Nghiem T. Diep

Duy M. H. Nguyen, Hoang Nguyen, Nghiem T. Diep et al. · eth-zurich

Obtaining large pre-trained models that can be fine-tuned to new tasks with limited annotated samples has remained an open challenge for medical imaging data. While pre-trained deep networks on ImageNet and vision-language foundation models trained on web-scale data are prevailing approaches, their effectiveness on medical tasks is limited due to the significant domain shift between natural and medical images. To bridge this gap, we introduce LVM-Med, the first family of deep networks trained on large-scale medical datasets. We have collected approximately 1.3 million medical images from 55 publicly available datasets, covering a large number of organs and modalities such as CT, MRI, X-ray, and Ultrasound. We benchmark several state-of-the-art self-supervised algorithms on this dataset and propose a novel self-supervised contrastive learning algorithm using a graph-matching formulation. The proposed approach makes three contributions: (i) it integrates prior pair-wise image similarity metrics based on local and global information; (ii) it captures the structural constraints of feature embeddings through a loss function constructed via a combinatorial graph-matching objective; and (iii) it can be trained efficiently end-to-end using modern gradient-estimation techniques for black-box solvers. We thoroughly evaluate the proposed LVM-Med on 15 downstream medical tasks ranging from segmentation and classification to object detection, and both for the in and out-of-distribution settings. LVM-Med empirically outperforms a number of state-of-the-art supervised, self-supervised, and foundation models. For challenging tasks such as Brain Tumor Classification or Diabetic Retinopathy Grading, LVM-Med improves previous vision-language models trained on 1 billion masks by 6-7% while using only a ResNet-50.

Duy Minh Ho Nguyen, Tan Ngoc Pham, Nghiem Tuong Diep et al.

Constructing a robust model that can effectively generalize to test samples under distribution shifts remains a significant challenge in the field of medical imaging. The foundational models for vision and language, pre-trained on extensive sets of natural image and text data, have emerged as a promising approach. It showcases impressive learning abilities across different tasks with the need for only a limited amount of annotated samples. While numerous techniques have focused on developing better fine-tuning strategies to adapt these models for specific domains, we instead examine their robustness to domain shifts in the medical image segmentation task. To this end, we compare the generalization performance to unseen domains of various pre-trained models after being fine-tuned on the same in-distribution dataset and show that foundation-based models enjoy better robustness than other architectures. From here, we further developed a new Bayesian uncertainty estimation for frozen models and used them as an indicator to characterize the model's performance on out-of-distribution (OOD) data, proving particularly beneficial for real-world applications. Our experiments not only reveal the limitations of current indicators like accuracy on the line or agreement on the line commonly used in natural image applications but also emphasize the promise of the introduced Bayesian uncertainty. Specifically, lower uncertainty predictions usually tend to higher out-of-distribution (OOD) performance.

Duy M. H. Nguyen, An T. Le, Trung Q. Nguyen et al.

Prompt learning methods are gaining increasing attention due to their ability to customize large vision-language models to new domains using pre-trained contextual knowledge and minimal training data. However, existing works typically rely on optimizing unified prompt inputs, often struggling with fine-grained classification tasks due to insufficient discriminative attributes. To tackle this, we consider a new framework based on a dual context of both domain-shared and class-specific contexts, where the latter is generated by Large Language Models (LLMs) such as GPTs. Such dual prompt methods enhance the model's feature representation by joining implicit and explicit factors encoded in LLM knowledge. Moreover, we formulate the Unbalanced Optimal Transport (UOT) theory to quantify the relationships between constructed prompts and visual tokens. Through partial matching, UOT can properly align discrete sets of visual tokens and prompt embeddings under different mass distributions, which is particularly valuable for handling irrelevant or noisy elements, ensuring that the preservation of mass does not restrict transport solutions. Furthermore, UOT's characteristics integrate seamlessly with image augmentation, expanding the training sample pool while maintaining a reasonable distance between perturbed images and prompt inputs. Extensive experiments across few-shot classification and adapter settings substantiate the superiority of our model over current state-of-the-art baselines.

Anh-Tien Nguyen, Duy Minh Ho Nguyen, Nghiem Tuong Diep et al.

