Multimodal large language models (MLLMs) are broadly empowering various fields. Despite their advancements, the explainability of MLLMs remains less explored, hindering deeper understanding, model credibility, and effective visualization. Unlike conventional vision models (e.g., CNNs, ViTs, CLIP) that produce a single output, MLLMs generate sequences of tokens progressively, where each generated token depends on the previous context. Therefore, earlier context tokens can introduce redundant activations that interfere with the explanation of later tokens beyond their original information. Existing studies often overlook this issue, but our observations reveal that these redundant correlations can significantly hurt the reliability of explanations. To address this, we propose an estimated causal inference method to mitigate the interference of context to achieve high-quality MLLM explanation, with a novel rank Gaussian filter to further reduce activation noises. We term this method Token Activation Map (TAM) to highlight the consideration of interactions between tokens. TAM also indicates that it excels at explaining multiple tokens of MLLM, which is different from the Class Activation Map (CAM) for a single prediction. Our TAM method significantly outperforms existing SoTA methods, showcasing high-quality visualization results that can be utilized for various scenarios, such as object localization, failure case analysis, video visualization, MLLMs visual comparison, and model understanding (e.g., color, shape, action, location, visual reasoning, multi-turn conversation, etc). The code is available at github.com/xmed-lab/TAM.

Source-free domain adaptation (SFDA) for segmentation aims at adapting a model trained in the source domain to perform well in the target domain with only the source model and unlabeled target data. Inspired by the recent success of Segment Anything Model (SAM) which exhibits the generality of segmenting images of various modalities and in different domains given human-annotated prompts like bounding boxes or points, we for the first time explore the potentials of Segment Anything Model for SFDA via automatedly finding an accurate bounding box prompt. We find that the bounding boxes directly generated with existing SFDA approaches are defective due to the domain gap. To tackle this issue, we propose a novel Dual Feature Guided (DFG) auto-prompting approach to search for the box prompt. Specifically, the source model is first trained in a feature aggregation phase, which not only preliminarily adapts the source model to the target domain but also builds a feature distribution well-prepared for box prompt search. In the second phase, based on two feature distribution observations, we gradually expand the box prompt with the guidance of the target model feature and the SAM feature to handle the class-wise clustered target features and the class-wise dispersed target features, respectively. To remove the potentially enlarged false positive regions caused by the over-confident prediction of the target model, the refined pseudo-labels produced by SAM are further postprocessed based on connectivity analysis. Experiments on 3D and 2D datasets indicate that our approach yields superior performance compared to conventional methods. Code is available at https://github.com/xmed-lab/DFG.

This paper presents a label-free gland segmentation, GlandSAM, which achieves comparable performance with supervised methods while no label is required during its training or inference phase. We observe that the Segment Anything model produces sub-optimal results on gland dataset: It either over-segments a gland into many fractions or under-segments the gland regions by confusing many of them with the background, due to the complex morphology of glands and lack of sufficient labels. To address this challenge, our GlandSAM innovatively injects two clues about gland morphology into SAM to guide the segmentation process: (1) Heterogeneity within glands and (2) Similarity with the background. Initially, we leverage the clues to decompose the intricate glands by selectively extracting a proposal for each gland sub-region of heterogeneous appearances. Then, we inject the morphology clues into SAM in a fine-tuning manner with a novel morphology-aware semantic grouping module that explicitly groups the high-level semantics of gland sub-regions. In this way, our GlandSAM could capture comprehensive knowledge about gland morphology, and produce well-delineated and complete segmentation results. Extensive experiments conducted on the GlaS dataset and the CRAG dataset reveal that GlandSAM outperforms state-of-the-art label-free methods by a significant margin. Notably, our GlandSAM even surpasses several fully-supervised methods that require pixel-wise labels for training, which highlights the remarkable performance and potential of GlandSAM in the realm of gland segmentation.

Semi-supervised semantic segmentation (SSSS) has been proposed to alleviate the burden of time-consuming pixel-level manual labeling, which leverages limited labeled data along with larger amounts of unlabeled data. Current state-of-the-art methods train the labeled data with ground truths and unlabeled data with pseudo labels. However, the two training flows are separate, which allows labeled data to dominate the training process, resulting in low-quality pseudo labels and, consequently, sub-optimal results. To alleviate this issue, we present AllSpark11The AllSpark is a powerful Cybertronian artifact in the film of Trans-formers: Revenge of the Fallen, which can be used to reborn the Trans-formers. It aligns well with our core idea., which reborns the labeled features from unlabeled ones with the channel-wise cross-attention mechanism. We further introduce a Semantic Memory along with a Channel Se-mantic Grouping strategy to ensure that unlabeled features adequately represent labeled features. The AllSpark shed new light on the architecture level designs of SSSS rather than framework level, which avoids increasingly complicated training pipeline designs. It can also be re-garded as a flexible bottleneck module that can be seam-lessly integrated into a general transformer-based segmentation model. The proposed AllSpark outperforms existing methods across all evaluation protocols on Pas-cal, Cityscapes and COCO benchmarks without bells-and-whistles. Code and model weights are available at: https://github.com/xmed-lab/AllSpark.

Predicting interactions between proteins is one of the most important yet challenging problems in structural bioinformatics. Intrinsically, potential function sites in protein surfaces are determined by both geometric and chemical features. However, existing works only consider handcrafted or individually learned chemical features from the atom type and extract geometric features independently. Here, we identify two key properties of effective protein surface learning: 1) relationship among atoms: atoms are linked with each other by covalent bonds to form biomolecules instead of appearing alone, leading to the significance of modeling the relationship among atoms in chemical feature learning. 2) hierarchical feature interaction: the neighboring residue effect validates the significance of hierarchical feature interaction among atoms and between surface points and atoms (or residues). In this paper, we present a principled framework based on deep learning techniques, namely Hierarchical Chemical and Geometric Feature Interaction Network (HCGNet), for protein surface analysis by bridging chemical and geometric features with hierarchical interactions. Extensive experiments demonstrate that our method outperforms the prior state-of-the-art method by 2.3% in site prediction task and 3.2 available at https://github.com/lyqun/HCGNet.

