Daily Papers

In healthcare, medical image segmentation is crucial for accurate disease diagnosis and the development of effective treatment strategies. Early detection can significantly aid in managing diseases and potentially prevent their progression. Machine learning, particularly deep convolutional neural networks, has emerged as a promising approach to addressing segmentation challenges. Traditional methods like U-Net use encoding blocks for local representation modeling and decoding blocks to uncover semantic relationships. However, these models often struggle with multi-scale objects exhibiting significant variations in texture and shape, and they frequently fail to capture long-range dependencies in the input data. Transformers designed for sequence-to-sequence predictions have been proposed as alternatives, utilizing global self-attention mechanisms. Yet, they can sometimes lack precise localization due to insufficient granular details. To overcome these limitations, we introduce TransDAE: a novel approach that reimagines the self-attention mechanism to include both spatial and channel-wise associations across the entire feature space, while maintaining computational efficiency. Additionally, TransDAE enhances the skip connection pathway with an inter-scale interaction module, promoting feature reuse and improving localization accuracy. Remarkably, TransDAE outperforms existing state-of-the-art methods on the Synaps multi-organ dataset, even without relying on pre-trained weights.

In this paper, we present UNet++, a new, more powerful architecture for medical image segmentation. Our architecture is essentially a deeply-supervised encoder-decoder network where the encoder and decoder sub-networks are connected through a series of nested, dense skip pathways. The re-designed skip pathways aim at reducing the semantic gap between the feature maps of the encoder and decoder sub-networks. We argue that the optimizer would deal with an easier learning task when the feature maps from the decoder and encoder networks are semantically similar. We have evaluated UNet++ in comparison with U-Net and wide U-Net architectures across multiple medical image segmentation tasks: nodule segmentation in the low-dose CT scans of chest, nuclei segmentation in the microscopy images, liver segmentation in abdominal CT scans, and polyp segmentation in colonoscopy videos. Our experiments demonstrate that UNet++ with deep supervision achieves an average IoU gain of 3.9 and 3.4 points over U-Net and wide U-Net, respectively.

Message passing neural networks (MPNNs) have been shown to suffer from the phenomenon of over-squashing that causes poor performance for tasks relying on long-range interactions. This can be largely attributed to message passing only occurring locally, over a node's immediate neighbours. Rewiring approaches attempting to make graphs 'more connected', and supposedly better suited to long-range tasks, often lose the inductive bias provided by distance on the graph since they make distant nodes communicate instantly at every layer. In this paper we propose a framework, applicable to any MPNN architecture, that performs a layer-dependent rewiring to ensure gradual densification of the graph. We also propose a delay mechanism that permits skip connections between nodes depending on the layer and their mutual distance. We validate our approach on several long-range tasks and show that it outperforms graph Transformers and multi-hop MPNNs.

Melanoma is caused by the abnormal growth of melanocytes in human skin. Like other cancers, this life-threatening skin cancer can be treated with early diagnosis. To support a diagnosis by automatic skin lesion segmentation, several Fully Convolutional Network (FCN) approaches, specifically the U-Net architecture, have been proposed. The U-Net model with a symmetrical architecture has exhibited superior performance in the segmentation task. However, the locality restriction of the convolutional operation incorporated in the U-Net architecture limits its performance in capturing long-range dependency, which is crucial for the segmentation task in medical images. To address this limitation, recently a Transformer based U-Net architecture that replaces the CNN blocks with the Swin Transformer module has been proposed to capture both local and global representation. In this paper, we propose Att-SwinU-Net, an attention-based Swin U-Net extension, for medical image segmentation. In our design, we seek to enhance the feature re-usability of the network by carefully designing the skip connection path. We argue that the classical concatenation operation utilized in the skip connection path can be further improved by incorporating an attention mechanism. By performing a comprehensive ablation study on several skin lesion segmentation datasets, we demonstrate the effectiveness of our proposed attention mechanism.

Segmentation of biomedical images can assist radiologists to make a better diagnosis and take decisions faster by helping in the detection of abnormalities, such as tumors. Manual or semi-automated segmentation, however, can be a time-consuming task. Most deep learning based automated segmentation methods are supervised and rely on manually segmented ground-truth. A possible solution for the problem would be an unsupervised deep learning based approach for automated segmentation, which this research work tries to address. We use a W-Net architecture and modified it, such that it can be applied to 3D volumes. In addition, to suppress noise in the segmentation we added attention gates to the skip connections. The loss for the segmentation output was calculated using soft N-Cuts and for the reconstruction output using SSIM. Conditional Random Fields were used as a post-processing step to fine-tune the results. The proposed method has shown promising results, with a dice coefficient of 0.88 for the liver segmentation compared against manual segmentation.

