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Dec 11

Dilated convolution with learnable spacings

Recent works indicate that convolutional neural networks (CNN) need large receptive fields (RF) to compete with visual transformers and their attention mechanism. In CNNs, RFs can simply be enlarged by increasing the convolution kernel sizes. Yet the number of trainable parameters, which scales quadratically with the kernel's size in the 2D case, rapidly becomes prohibitive, and the training is notoriously difficult. This paper presents a new method to increase the RF size without increasing the number of parameters. The dilated convolution (DC) has already been proposed for the same purpose. DC can be seen as a convolution with a kernel that contains only a few non-zero elements placed on a regular grid. Here we present a new version of the DC in which the spacings between the non-zero elements, or equivalently their positions, are no longer fixed but learnable via backpropagation thanks to an interpolation technique. We call this method "Dilated Convolution with Learnable Spacings" (DCLS) and generalize it to the n-dimensional convolution case. However, our main focus here will be on the 2D case. We first tried our approach on ResNet50: we drop-in replaced the standard convolutions with DCLS ones, which increased the accuracy of ImageNet1k classification at iso-parameters, but at the expense of the throughput. Next, we used the recent ConvNeXt state-of-the-art convolutional architecture and drop-in replaced the depthwise convolutions with DCLS ones. This not only increased the accuracy of ImageNet1k classification but also of typical downstream and robustness tasks, again at iso-parameters but this time with negligible cost on throughput, as ConvNeXt uses separable convolutions. Conversely, classic DC led to poor performance with both ResNet50 and ConvNeXt. The code of the method is available at: https://github.com/K-H-Ismail/Dilated-Convolution-with-Learnable-Spacings-PyTorch.

  • 3 authors
·
Dec 7, 2021

Optimal Weighted Convolution for Classification and Denosing

We introduce a novel weighted convolution operator that enhances traditional convolutional neural networks (CNNs) by integrating a spatial density function into the convolution operator. This extension enables the network to differentially weight neighbouring pixels based on their relative position to the reference pixel, improving spatial characterisation and feature extraction. The proposed operator maintains the same number of trainable parameters and is fully compatible with existing CNN architectures. Although developed for 2D image data, the framework is generalisable to signals on regular grids of arbitrary dimensions, such as 3D volumetric data or 1D time series. We propose an efficient implementation of the weighted convolution by pre-computing the density function and achieving execution times comparable to standard convolution layers. We evaluate our method on two deep learning tasks: image classification using the CIFAR-100 dataset [KH+09] and image denoising using the DIV2K dataset [AT17]. Experimental results with state-of-the-art classification (e.g., VGG [SZ15], ResNet [HZRS16]) and denoising (e.g., DnCNN [ZZC+17], NAFNet [CCZS22]) methods show that the weighted convolution improves performance with respect to standard convolution across different quantitative metrics. For example, VGG achieves an accuracy of 66.94% with weighted convolution versus 56.89% with standard convolution on the classification problem, while DnCNN improves the PSNR value from 20.17 to 22.63 on the denoising problem. All models were trained on the CINECA Leonardo cluster to reduce the execution time and improve the tuning of the density function values. The PyTorch implementation of the weighted convolution is publicly available at: https://github.com/cammarasana123/weightedConvolution2.0.

  • 2 authors
·
May 30

Improving anatomical plausibility in medical image segmentation via hybrid graph neural networks: applications to chest x-ray analysis

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.

  • 5 authors
·
Mar 21, 2022

SkyReconNet: A Cross-Resolution Contextual Integration Framework for Inpainting with Application to Enhanced CMB Map Reconstruction

We introduce a novel neural network, SkyReconNet, which combines the expanded receptive fields of dilated convolutional layers along with standard convolutions, to capture both the global and local features for reconstructing the missing information in an image. We implement our network to inpaint the masked regions in a full-sky Cosmic Microwave Background (CMB) map. Inpainting CMB maps is a particularly formidable challenge when dealing with extensive and irregular masks, such as galactic masks which can obscure substantial fractions of the sky. The hybrid design of SkyReconNet leverages the strengths of standard and dilated convolutions to accurately predict CMB fluctuations in the masked regions, by effectively utilizing the information from surrounding unmasked areas. During training, the network optimizes its weights by minimizing a composite loss function that combines the Structural Similarity Index Measure (SSIM) and mean squared error (MSE). SSIM preserves the essential structural features of the CMB, ensuring an accurate and coherent reconstruction of the missing CMB fluctuations, while MSE minimizes the pixel-wise deviations, enhancing the overall accuracy of the predictions. The predicted CMB maps and their corresponding angular power spectra align closely with the targets, achieving the performance limited only by the fundamental uncertainty of cosmic variance. The network's generic architecture enables application to other physics-based challenges involving data with missing or defective pixels, systematic artefacts etc. Our results demonstrate its effectiveness in addressing the challenges posed by large irregular masks, offering a significant inpainting tool not only for CMB analyses but also for image-based experiments across disciplines where such data imperfections are prevalent.