Out-of-distribution (OOD) detection refers to training the model on an in-distribution (ID) dataset to classify whether the input images come from unknown classes. Considerable effort has been invested in designing various OOD detection methods based on either convolutional neural networks or transformers. However, zero-shot OOD detection methods driven by CLIP, which only require class names for ID, have received less attention. This paper presents a novel method, namely CLIP saying "no" (CLIPN), which empowers the logic of saying "no" within CLIP. Our key motivation is to equip CLIP with the capability of distinguishing OOD and ID samples using positive-semantic prompts and negation-semantic prompts. Specifically, we design a novel learnable "no" prompt and a "no" text encoder to capture negation semantics within images. Subsequently, we introduce two loss functions: the image-text binary-opposite loss and the text semantic-opposite loss, which we use to teach CLIPN to associate images with "no" prompts, thereby enabling it to identify unknown samples. Furthermore, we propose two threshold-free inference algorithms to perform OOD detection by utilizing negation semantics from "no" prompts and the text encoder. Experimental results on 9 benchmark datasets (3 ID datasets and 6 OOD datasets) for the OOD detection task demonstrate that CLIPN, based on ViT-B-16, outperforms 7 well-used algorithms by at least 2.34% and 11.64% in terms of AUROC and FPR95 for zero-shot OOD detection on ImageNet-1K. Our CLIPN can serve as a solid foundation for effectively leveraging CLIP in downstream OOD tasks. The code is available on https://github.com/xmed-lab/CLIPN.

Weakly-Supervised Semantic Segmentation (WSSS) segments objects without heavy burden of dense annotation. While as a price, generated pseudo-masks exist obvious noisy pixels, which result in sub-optimal segmentation models trained over these pseudo-masks. But rare studies notice or work on this problem, even these noisy pixels are inevitable after their improvements on pseudo-mask. So we try to improve WSSS in the aspect of noise mitigation. And we observe that many noisy pixels are of high confidences, especially when the response range is too wide or narrow, presenting an uncertain status. Thus, in this paper, we simulate noisy variations of response by scaling the prediction map in multiple times for uncertainty estimation. The uncertainty is then used to weight the segmentation loss to mitigate noisy supervision signals. We call this method URN, abbreviated from Uncertainty estimation via Response scaling for Noise mitigation. Experiments validate the benefits of URN, and our method achieves state-of-the-art results at 71.2% and 41.5% on PASCAL VOC 2012 and MS COCO 2014 respectively, without extra models like saliency detection. Code is available at https://github.com/XMed-Lab/URN.

Most weakly supervised semantic segmentation (WSSS) methods follow the pipeline that generates pseudo-masks initially and trains the segmentation model with the pseudo-masks in fully supervised manner after. However, we find some matters related to the pseudo-masks, including high quality pseudo-masks generation from class activation maps (CAMs), and training with noisy pseudo-mask supervision. For these matters, we propose the following designs to push the performance to new state-of-art: (i) Coefficient of Variation Smoothing to smooth the CAMs adaptively; (ii) Proportional Pseudo-mask Generation to project the expanded CAMs to pseudo-mask based on a new metric indicating the importance of each class on each location, instead of the scores trained from binary classifiers. (iii) Pretended Under-Fitting strategy to suppress the influence of noise in pseudo-mask; (iv) Cyclic Pseudo-mask to boost the pseudo-masks during training of fully supervised semantic segmentation (FSSS). Experiments based on our methods achieve new state-of-art results on two changeling weakly supervised semantic segmentation datasets, pushing the mIoU to 70.0% and 40.2% on PAS-CAL VOC 2012 and MS COCO 2014 respectively. Codes including segmentation framework are released at https://github.com/Eli-YiLi/PMM

Successful visual recognition networks benefit from aggregating information spanning from a wide range of scales. Previous research has investigated information fusion of connected layers or multiple branches in a block, seeking to strengthen the power of multi-scale representations. Despite their great successes, existing practices often allocate the neurons for each scale manually, and keep the same ratio in all aggregation blocks of an entire network, rendering suboptimal performance. In this paper, we propose to learn the neuron allocation for aggregating multi-scale information in different building blocks of a deep network. The most informative output neurons in each block are preserved while others are discarded, and thus neurons for multiple scales are competitively and adaptively allocated. Our scale aggregation network (ScaleNet) is constructed by repeating a scale aggregation (SA) block that concatenates feature maps at a wide range of scales. Feature maps for each scale are generated by a stack of downsampling, convolution and upsampling operations. The data-driven neuron allocation and SA block achieve strong representational power at the cost of considerably low computational complexity. The proposed ScaleNet, by replacing all 3×3 convolutions in ResNet with our SA blocks, achieves better performance than ResNet and its outstanding variants like ResNeXt and SE-ResNet, in the same computational complexity. On ImageNet classification, ScaleNets absolutely reduce the top-1 error rate of ResNets by 1.12 (101 layers) and 1.82 (50 layers). On COCO object detection, ScaleNets absolutely improve the mAP with backbone of ResNets by 3.6 and 4.6 on Faster-RCNN, respectively. Code and models are released on https://github.com/Eli-YiLi/ScaleNet.