With the incorporation of the UNet architecture, diffusion probabilistic models have become a dominant force in image generation tasks. One key design in UNet is the skip connections between the encoder and decoder blocks. Although skip connections have been shown to improve training stability and model performance, we reveal that such shortcuts can be a limiting factor for the complexity of the transformation. As the sampling steps decrease, the generation process and the role of the UNet get closer to the push-forward transformations from Gaussian distribution to the target, posing a challenge for the network's complexity. To address this challenge, we propose Skip-Tuning, a simple yet surprisingly effective training-free tuning method on the skip connections. Our method can achieve 100% FID improvement for pretrained EDM on ImageNet 64 with only 19 NFEs (1.75), breaking the limit of ODE samplers regardless of sampling steps. Surprisingly, the improvement persists when we increase the number of sampling steps and can even surpass the best result from EDM-2 (1.58) with only 39 NFEs (1.57). Comprehensive exploratory experiments are conducted to shed light on the surprising effectiveness. We observe that while Skip-Tuning increases the score-matching losses in the pixel space, the losses in the feature space are reduced, particularly at intermediate noise levels, which coincide with the most effective range accounting for image quality improvement.

Anatomical segmentation is a fundamental task in medical image computing, generally tackled with fully convolutional neural networks which produce dense segmentation masks. These models are often trained with loss functions such as cross-entropy or Dice, which assume pixels to be independent of each other, thus ignoring topological errors and anatomical inconsistencies. We address this limitation by moving from pixel-level to graph representations, which allow to naturally incorporate anatomical constraints by construction. To this end, we introduce HybridGNet, an encoder-decoder neural architecture that leverages standard convolutions for image feature encoding and graph convolutional neural networks (GCNNs) to decode plausible representations of anatomical structures. We also propose a novel image-to-graph skip connection layer which allows localized features to flow from standard convolutional blocks to GCNN blocks, and show that it improves segmentation accuracy. The proposed architecture is extensively evaluated in a variety of domain shift and image occlusion scenarios, and audited considering different types of demographic domain shift. Our comprehensive experimental setup compares HybridGNet with other landmark and pixel-based models for anatomical segmentation in chest x-ray images, and shows that it produces anatomically plausible results in challenging scenarios where other models tend to fail.

Data and pipeline parallelism are ubiquitous for training of Large Language Models (LLM) on distributed nodes. Driven by the need for cost-effective training, recent work explores efficient communication arrangement for end to end training. Motivated by LLM's resistance to layer skipping and layer reordering, in this paper, we explore stage (several consecutive layers) skipping in pipeline training, and challenge the conventional practice of sequential pipeline execution. We derive convergence and throughput constraints (guidelines) for pipelining with skipping and swapping pipeline stages. Based on these constraints, we propose SkipPipe, the first partial pipeline framework to reduce the end-to-end training time for LLMs while preserving the convergence. The core of SkipPipe is a path scheduling algorithm that optimizes the paths for individual microbatches and reduces idle time (due to microbatch collisions) on the distributed nodes, complying with the given stage skipping ratio. We extensively evaluate SkipPipe on LLaMa models from 500M to 8B parameters on up to 20 nodes. Our results show that SkipPipe reduces training iteration time by up to 55% compared to full pipeline. Our partial pipeline training also improves resistance to layer omission during inference, experiencing a drop in perplexity of only 7% when running only half the model. Our code is available at https://github.com/gensyn-ai/skippipe.

Prompt tuning (PT) has long been recognized as an effective and efficient paradigm for transferring large pre-trained vision-language models (VLMs) to downstream tasks by learning a tiny set of context vectors. Nevertheless, in this work, we reveal that freezing the parameters of VLMs during learning the context vectors neither facilitates the transferability of pre-trained knowledge nor improves the memory and time efficiency significantly. Upon further investigation, we find that reducing both the length and width of the feature-gradient propagation flows of the full fine-tuning (FT) baseline is key to achieving effective and efficient knowledge transfer. Motivated by this, we propose Skip Tuning, a novel paradigm for adapting VLMs to downstream tasks. Unlike existing PT or adapter-based methods, Skip Tuning applies Layer-wise Skipping (LSkip) and Class-wise Skipping (CSkip) upon the FT baseline without introducing extra context vectors or adapter modules. Extensive experiments across a wide spectrum of benchmarks demonstrate the superior effectiveness and efficiency of our Skip Tuning over both PT and adapter-based methods. Code: https://github.com/Koorye/SkipTuning.