  • 3 authors
·
Jan 10

Dilated Convolution with Learnable Spacings

This thesis presents and evaluates the Dilated Convolution with Learnable Spacings (DCLS) method. Through various supervised learning experiments in the fields of computer vision, audio, and speech processing, the DCLS method proves to outperform both standard and advanced convolution techniques. The research is organized into several steps, starting with an analysis of the literature and existing convolution techniques that preceded the development of the DCLS method. We were particularly interested in the methods that are closely related to our own and that remain essential to capture the nuances and uniqueness of our approach. The cornerstone of our study is the introduction and application of the DCLS method to convolutional neural networks (CNNs), as well as to hybrid architectures that rely on both convolutional and visual attention approaches. DCLS is shown to be particularly effective in tasks such as classification, semantic segmentation, and object detection. Initially using bilinear interpolation, the study also explores other interpolation methods, finding that Gaussian interpolation slightly improves performance. The DCLS method is further applied to spiking neural networks (SNNs) to enable synaptic delay learning within a neural network that could eventually be transferred to so-called neuromorphic chips. The results show that the DCLS method stands out as a new state-of-the-art technique in SNN audio classification for certain benchmark tasks in this field. These tasks involve datasets with a high temporal component. In addition, we show that DCLS can significantly improve the accuracy of artificial neural networks for the multi-label audio classification task. We conclude with a discussion of the chosen experimental setup, its limitations, the limitations of our method, and our results.

  • 1 authors
·
Aug 10, 2024

MOAT: Alternating Mobile Convolution and Attention Brings Strong Vision Models

This paper presents MOAT, a family of neural networks that build on top of MObile convolution (i.e., inverted residual blocks) and ATtention. Unlike the current works that stack separate mobile convolution and transformer blocks, we effectively merge them into a MOAT block. Starting with a standard Transformer block, we replace its multi-layer perceptron with a mobile convolution block, and further reorder it before the self-attention operation. The mobile convolution block not only enhances the network representation capacity, but also produces better downsampled features. Our conceptually simple MOAT networks are surprisingly effective, achieving 89.1% / 81.5% top-1 accuracy on ImageNet-1K / ImageNet-1K-V2 with ImageNet22K pretraining. Additionally, MOAT can be seamlessly applied to downstream tasks that require large resolution inputs by simply converting the global attention to window attention. Thanks to the mobile convolution that effectively exchanges local information between pixels (and thus cross-windows), MOAT does not need the extra window-shifting mechanism. As a result, on COCO object detection, MOAT achieves 59.2% box AP with 227M model parameters (single-scale inference, and hard NMS), and on ADE20K semantic segmentation, MOAT attains 57.6% mIoU with 496M model parameters (single-scale inference). Finally, the tiny-MOAT family, obtained by simply reducing the channel sizes, also surprisingly outperforms several mobile-specific transformer-based models on ImageNet. The tiny-MOAT family is also benchmarked on downstream tasks, serving as a baseline for the community. We hope our simple yet effective MOAT will inspire more seamless integration of convolution and self-attention. Code is publicly available.

  • 8 authors
·
Oct 4, 2022

Adaptive Rotated Convolution for Rotated Object Detection

Rotated object detection aims to identify and locate objects in images with arbitrary orientation. In this scenario, the oriented directions of objects vary considerably across different images, while multiple orientations of objects exist within an image. This intrinsic characteristic makes it challenging for standard backbone networks to extract high-quality features of these arbitrarily orientated objects. In this paper, we present Adaptive Rotated Convolution (ARC) module to handle the aforementioned challenges. In our ARC module, the convolution kernels rotate adaptively to extract object features with varying orientations in different images, and an efficient conditional computation mechanism is introduced to accommodate the large orientation variations of objects within an image. The two designs work seamlessly in rotated object detection problem. Moreover, ARC can conveniently serve as a plug-and-play module in various vision backbones to boost their representation ability to detect oriented objects accurately. Experiments on commonly used benchmarks (DOTA and HRSC2016) demonstrate that equipped with our proposed ARC module in the backbone network, the performance of multiple popular oriented object detectors is significantly improved (e.g. +3.03% mAP on Rotated RetinaNet and +4.16% on CFA). Combined with the highly competitive method Oriented R-CNN, the proposed approach achieves state-of-the-art performance on the DOTA dataset with 81.77% mAP.

  • 9 authors
·
Mar 14, 2023 1

What Makes Convolutional Models Great on Long Sequence Modeling?

Convolutional models have been widely used in multiple domains. However, most existing models only use local convolution, making the model unable to handle long-range dependency efficiently. Attention overcomes this problem by aggregating global information but also makes the computational complexity quadratic to the sequence length. Recently, Gu et al. [2021] proposed a model called S4 inspired by the state space model. S4 can be efficiently implemented as a global convolutional model whose kernel size equals the input sequence length. S4 can model much longer sequences than Transformers and achieve significant gains over SoTA on several long-range tasks. Despite its empirical success, S4 is involved. It requires sophisticated parameterization and initialization schemes. As a result, S4 is less intuitive and hard to use. Here we aim to demystify S4 and extract basic principles that contribute to the success of S4 as a global convolutional model. We focus on the structure of the convolution kernel and identify two critical but intuitive principles enjoyed by S4 that are sufficient to make up an effective global convolutional model: 1) The parameterization of the convolutional kernel needs to be efficient in the sense that the number of parameters should scale sub-linearly with sequence length. 2) The kernel needs to satisfy a decaying structure that the weights for convolving with closer neighbors are larger than the more distant ones. Based on the two principles, we propose a simple yet effective convolutional model called Structured Global Convolution (SGConv). SGConv exhibits strong empirical performance over several tasks: 1) With faster speed, SGConv surpasses S4 on Long Range Arena and Speech Command datasets. 2) When plugging SGConv into standard language and vision models, it shows the potential to improve both efficiency and performance.