Whole slide pathology image classification presents challenges due to gigapixel image sizes and limited annotation labels, hindering model generalization. This paper introduces a prompt learning method to adapt large vision-language models for few-shot pathology classification. We first extend the Prov-GigaPath vision foundation model, pre-trained on 1.3 billion pathology image tiles, into a vision-language model by adding adaptors and aligning it with medical text encoders via contrastive learning on 923K image-text pairs. The model is then used to extract visual features and text embeddings from few-shot annotations and fine-tunes with learnable prompt embeddings. Unlike prior methods that combine prompts with frozen features using prefix embeddings or self-attention, we propose multi-granular attention that compares interactions between learnable prompts with individual image patches and groups of them. This approach improves the model's ability to capture both fine-grained details and broader context, enhancing its recognition of complex patterns across sub-regions. To further improve accuracy, we leverage (unbalanced) optimal transport-based visual-text distance to secure model robustness by mitigating perturbations that might occur during the data augmentation process. Empirical experiments on lung, kidney, and breast pathology modalities validate the effectiveness of our approach; thereby, we surpass several of the latest competitors and consistently improve performance across diverse architectures, including CLIP, PLIP, and Prov-GigaPath integrated PLIP.

Nghiem T. Diep, Huy Nguyen, Chau Nguyen et al.

The LLaMA-Adapter has recently emerged as an efficient fine-tuning technique for LLaMA models, leveraging zero-initialized attention to stabilize training and enhance performance. However, despite its empirical success, the theoretical foundations of zero-initialized attention remain largely unexplored. In this paper, we provide a rigorous theoretical analysis, establishing a connection between zero-initialized attention and mixture-of-expert models. We prove that both linear and non-linear prompts, along with gating functions, can be optimally estimated, with non-linear prompts offering greater flexibility for future applications. Empirically, we validate our findings on the open LLM benchmarks, demonstrating that non-linear prompts outperform linear ones. Notably, even with limited training data, both prompt types consistently surpass vanilla attention, highlighting the robustness and adaptability of zero-initialized attention.

Nghiem T. Diep, Hien Dang, Tuan Truong et al.

Parameter-efficient fine-tuning (PEFT) methods have become the standard paradigm for adapting large-scale models. Among these techniques, Weight-Decomposed Low-Rank Adaptation (DoRA) has been shown to improve both the learning capacity and training stability of the vanilla Low-Rank Adaptation (LoRA) method by explicitly decomposing pre-trained weights into magnitude and directional components. In this work, we propose DoRAN, a new variant of DoRA designed to further stabilize training and boost the sample efficiency of DoRA. Our approach includes two key stages: (i) injecting noise into the denominator of DoRA's weight decomposition, which serves as an adaptive regularizer to mitigate instabilities; and (ii) replacing static low-rank matrices with auxiliary networks that generate them dynamically, enabling parameter coupling across layers and yielding better sample efficiency in both theory and practice. Comprehensive experiments on vision and language benchmarks show that DoRAN consistently outperforms LoRA, DoRA, and other PEFT baselines. These results underscore the effectiveness of combining stabilization through noise-based regularization with network-based parameter generation, offering a promising direction for robust and efficient fine-tuning of foundation models.

Nghiem T. Diep, Dung Le, Tuan Truong et al.

Low-Rank Adaptation (LoRA) is a parameter-efficient fine-tuning (PEFT) technique that adapts large pre-trained models by adding low-rank matrices to their weight updates. However, in the context of fine-tuning multi-head self-attention (MHA), LoRA has been employed to adapt each attention head separately, thereby overlooking potential synergies across different heads. To mitigate this issue, we propose a novel Hyper-shared Low-Rank Adaptation (HoRA) method, which utilizes joint hypernetworks to generate low-rank matrices across attention heads. By coupling their adaptation through a shared generator, HoRA encourages cross-head information sharing, and thus directly addresses the aforementioned limitation of LoRA. By comparing LoRA and HoRA through the lens of hierarchical mixture of experts, our theoretical findings reveal that the latter achieves superior sample efficiency to the former. Furthermore, through extensive experiments across diverse language and vision benchmarks, we demonstrate that HoRA outperforms LoRA and other PEFT methods while requiring only a marginal increase in the number of trainable parameters.

Khang Tran, Hieu Cao, Thinh Pham et al.

Regression is essential across many domains but remains challenging in high-dimensional settings, where existing methods often lose spatial structure or demand heavy storage. In this work, we address the problem of matrix-valued regression, where each sample is naturally represented as a matrix. We propose MELCOT, a hybrid model that integrates a classical machine learning-based Marginal Estimation (ME) block with a deep learning-based Learnable-Cost Optimal Transport (LCOT) block. The ME block estimates data marginals to preserve spatial information, while the LCOT block learns complex global features. This design enables MELCOT to inherit the strengths of both classical and deep learning methods. Extensive experiments across diverse datasets and domains demonstrate that MELCOT consistently outperforms all baselines while remaining highly efficient.