselines on Front3D and ScanNet datasets with an absolute performance improvement of over 20% AP50 and 8% AP25 for 3D object detection.

  • 6 authors
·
Apr 1, 2024 2

Unsupervised Real-World Denoising: Sparsity is All You Need

Supervised training for real-world denoising presents challenges due to the difficulty of collecting large datasets of paired noisy and clean images. Recent methods have attempted to address this by utilizing unpaired datasets of clean and noisy images. Some approaches leverage such unpaired data to train denoisers in a supervised manner by generating synthetic clean-noisy pairs. However, these methods often fall short due to the distribution gap between synthetic and real noisy images. To mitigate this issue, we propose a solution based on input sparsification, specifically using random input masking. Our method, which we refer to as Mask, Inpaint and Denoise (MID), trains a denoiser to simultaneously denoise and inpaint synthetic clean-noisy pairs. On one hand, input sparsification reduces the gap between synthetic and real noisy images. On the other hand, an inpainter trained in a supervised manner can still accurately reconstruct sparse inputs by predicting missing clean pixels using the remaining unmasked pixels. Our approach begins with a synthetic Gaussian noise sampler and iteratively refines it using a noise dataset derived from the denoiser's predictions. The noise dataset is created by subtracting predicted pseudo-clean images from real noisy images at each iteration. The core intuition is that improving the denoiser results in a more accurate noise dataset and, consequently, a better noise sampler. We validate our method through extensive experiments on real-world noisy image datasets, demonstrating competitive performance compared to existing unsupervised denoising methods.

  • 2 authors
·
Mar 27

Synthio: Augmenting Small-Scale Audio Classification Datasets with Synthetic Data

We present Synthio, a novel approach for augmenting small-scale audio classification datasets with synthetic data. Our goal is to improve audio classification accuracy with limited labeled data. Traditional data augmentation techniques, which apply artificial transformations (e.g., adding random noise or masking segments), struggle to create data that captures the true diversity present in real-world audios. To address this shortcoming, we propose to augment the dataset with synthetic audio generated from text-to-audio (T2A) diffusion models. However, synthesizing effective augmentations is challenging because not only should the generated data be acoustically consistent with the underlying small-scale dataset, but they should also have sufficient compositional diversity. To overcome the first challenge, we align the generations of the T2A model with the small-scale dataset using preference optimization. This ensures that the acoustic characteristics of the generated data remain consistent with the small-scale dataset. To address the second challenge, we propose a novel caption generation technique that leverages the reasoning capabilities of Large Language Models to (1) generate diverse and meaningful audio captions and (2) iteratively refine their quality. The generated captions are then used to prompt the aligned T2A model. We extensively evaluate Synthio on ten datasets and four simulated limited-data settings. Results indicate our method consistently outperforms all baselines by 0.1%-39% using a T2A model trained only on weakly-captioned AudioSet.

  • 6 authors
·
Oct 2, 2024 2

Attentive Mask CLIP

Image token removal is an efficient augmentation strategy for reducing the cost of computing image features. However, this efficient augmentation strategy has been found to adversely affect the accuracy of CLIP-based training. We hypothesize that removing a large portion of image tokens may improperly discard the semantic content associated with a given text description, thus constituting an incorrect pairing target in CLIP training. To address this issue, we propose an attentive token removal approach for CLIP training, which retains tokens with a high semantic correlation to the text description. The correlation scores are computed in an online fashion using the EMA version of the visual encoder. Our experiments show that the proposed attentive masking approach performs better than the previous method of random token removal for CLIP training. The approach also makes it efficient to apply multiple augmentation views to the image, as well as introducing instance contrastive learning tasks between these views into the CLIP framework. Compared to other CLIP improvements that combine different pre-training targets such as SLIP and MaskCLIP, our method is not only more effective, but also much more efficient. Specifically, using ViT-B and YFCC-15M dataset, our approach achieves 43.9% top-1 accuracy on ImageNet-1K zero-shot classification, as well as 62.7/42.1 and 38.0/23.2 I2T/T2I retrieval accuracy on Flickr30K and MS COCO, which are +1.1%, +5.5/+0.9, and +4.4/+1.3 higher than the SLIP method, while being 2.30times faster. An efficient version of our approach running 1.16times faster than the plain CLIP model achieves significant gains of +5.3%, +11.3/+8.0, and +9.5/+4.9 on these benchmarks.

  • 11 authors
·
Dec 16, 2022

Interpretable graph-based models on multimodal biomedical data integration: A technical review and benchmarking

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet clinical uptake requires regulator-ready interpretability. We present the first technical survey of interpretable graph based models for multimodal biomedical data, covering 26 studies published between Jan 2019 and Sep 2024. Most target disease classification, notably cancer and rely on static graphs from simple similarity measures, while graph-native explainers are rare; post-hoc methods adapted from non-graph domains such as gradient saliency, and SHAP predominate. We group existing approaches into four interpretability families, outline trends such as graph-in-graph hierarchies, knowledge-graph edges, and dynamic topology learning, and perform a practical benchmark. Using an Alzheimer disease cohort, we compare Sensitivity Analysis, Gradient Saliency, SHAP and Graph Masking. SHAP and Sensitivity Analysis recover the broadest set of known AD pathways and Gene-Ontology terms, whereas Gradient Saliency and Graph Masking surface complementary metabolic and transport signatures. Permutation tests show all four beat random gene sets, but with distinct trade-offs: SHAP and Graph Masking offer deeper biology at higher compute cost, while Gradient Saliency and Sensitivity Analysis are quicker though coarser. We also provide a step-by-step flowchart covering graph construction, explainer choice and resource budgeting to help researchers balance transparency and performance. This review synthesises the state of interpretable graph learning for multimodal medicine, benchmarks leading techniques, and charts future directions, from advanced XAI tools to under-studied diseases, serving as a concise reference for method developers and translational scientists.

  • 6 authors
·
May 3