  • 5 authors
·
Oct 17, 2022

Spherical convolutions on molecular graphs for protein model quality assessment

Processing information on 3D objects requires methods stable to rigid-body transformations, in particular rotations, of the input data. In image processing tasks, convolutional neural networks achieve this property using rotation-equivariant operations. However, contrary to images, graphs generally have irregular topology. This makes it challenging to define a rotation-equivariant convolution operation on these structures. In this work, we propose Spherical Graph Convolutional Network (S-GCN) that processes 3D models of proteins represented as molecular graphs. In a protein molecule, individual amino acids have common topological elements. This allows us to unambiguously associate each amino acid with a local coordinate system and construct rotation-equivariant spherical filters that operate on angular information between graph nodes. Within the framework of the protein model quality assessment problem, we demonstrate that the proposed spherical convolution method significantly improves the quality of model assessment compared to the standard message-passing approach. It is also comparable to state-of-the-art methods, as we demonstrate on Critical Assessment of Structure Prediction (CASP) benchmarks. The proposed technique operates only on geometric features of protein 3D models. This makes it universal and applicable to any other geometric-learning task where the graph structure allows constructing local coordinate systems.

  • 3 authors
·
Nov 16, 2020

Compressed Convolutional Attention: Efficient Attention in a Compressed Latent Space

Multi-headed Attention's (MHA) quadratic compute and linearly growing KV-cache make long-context transformers expensive to train and serve. Prior works such as Grouped Query Attention (GQA) and Multi-Latent Attention (MLA) shrink the cache, speeding decode, but leave compute, which determines prefill and training speed, largely unchanged. We introduce Compressed Convolutional Attention (CCA), a novel attention method which down-projects queries, keys, and values and performs the entire attention operation inside the shared latent space. This simple design dramatically cuts parameters, KV-cache, and FLOPs all at once by the desired compression factor. Because CCA is orthogonal to head-sharing, we combine the two to form Compressed Convolutional Grouped Query Attention (CCGQA), which further tightens the compute-bandwidth Pareto frontier so that users can tune compression toward either FLOP or memory limits without sacrificing quality. Experiments show that CCGQA consistently outperforms both GQA and MLA at equal KV-cache compression on dense and MoE models. Additionally, we show that CCGQA outperforms all other attention methods on MoE models with half the KV-cache of GQA and MLA, achieving an 8x KV-cache compression with no drop in performance compared to standard MHA. CCA and CCGQA also dramatically reduce the FLOP cost of attention which leads to substantially faster training and prefill than existing methods. On H100 GPUs, our fused CCA/CCGQA kernel reduces prefill latency by about 1.7x at a sequence length of 16k relative to MHA, and accelerates backward by about 1.3x.

  • 5 authors
·
Oct 6

TiC: Exploring Vision Transformer in Convolution

While models derived from Vision Transformers (ViTs) have been phonemically surging, pre-trained models cannot seamlessly adapt to arbitrary resolution images without altering the architecture and configuration, such as sampling the positional encoding, limiting their flexibility for various vision tasks. For instance, the Segment Anything Model (SAM) based on ViT-Huge requires all input images to be resized to 1024times1024. To overcome this limitation, we propose the Multi-Head Self-Attention Convolution (MSA-Conv) that incorporates Self-Attention within generalized convolutions, including standard, dilated, and depthwise ones. Enabling transformers to handle images of varying sizes without retraining or rescaling, the use of MSA-Conv further reduces computational costs compared to global attention in ViT, which grows costly as image size increases. Later, we present the Vision Transformer in Convolution (TiC) as a proof of concept for image classification with MSA-Conv, where two capacity enhancing strategies, namely Multi-Directional Cyclic Shifted Mechanism and Inter-Pooling Mechanism, have been proposed, through establishing long-distance connections between tokens and enlarging the effective receptive field. Extensive experiments have been carried out to validate the overall effectiveness of TiC. Additionally, ablation studies confirm the performance improvement made by MSA-Conv and the two capacity enhancing strategies separately. Note that our proposal aims at studying an alternative to the global attention used in ViT, while MSA-Conv meets our goal by making TiC comparable to state-of-the-art on ImageNet-1K. Code will be released at https://github.com/zs670980918/MSA-Conv.