With the advent of AI and computer vision techniques, the quest for automated and efficient floor plan designs has gained momentum. This paper presents a novel approach using skip-connected neural networks integrated with layout graphs. The skip-connected layers capture multi-scale floor plan information, and the encoder-decoder networks with GNN facilitate pixel-level probability-based generation. Validated on the MSD dataset, our approach achieved a 93.9 mIoU score in the 1st CVAAD workshop challenge. Code and pre-trained models are publicly available at https://github.com/yuntaeJ/SkipNet-FloorPlanGe.

We present SlowFast networks for video recognition. Our model involves (i) a Slow pathway, operating at low frame rate, to capture spatial semantics, and (ii) a Fast pathway, operating at high frame rate, to capture motion at fine temporal resolution. The Fast pathway can be made very lightweight by reducing its channel capacity, yet can learn useful temporal information for video recognition. Our models achieve strong performance for both action classification and detection in video, and large improvements are pin-pointed as contributions by our SlowFast concept. We report state-of-the-art accuracy on major video recognition benchmarks, Kinetics, Charades and AVA. Code has been made available at: https://github.com/facebookresearch/SlowFast

Multi-layer perceptrons (MLPs) conventionally follow a narrow-wide-narrow design where skip connections operate at the input/output dimensions while processing occurs in expanded hidden spaces. We challenge this convention by proposing wide-narrow-wide (Hourglass) MLP blocks where skip connections operate at expanded dimensions while residual computation flows through narrow bottlenecks. This inversion leverages higher-dimensional spaces for incremental refinement while maintaining computational efficiency through parameter-matched designs. Implementing Hourglass MLPs requires an initial projection to lift input signals to expanded dimensions. We propose that this projection can remain fixed at random initialization throughout training, enabling efficient training and inference implementations. We evaluate both architectures on generative tasks over popular image datasets, characterizing performance-parameter Pareto frontiers through systematic architectural search. Results show that Hourglass architectures consistently achieve superior Pareto frontiers compared to conventional designs. As parameter budgets increase, optimal Hourglass configurations favor deeper networks with wider skip connections and narrower bottlenecks-a scaling pattern distinct from conventional MLPs. Our findings suggest reconsidering skip connection placement in modern architectures, with potential applications extending to Transformers and other residual networks.

Fiber tractography is a cornerstone of neuroimaging, enabling the detailed mapping of the brain's white matter pathways through diffusion MRI. This is crucial for understanding brain connectivity and function, making it a valuable tool in neurological applications. Despite its importance, tractography faces challenges due to its complexity and susceptibility to false positives, misrepresenting vital pathways. To address these issues, recent strategies have shifted towards deep learning, utilizing supervised learning, which depends on precise ground truth, or reinforcement learning, which operates without it. In this work, we propose Tract-RLFormer, a network utilizing both supervised and reinforcement learning, in a two-stage policy refinement process that markedly improves the accuracy and generalizability across various data-sets. By employing a tract-specific approach, our network directly delineates the tracts of interest, bypassing the traditional segmentation process. Through rigorous validation on datasets such as TractoInferno, HCP, and ISMRM-2015, our methodology demonstrates a leap forward in tractography, showcasing its ability to accurately map the brain's white matter tracts.

While deeper convolutional networks are needed to achieve maximum accuracy in visual perception tasks, for many inputs shallower networks are sufficient. We exploit this observation by learning to skip convolutional layers on a per-input basis. We introduce SkipNet, a modified residual network, that uses a gating network to selectively skip convolutional blocks based on the activations of the previous layer. We formulate the dynamic skipping problem in the context of sequential decision making and propose a hybrid learning algorithm that combines supervised learning and reinforcement learning to address the challenges of non-differentiable skipping decisions. We show SkipNet reduces computation by 30-90% while preserving the accuracy of the original model on four benchmark datasets and outperforms the state-of-the-art dynamic networks and static compression methods. We also qualitatively evaluate the gating policy to reveal a relationship between image scale and saliency and the number of layers skipped.