DACAT: Dual-stream Adaptive Clip-aware Time Modeling for Robust Online Surgical Phase Recognition

Surgical phase recognition has become a crucial requirement in laparoscopic surgery, enabling various clinical applications like surgical risk forecasting. Current methods typically identify the surgical phase using individual frame-wise embeddings as the fundamental unit for time modeling. However, this approach is overly sensitive to current observations, often resulting in discontinuous and erroneous predictions within a complete surgical phase. In this paper, we propose DACAT, a novel dual-stream model that adaptively learns clip-aware context information to enhance the temporal relationship. In one stream, DACAT pretrains a frame encoder, caching all historical frame-wise features. In the other stream, DACAT fine-tunes a new frame encoder to extract the frame-wise feature at the current moment. Additionally, a max clip-response read-out (Max-R) module is introduced to bridge the two streams by using the current frame-wise feature to adaptively fetch the most relevant past clip from the feature cache. The clip-aware context feature is then encoded via cross-attention between the current frame and its fetched adaptive clip, and further utilized to enhance the time modeling for accurate online surgical phase recognition. The benchmark results on three public datasets, i.e., Cholec80, M2CAI16, and AutoLaparo, demonstrate the superiority of our proposed DACAT over existing state-of-the-art methods, with improvements in Jaccard scores of at least 4.5%, 4.6%, and 2.7%, respectively. Our code and models have been released at https://github.com/kk42yy/DACAT.

Decoupling Feature Representations of Ego and Other Modalities for Incomplete Multi-modal Brain Tumor Segmentation

Multi-modal brain tumor segmentation typically involves four magnetic resonance imaging (MRI) modalities, while incomplete modalities significantly degrade performance. Existing solutions employ explicit or implicit modality adaptation, aligning features across modalities or learning a fused feature robust to modality incompleteness. They share a common goal of encouraging each modality to express both itself and the others. However, the two expression abilities are entangled as a whole in a seamless feature space, resulting in prohibitive learning burdens. In this paper, we propose DeMoSeg to enhance the modality adaptation by Decoupling the task of representing the ego and other Modalities for robust incomplete multi-modal Segmentation. The decoupling is super lightweight by simply using two convolutions to map each modality onto four feature sub-spaces. The first sub-space expresses itself (Self-feature), while the remaining sub-spaces substitute for other modalities (Mutual-features). The Self- and Mutual-features interactively guide each other through a carefully-designed Channel-wised Sparse Self-Attention (CSSA). After that, a Radiologist-mimic Cross-modality expression Relationships (RCR) is introduced to have available modalities provide Self-feature and also `lend' their Mutual-features to compensate for the absent ones by exploiting the clinical prior knowledge. The benchmark results on BraTS2020, BraTS2018 and BraTS2015 verify the DeMoSeg's superiority thanks to the alleviated modality adaptation difficulty. Concretely, for BraTS2020, DeMoSeg increases Dice by at least 0.92%, 2.95% and 4.95% on whole tumor, tumor core and enhanced tumor regions, respectively, compared to other state-of-the-arts. Codes are at https://github.com/kk42yy/DeMoSeg

SALI: Short-term Alignment and Long-term Interaction Network for Colonoscopy Video Polyp Segmentation

Colonoscopy videos provide richer information in polyp segmentation for rectal cancer diagnosis. However, the endoscope's fast moving and close-up observing make the current methods suffer from large spatial incoherence and continuous low-quality frames, and thus yield limited segmentation accuracy. In this context, we focus on robust video polyp segmentation by enhancing the adjacent feature consistency and rebuilding the reliable polyp representation. To achieve this goal, we in this paper propose SALI network, a hybrid of Short-term Alignment Module (SAM) and Long-term Interaction Module (LIM). The SAM learns spatial-aligned features of adjacent frames via deformable convolution and further harmonizes them to capture more stable short-term polyp representation. In case of low-quality frames, the LIM stores the historical polyp representations as a long-term memory bank, and explores the retrospective relations to interactively rebuild more reliable polyp features for the current segmentation. Combing SAM and LIM, the SALI network of video segmentation shows a great robustness to the spatial variations and low-visual cues. Benchmark on the large-scale SUNSEG verifies the superiority of SALI over the current state-of-the-arts by improving Dice by 2.1%, 2.5%, 4.1% and 1.9%, for the four test sub-sets, respectively. Codes are at https://github.com/Scatteredrain/SALI.