  • 4 authors
·
Oct 6, 2023

ConvShareViT: Enhancing Vision Transformers with Convolutional Attention Mechanisms for Free-Space Optical Accelerators

This paper introduces ConvShareViT, a novel deep learning architecture that adapts Vision Transformers (ViTs) to the 4f free-space optical system. ConvShareViT replaces linear layers in multi-head self-attention (MHSA) and Multilayer Perceptrons (MLPs) with a depthwise convolutional layer with shared weights across input channels. Through the development of ConvShareViT, the behaviour of convolutions within MHSA and their effectiveness in learning the attention mechanism were analysed systematically. Experimental results demonstrate that certain configurations, particularly those using valid-padded shared convolutions, can successfully learn attention, achieving comparable attention scores to those obtained with standard ViTs. However, other configurations, such as those using same-padded convolutions, show limitations in attention learning and operate like regular CNNs rather than transformer models. ConvShareViT architectures are specifically optimised for the 4f optical system, which takes advantage of the parallelism and high-resolution capabilities of optical systems. Results demonstrate that ConvShareViT can theoretically achieve up to 3.04 times faster inference than GPU-based systems. This potential acceleration makes ConvShareViT an attractive candidate for future optical deep learning applications and proves that our ViT (ConvShareViT) can be employed using only the convolution operation, via the necessary optimisation of the ViT to balance performance and complexity.

  • 3 authors
·
Apr 15

Towards Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-based Convolutional Encoders

In line with recent advances in neural drug design and sensitivity prediction, we propose a novel architecture for interpretable prediction of anticancer compound sensitivity using a multimodal attention-based convolutional encoder. Our model is based on the three key pillars of drug sensitivity: compounds' structure in the form of a SMILES sequence, gene expression profiles of tumors and prior knowledge on intracellular interactions from protein-protein interaction networks. We demonstrate that our multiscale convolutional attention-based (MCA) encoder significantly outperforms a baseline model trained on Morgan fingerprints, a selection of encoders based on SMILES as well as previously reported state of the art for multimodal drug sensitivity prediction (R2 = 0.86 and RMSE = 0.89). Moreover, the explainability of our approach is demonstrated by a thorough analysis of the attention weights. We show that the attended genes significantly enrich apoptotic processes and that the drug attention is strongly correlated with a standard chemical structure similarity index. Finally, we report a case study of two receptor tyrosine kinase (RTK) inhibitors acting on a leukemia cell line, showcasing the ability of the model to focus on informative genes and submolecular regions of the two compounds. The demonstrated generalizability and the interpretability of our model testify its potential for in-silico prediction of anticancer compound efficacy on unseen cancer cells, positioning it as a valid solution for the development of personalized therapies as well as for the evaluation of candidate compounds in de novo drug design.

  • 6 authors
·
Apr 25, 2019

Barlow-Swin: Toward a novel siamese-based segmentation architecture using Swin-Transformers

Medical image segmentation is a critical task in clinical workflows, particularly for the detection and delineation of pathological regions. While convolutional architectures like U-Net have become standard for such tasks, their limited receptive field restricts global context modeling. Recent efforts integrating transformers have addressed this, but often result in deep, computationally expensive models unsuitable for real-time use. In this work, we present a novel end-to-end lightweight architecture designed specifically for real-time binary medical image segmentation. Our model combines a Swin Transformer-like encoder with a U-Net-like decoder, connected via skip pathways to preserve spatial detail while capturing contextual information. Unlike existing designs such as Swin Transformer or U-Net, our architecture is significantly shallower and competitively efficient. To improve the encoder's ability to learn meaningful features without relying on large amounts of labeled data, we first train it using Barlow Twins, a self-supervised learning method that helps the model focus on important patterns by reducing unnecessary repetition in the learned features. After this pretraining, we fine-tune the entire model for our specific task. Experiments on benchmark binary segmentation tasks demonstrate that our model achieves competitive accuracy with substantially reduced parameter count and faster inference, positioning it as a practical alternative for deployment in real-time and resource-limited clinical environments. The code for our method is available at Github repository: https://github.com/mkianih/Barlow-Swin.

  • 5 authors
·
Sep 8

Learning Features with Parameter-Free Layers

Trainable layers such as convolutional building blocks are the standard network design choices by learning parameters to capture the global context through successive spatial operations. When designing an efficient network, trainable layers such as the depthwise convolution is the source of efficiency in the number of parameters and FLOPs, but there was little improvement to the model speed in practice. This paper argues that simple built-in parameter-free operations can be a favorable alternative to the efficient trainable layers replacing spatial operations in a network architecture. We aim to break the stereotype of organizing the spatial operations of building blocks into trainable layers. Extensive experimental analyses based on layer-level studies with fully-trained models and neural architecture searches are provided to investigate whether parameter-free operations such as the max-pool are functional. The studies eventually give us a simple yet effective idea for redesigning network architectures, where the parameter-free operations are heavily used as the main building block without sacrificing the model accuracy as much. Experimental results on the ImageNet dataset demonstrate that the network architectures with parameter-free operations could enjoy the advantages of further efficiency in terms of model speed, the number of the parameters, and FLOPs. Code and ImageNet pretrained models are available at https://github.com/naver-ai/PfLayer.

  • 4 authors
·
Feb 6, 2022

AutoNeural: Co-Designing Vision-Language Models for NPU Inference

While Neural Processing Units (NPUs) offer high theoretical efficiency for edge AI, state-of-the-art Vision--Language Models (VLMs) tailored for GPUs often falter on these substrates. We attribute this hardware-model mismatch to two primary factors: the quantization brittleness of Vision Transformers (ViTs) and the I/O-bound nature of autoregressive attention mechanisms, which fail to utilize the high arithmetic throughput of NPUs. To bridge this gap, we propose AutoNeural, an NPU-native VLM architecture co-designed for integer-only inference. We replace the standard ViT encoder with a MobileNetV5-style backbone utilizing depthwise separable convolutions, which ensures bounded activation distributions for stable INT4/8/16 quantization. Complementing this, our language backbone integrates State-Space Model (SSM) principles with Transformer layers, employing efficient gated convolutions to achieve linear-time complexity. This hybrid design eliminates the heavy memory I/O overhead of Key-Value caching during generation. Our approach delivers substantial efficiency gains, reducing quantization error of vision encoder by up to 7x and end-to-end latency by 14x compared to conventional baselines. The AutoNeural also delivers 3x decoding speed and 4x longer context window than the baseline. We validate these improvements via a real-world automotive case study on the Qualcomm SA8295P SoC, demonstrating real-time performance for cockpit applications. Our results highlight that rethinking model topology specifically for NPU constraints is a prerequisite for robust multi-modal edge intelligence.

NexaAI Nexa AI
·
Dec 2 2

Multi-scale self-guided attention for medical image segmentation

Even though convolutional neural networks (CNNs) are driving progress in medical image segmentation, standard models still have some drawbacks. First, the use of multi-scale approaches, i.e., encoder-decoder architectures, leads to a redundant use of information, where similar low-level features are extracted multiple times at multiple scales. Second, long-range feature dependencies are not efficiently modeled, resulting in non-optimal discriminative feature representations associated with each semantic class. In this paper we attempt to overcome these limitations with the proposed architecture, by capturing richer contextual dependencies based on the use of guided self-attention mechanisms. This approach is able to integrate local features with their corresponding global dependencies, as well as highlight interdependent channel maps in an adaptive manner. Further, the additional loss between different modules guides the attention mechanisms to neglect irrelevant information and focus on more discriminant regions of the image by emphasizing relevant feature associations. We evaluate the proposed model in the context of semantic segmentation on three different datasets: abdominal organs, cardiovascular structures and brain tumors. A series of ablation experiments support the importance of these attention modules in the proposed architecture. In addition, compared to other state-of-the-art segmentation networks our model yields better segmentation performance, increasing the accuracy of the predictions while reducing the standard deviation. This demonstrates the efficiency of our approach to generate precise and reliable automatic segmentations of medical images. Our code is made publicly available at https://github.com/sinAshish/Multi-Scale-Attention

  • 2 authors
·
Jun 6, 2019

B-cosification: Transforming Deep Neural Networks to be Inherently Interpretable

B-cos Networks have been shown to be effective for obtaining highly human interpretable explanations of model decisions by architecturally enforcing stronger alignment between inputs and weight. B-cos variants of convolutional networks (CNNs) and vision transformers (ViTs), which primarily replace linear layers with B-cos transformations, perform competitively to their respective standard variants while also yielding explanations that are faithful by design. However, it has so far been necessary to train these models from scratch, which is increasingly infeasible in the era of large, pre-trained foundation models. In this work, inspired by the architectural similarities in standard DNNs and B-cos networks, we propose 'B-cosification', a novel approach to transform existing pre-trained models to become inherently interpretable. We perform a thorough study of design choices to perform this conversion, both for convolutional neural networks and vision transformers. We find that B-cosification can yield models that are on par with B-cos models trained from scratch in terms of interpretability, while often outperforming them in terms of classification performance at a fraction of the training cost. Subsequently, we apply B-cosification to a pretrained CLIP model, and show that, even with limited data and compute cost, we obtain a B-cosified version that is highly interpretable and competitive on zero shot performance across a variety of datasets. We release our code and pre-trained model weights at https://github.com/shrebox/B-cosification.

Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images

Semantic segmentation of brain tumors is a fundamental medical image analysis task involving multiple MRI imaging modalities that can assist clinicians in diagnosing the patient and successively studying the progression of the malignant entity. In recent years, Fully Convolutional Neural Networks (FCNNs) approaches have become the de facto standard for 3D medical image segmentation. The popular "U-shaped" network architecture has achieved state-of-the-art performance benchmarks on different 2D and 3D semantic segmentation tasks and across various imaging modalities. However, due to the limited kernel size of convolution layers in FCNNs, their performance of modeling long-range information is sub-optimal, and this can lead to deficiencies in the segmentation of tumors with variable sizes. On the other hand, transformer models have demonstrated excellent capabilities in capturing such long-range information in multiple domains, including natural language processing and computer vision. Inspired by the success of vision transformers and their variants, we propose a novel segmentation model termed Swin UNEt TRansformers (Swin UNETR). Specifically, the task of 3D brain tumor semantic segmentation is reformulated as a sequence to sequence prediction problem wherein multi-modal input data is projected into a 1D sequence of embedding and used as an input to a hierarchical Swin transformer as the encoder. The swin transformer encoder extracts features at five different resolutions by utilizing shifted windows for computing self-attention and is connected to an FCNN-based decoder at each resolution via skip connections. We have participated in BraTS 2021 segmentation challenge, and our proposed model ranks among the top-performing approaches in the validation phase. Code: https://monai.io/research/swin-unetr

  • 6 authors
·
Jan 4, 2022

IVD-Net: Intervertebral disc localization and segmentation in MRI with a multi-modal UNet