Improving Paratope and Epitope Prediction by Multi-Modal Contrastive Learning and Interaction Informativeness Estimation

Accurately predicting antibody-antigen binding residues, i.e., paratopes and epitopes, is crucial in antibody design. However, existing methods solely focus on uni-modal data (either sequence or structure), disregarding the complementary information present in multi-modal data, and most methods predict paratopes and epitopes separately, overlooking their specific spatial interactions. In this paper, we propose a novel Multi-modal contrastive learning and Interaction informativeness estimation-based method for Paratope and Epitope prediction, named MIPE, by using both sequence and structure data of antibodies and antigens. MIPE implements a multi-modal contrastive learning strategy, which maximizes representations of binding and non-binding residues within each modality and meanwhile aligns uni-modal representations towards effective modal representations. To exploit the spatial interaction information, MIPE also incorporates an interaction informativeness estimation that computes the estimated interaction matrices between antibodies and antigens, thereby approximating them to the actual ones. Extensive experiments demonstrate the superiority of our method compared to baselines. Additionally, the ablation studies and visualizations demonstrate the superiority of MIPE owing to the better representations acquired through multi-modal contrastive learning and the interaction patterns comprehended by the interaction informativeness estimation.

Towards Understanding How Transformer Perform Multi-step Reasoning with Matching Operation

Large language models have consistently struggled with complex reasoning tasks, such as mathematical problem-solving. Investigating the internal reasoning mechanisms of these models can help us design better model architectures and training strategies, ultimately enhancing their reasoning capabilities. In this study, we examine the matching mechanism employed by Transformer for multi-step reasoning on a constructed dataset. We investigate factors that influence the model's matching mechanism and discover that small initialization and post-LayerNorm can facilitate the formation of the matching mechanism, thereby enhancing the model's reasoning ability. Moreover, we propose a method to improve the model's reasoning capability by adding orthogonal noise. Finally, we investigate the parallel reasoning mechanism of Transformers and propose a conjecture on the upper bound of the model's reasoning ability based on this phenomenon. These insights contribute to a deeper understanding of the reasoning processes in large language models and guide designing more effective reasoning architectures and training strategies.

Exploring Graph-based Knowledge: Multi-Level Feature Distillation via Channels Relational Graph

In visual tasks, large teacher models capture essential features and deep information, enhancing performance. However, distilling this information into smaller student models often leads to performance loss due to structural differences and capacity limitations. To tackle this, we propose a distillation framework based on graph knowledge, including a multi-level feature alignment strategy and an attention-guided mechanism to provide a targeted learning trajectory for the student model. We emphasize spectral embedding (SE) as a key technique in our distillation process, which merges the student's feature space with the relational knowledge and structural complexities similar to the teacher network. This method captures the teacher's understanding in a graph-based representation, enabling the student model to more accurately mimic the complex structural dependencies present in the teacher model. Compared to methods that focus only on specific distillation areas, our strategy not only considers key features within the teacher model but also endeavors to capture the relationships and interactions among feature sets, encoding these complex pieces of information into a graph structure to understand and utilize the dynamic relationships among these pieces of information from a global perspective. Experiments show that our method outperforms previous feature distillation methods on the CIFAR-100, MS-COCO, and Pascal VOC datasets, proving its efficiency and applicability.

Initialization is Critical to Whether Transformers Fit Composite Functions by Inference or Memorizing

Transformers have shown impressive capabilities across various tasks, but their performance on compositional problems remains a topic of debate. In this work, we investigate the mechanisms of how transformers behave on unseen compositional tasks using anchor functions. We discover that the parameter initialization scale plays a critical role in determining whether the model learns inferential solutions, which capture the underlying compositional primitives, or symmetric solutions, which simply memorize mappings without understanding the compositional structure. By analyzing the information flow and vector representations within the model, we reveal the distinct mechanisms underlying these solution types. We further find that inferential solutions exhibit low complexity bias, which we hypothesize is a key factor enabling them to learn individual mappings for single anchors. Building upon our understanding of these mechanisms, we can predict the learning behavior of models with different initialization scales when faced with data of varying inferential complexity. Our findings provide valuable insights into the role of initialization scale in shaping the type of solution learned by transformers and their ability to learn and generalize compositional functions.