Accurate localization and segmentation of intervertebral disc (IVD) is crucial for the assessment of spine disease diagnosis. Despite the technological advances in medical imaging, IVD localization and segmentation are still manually performed, which is time-consuming and prone to errors. If, in addition, multi-modal imaging is considered, the burden imposed on disease assessments increases substantially. In this paper, we propose an architecture for IVD localization and segmentation in multi-modal MRI, which extends the well-known UNet. Compared to single images, multi-modal data brings complementary information, contributing to better data representation and discriminative power. Our contributions are three-fold. First, how to effectively integrate and fully leverage multi-modal data remains almost unexplored. In this work, each MRI modality is processed in a different path to better exploit their unique information. Second, inspired by HyperDenseNet, the network is densely-connected both within each path and across different paths, granting the model the freedom to learn where and how the different modalities should be processed and combined. Third, we improved standard U-Net modules by extending inception modules with two dilated convolutions blocks of different scale, which helps handling multi-scale context. We report experiments over the data set of the public MICCAI 2018 Challenge on Automatic Intervertebral Disc Localization and Segmentation, with 13 multi-modal MRI images used for training and 3 for validation. We trained IVD-Net on an NVidia TITAN XP GPU with 16 GBs RAM, using ADAM as optimizer and a learning rate of 10e-5 during 200 epochs. Training took about 5 hours, and segmentation of a whole volume about 2-3 seconds, on average. Several baselines, with different multi-modal fusion strategies, were used to demonstrate the effectiveness of the proposed architecture.

  • 3 authors
·
Nov 19, 2018

LoRA-based methods on Unet for transfer learning in Subarachnoid Hematoma Segmentation

Aneurysmal subarachnoid hemorrhage (SAH) is a life-threatening neurological emergency with mortality rates exceeding 30%. Transfer learning from related hematoma types represents a potentially valuable but underexplored approach. Although Unet architectures remain the gold standard for medical image segmentation due to their effectiveness on limited datasets, Low-Rank Adaptation (LoRA) methods for parameter-efficient transfer learning have been rarely applied to convolutional neural networks in medical imaging contexts. We implemented a Unet architecture pre-trained on computed tomography scans from 124 traumatic brain injury patients across multiple institutions, then fine-tuned on 30 aneurysmal SAH patients from the University of Michigan Health System using 3-fold cross-validation. We developed a novel CP-LoRA method based on tensor CP-decomposition and introduced DoRA variants (DoRA-C, convDoRA, CP-DoRA) that decompose weight matrices into magnitude and directional components. We compared these approaches against existing LoRA methods (LoRA-C, convLoRA) and standard fine-tuning strategies across different modules on a multi-view Unet model. LoRA-based methods consistently outperformed standard Unet fine-tuning. Performance varied by hemorrhage volume, with all methods showing improved accuracy for larger volumes. CP-LoRA achieved comparable performance to existing methods while using significantly fewer parameters. Over-parameterization with higher ranks consistently yielded better performance than strictly low-rank adaptations. This study demonstrates that transfer learning between hematoma types is feasible and that LoRA-based methods significantly outperform conventional Unet fine-tuning for aneurysmal SAH segmentation.

  • 7 authors
·
Aug 3

VMFormer: End-to-End Video Matting with Transformer

Video matting aims to predict the alpha mattes for each frame from a given input video sequence. Recent solutions to video matting have been dominated by deep convolutional neural networks (CNN) for the past few years, which have become the de-facto standard for both academia and industry. However, they have inbuilt inductive bias of locality and do not capture global characteristics of an image due to the CNN-based architectures. They also lack long-range temporal modeling considering computational costs when dealing with feature maps of multiple frames. In this paper, we propose VMFormer: a transformer-based end-to-end method for video matting. It makes predictions on alpha mattes of each frame from learnable queries given a video input sequence. Specifically, it leverages self-attention layers to build global integration of feature sequences with short-range temporal modeling on successive frames. We further apply queries to learn global representations through cross-attention in the transformer decoder with long-range temporal modeling upon all queries. In the prediction stage, both queries and corresponding feature maps are used to make the final prediction of alpha matte. Experiments show that VMFormer outperforms previous CNN-based video matting methods on the composited benchmarks. To our best knowledge, it is the first end-to-end video matting solution built upon a full vision transformer with predictions on the learnable queries. The project is open-sourced at https://chrisjuniorli.github.io/project/VMFormer/

  • 6 authors
·
Aug 26, 2022

More is Better in Modern Machine Learning: when Infinite Overparameterization is Optimal and Overfitting is Obligatory

In our era of enormous neural networks, empirical progress has been driven by the philosophy that more is better. Recent deep learning practice has found repeatedly that larger model size, more data, and more computation (resulting in lower training loss) improves performance. In this paper, we give theoretical backing to these empirical observations by showing that these three properties hold in random feature (RF) regression, a class of models equivalent to shallow networks with only the last layer trained. Concretely, we first show that the test risk of RF regression decreases monotonically with both the number of features and the number of samples, provided the ridge penalty is tuned optimally. In particular, this implies that infinite width RF architectures are preferable to those of any finite width. We then proceed to demonstrate that, for a large class of tasks characterized by powerlaw eigenstructure, training to near-zero training loss is obligatory: near-optimal performance can only be achieved when the training error is much smaller than the test error. Grounding our theory in real-world data, we find empirically that standard computer vision tasks with convolutional neural tangent kernels clearly fall into this class. Taken together, our results tell a simple, testable story of the benefits of overparameterization, overfitting, and more data in random feature models.

  • 4 authors
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Nov 24, 2023

DrivAerNet: A Parametric Car Dataset for Data-Driven Aerodynamic Design and Graph-Based Drag Prediction

This study introduces DrivAerNet, a large-scale high-fidelity CFD dataset of 3D industry-standard car shapes, and RegDGCNN, a dynamic graph convolutional neural network model, both aimed at aerodynamic car design through machine learning. DrivAerNet, with its 4000 detailed 3D car meshes using 0.5 million surface mesh faces and comprehensive aerodynamic performance data comprising of full 3D pressure, velocity fields, and wall-shear stresses, addresses the critical need for extensive datasets to train deep learning models in engineering applications. It is 60\% larger than the previously available largest public dataset of cars, and is the only open-source dataset that also models wheels and underbody. RegDGCNN leverages this large-scale dataset to provide high-precision drag estimates directly from 3D meshes, bypassing traditional limitations such as the need for 2D image rendering or Signed Distance Fields (SDF). By enabling fast drag estimation in seconds, RegDGCNN facilitates rapid aerodynamic assessments, offering a substantial leap towards integrating data-driven methods in automotive design. Together, DrivAerNet and RegDGCNN promise to accelerate the car design process and contribute to the development of more efficient vehicles. To lay the groundwork for future innovations in the field, the dataset and code used in our study are publicly accessible at https://github.com/Mohamedelrefaie/DrivAerNet

  • 3 authors
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Mar 12, 2024

Fast Sparse ConvNets

Historically, the pursuit of efficient inference has been one of the driving forces behind research into new deep learning architectures and building blocks. Some recent examples include: the squeeze-and-excitation module, depthwise separable convolutions in Xception, and the inverted bottleneck in MobileNet v2. Notably, in all of these cases, the resulting building blocks enabled not only higher efficiency, but also higher accuracy, and found wide adoption in the field. In this work, we further expand the arsenal of efficient building blocks for neural network architectures; but instead of combining standard primitives (such as convolution), we advocate for the replacement of these dense primitives with their sparse counterparts. While the idea of using sparsity to decrease the parameter count is not new, the conventional wisdom is that this reduction in theoretical FLOPs does not translate into real-world efficiency gains. We aim to correct this misconception by introducing a family of efficient sparse kernels for ARM and WebAssembly, which we open-source for the benefit of the community as part of the XNNPACK library. Equipped with our efficient implementation of sparse primitives, we show that sparse versions of MobileNet v1, MobileNet v2 and EfficientNet architectures substantially outperform strong dense baselines on the efficiency-accuracy curve. On Snapdragon 835 our sparse networks outperform their dense equivalents by 1.3-2.4times -- equivalent to approximately one entire generation of MobileNet-family improvement. We hope that our findings will facilitate wider adoption of sparsity as a tool for creating efficient and accurate deep learning architectures.

  • 4 authors
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Nov 21, 2019

Scale-Equalizing Pyramid Convolution for Object Detection

Feature pyramid has been an efficient method to extract features at different scales. Development over this method mainly focuses on aggregating contextual information at different levels while seldom touching the inter-level correlation in the feature pyramid. Early computer vision methods extracted scale-invariant features by locating the feature extrema in both spatial and scale dimension. Inspired by this, a convolution across the pyramid level is proposed in this study, which is termed pyramid convolution and is a modified 3-D convolution. Stacked pyramid convolutions directly extract 3-D (scale and spatial) features and outperforms other meticulously designed feature fusion modules. Based on the viewpoint of 3-D convolution, an integrated batch normalization that collects statistics from the whole feature pyramid is naturally inserted after the pyramid convolution. Furthermore, we also show that the naive pyramid convolution, together with the design of RetinaNet head, actually best applies for extracting features from a Gaussian pyramid, whose properties can hardly be satisfied by a feature pyramid. In order to alleviate this discrepancy, we build a scale-equalizing pyramid convolution (SEPC) that aligns the shared pyramid convolution kernel only at high-level feature maps. Being computationally efficient and compatible with the head design of most single-stage object detectors, the SEPC module brings significant performance improvement (>4AP increase on MS-COCO2017 dataset) in state-of-the-art one-stage object detectors, and a light version of SEPC also has sim3.5AP gain with only around 7% inference time increase. The pyramid convolution also functions well as a stand-alone module in two-stage object detectors and is able to improve the performance by sim2AP. The source code can be found at https://github.com/jshilong/SEPC.