StyleSeg V2: Towards Robust One-shot Segmentation of Brain Tissue via Optimization-free Registration Error Perception

One-shot segmentation of brain tissue requires training registration-segmentation (reg-seg) dual-model iteratively, where reg-model aims to provide pseudo masks of unlabeled images for seg-model by warping a carefully-labeled atlas. However, the imperfect reg-model induces image-mask misalignment, poisoning the seg-model subsequently. Recent StyleSeg bypasses this bottleneck by replacing the unlabeled images with their warped copies of atlas, but needs to borrow the diverse image patterns via style transformation. Here, we present StyleSeg V2, inherited from StyleSeg but granted the ability of perceiving the registration errors. The motivation is that good registration behaves in a mirrored fashion for mirrored images. Therefore, almost at no cost, StyleSeg V2 can have reg-model itself "speak out" incorrectly-aligned regions by simply mirroring (symmetrically flipping the brain) its input, and the registration errors are symmetric inconsistencies between the outputs of original and mirrored inputs. Consequently, StyleSeg V2 allows the seg-model to make use of correctly-aligned regions of unlabeled images and also enhances the fidelity of style-transformed warped atlas image by weighting the local transformation strength according to registration errors. The experimental results on three public datasets demonstrate that our proposed StyleSeg V2 outperforms other state-of-the-arts by considerable margins, and exceeds StyleSeg by increasing the average Dice by at least 2.4%.

Loss Jump During Loss Switch in Solving PDEs with Neural Networks

Using neural networks to solve partial differential equations (PDEs) is gaining popularity as an alternative approach in the scientific computing community. Neural networks can integrate different types of information into the loss function. These include observation data, governing equations, and variational forms, etc. These loss functions can be broadly categorized into two types: observation data loss directly constrains and measures the model output, while other loss functions indirectly model the performance of the network, which can be classified as model loss. However, this alternative approach lacks a thorough understanding of its underlying mechanisms, including theoretical foundations and rigorous characterization of various phenomena. This work focuses on investigating how different loss functions impact the training of neural networks for solving PDEs. We discover a stable loss-jump phenomenon: when switching the loss function from the data loss to the model loss, which includes different orders of derivative information, the neural network solution significantly deviates from the exact solution immediately. Further experiments reveal that this phenomenon arises from the different frequency preferences of neural networks under different loss functions. We theoretically analyze the frequency preference of neural networks under model loss. This loss-jump phenomenon provides a valuable perspective for examining the underlying mechanisms of neural networks in solving PDEs.

MonoPCC: Photometric-invariant Cycle Constraint for Monocular Depth Estimation of Endoscopic Images

Photometric constraint is indispensable for self-supervised monocular depth estimation. It involves warping a source image onto a target view using estimated depth&pose, and then minimizing the difference between the warped and target images. However, the endoscopic built-in light causes significant brightness fluctuations, and thus makes the photometric constraint unreliable. Previous efforts only mitigate this relying on extra models to calibrate image brightness. In this paper, we propose MonoPCC to address the brightness inconsistency radically by reshaping the photometric constraint into a cycle form. Instead of only warping the source image, MonoPCC constructs a closed loop consisting of two opposite forward-backward warping paths: from target to source and then back to target. Thus, the target image finally receives an image cycle-warped from itself, which naturally makes the constraint invariant to brightness changes. Moreover, MonoPCC transplants the source image's phase-frequency into the intermediate warped image to avoid structure lost, and also stabilizes the training via an exponential moving average (EMA) strategy to avoid frequent changes in the forward warping. The comprehensive and extensive experimental results on three datasets demonstrate that our proposed MonoPCC shows a great robustness to the brightness inconsistency, and exceeds other state-of-the-arts by reducing the absolute relative error by at least 7.27%.