  • 5 authors
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May 6, 2020

A ConvNet for the 2020s

The "Roaring 20s" of visual recognition began with the introduction of Vision Transformers (ViTs), which quickly superseded ConvNets as the state-of-the-art image classification model. A vanilla ViT, on the other hand, faces difficulties when applied to general computer vision tasks such as object detection and semantic segmentation. It is the hierarchical Transformers (e.g., Swin Transformers) that reintroduced several ConvNet priors, making Transformers practically viable as a generic vision backbone and demonstrating remarkable performance on a wide variety of vision tasks. However, the effectiveness of such hybrid approaches is still largely credited to the intrinsic superiority of Transformers, rather than the inherent inductive biases of convolutions. In this work, we reexamine the design spaces and test the limits of what a pure ConvNet can achieve. We gradually "modernize" a standard ResNet toward the design of a vision Transformer, and discover several key components that contribute to the performance difference along the way. The outcome of this exploration is a family of pure ConvNet models dubbed ConvNeXt. Constructed entirely from standard ConvNet modules, ConvNeXts compete favorably with Transformers in terms of accuracy and scalability, achieving 87.8% ImageNet top-1 accuracy and outperforming Swin Transformers on COCO detection and ADE20K segmentation, while maintaining the simplicity and efficiency of standard ConvNets.

  • 6 authors
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Jan 10, 2022

Quantizing deep convolutional networks for efficient inference: A whitepaper

We present an overview of techniques for quantizing convolutional neural networks for inference with integer weights and activations. Per-channel quantization of weights and per-layer quantization of activations to 8-bits of precision post-training produces classification accuracies within 2% of floating point networks for a wide variety of CNN architectures. Model sizes can be reduced by a factor of 4 by quantizing weights to 8-bits, even when 8-bit arithmetic is not supported. This can be achieved with simple, post training quantization of weights.We benchmark latencies of quantized networks on CPUs and DSPs and observe a speedup of 2x-3x for quantized implementations compared to floating point on CPUs. Speedups of up to 10x are observed on specialized processors with fixed point SIMD capabilities, like the Qualcomm QDSPs with HVX. Quantization-aware training can provide further improvements, reducing the gap to floating point to 1% at 8-bit precision. Quantization-aware training also allows for reducing the precision of weights to four bits with accuracy losses ranging from 2% to 10%, with higher accuracy drop for smaller networks.We introduce tools in TensorFlow and TensorFlowLite for quantizing convolutional networks and review best practices for quantization-aware training to obtain high accuracy with quantized weights and activations. We recommend that per-channel quantization of weights and per-layer quantization of activations be the preferred quantization scheme for hardware acceleration and kernel optimization. We also propose that future processors and hardware accelerators for optimized inference support precisions of 4, 8 and 16 bits.

  • 1 authors
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Jun 21, 2018

Existence, Stability and Scalability of Orthogonal Convolutional Neural Networks

Imposing orthogonality on the layers of neural networks is known to facilitate the learning by limiting the exploding/vanishing of the gradient; decorrelate the features; improve the robustness. This paper studies the theoretical properties of orthogonal convolutional layers.We establish necessary and sufficient conditions on the layer architecture guaranteeing the existence of an orthogonal convolutional transform. The conditions prove that orthogonal convolutional transforms exist for almost all architectures used in practice for 'circular' padding.We also exhibit limitations with 'valid' boundary conditions and 'same' boundary conditions with zero-padding.Recently, a regularization term imposing the orthogonality of convolutional layers has been proposed, and impressive empirical results have been obtained in different applications (Wang et al. 2020).The second motivation of the present paper is to specify the theory behind this.We make the link between this regularization term and orthogonality measures. In doing so, we show that this regularization strategy is stable with respect to numerical and optimization errors and that, in the presence of small errors and when the size of the signal/image is large, the convolutional layers remain close to isometric.The theoretical results are confirmed with experiments and the landscape of the regularization term is studied. Experiments on real data sets show that when orthogonality is used to enforce robustness, the parameter multiplying the regularization termcan be used to tune a tradeoff between accuracy and orthogonality, for the benefit of both accuracy and robustness.Altogether, the study guarantees that the regularization proposed in Wang et al. (2020) is an efficient, flexible and stable numerical strategy to learn orthogonal convolutional layers.

  • 3 authors
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Aug 12, 2021

DiCo: Revitalizing ConvNets for Scalable and Efficient Diffusion Modeling

Diffusion Transformer (DiT), a promising diffusion model for visual generation, demonstrates impressive performance but incurs significant computational overhead. Intriguingly, analysis of pre-trained DiT models reveals that global self-attention is often redundant, predominantly capturing local patterns-highlighting the potential for more efficient alternatives. In this paper, we revisit convolution as an alternative building block for constructing efficient and expressive diffusion models. However, naively replacing self-attention with convolution typically results in degraded performance. Our investigations attribute this performance gap to the higher channel redundancy in ConvNets compared to Transformers. To resolve this, we introduce a compact channel attention mechanism that promotes the activation of more diverse channels, thereby enhancing feature diversity. This leads to Diffusion ConvNet (DiCo), a family of diffusion models built entirely from standard ConvNet modules, offering strong generative performance with significant efficiency gains. On class-conditional ImageNet benchmarks, DiCo outperforms previous diffusion models in both image quality and generation speed. Notably, DiCo-XL achieves an FID of 2.05 at 256x256 resolution and 2.53 at 512x512, with a 2.7x and 3.1x speedup over DiT-XL/2, respectively. Furthermore, our largest model, DiCo-H, scaled to 1B parameters, reaches an FID of 1.90 on ImageNet 256x256-without any additional supervision during training. Code: https://github.com/shallowdream204/DiCo.

  • 6 authors
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May 16 2