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Dec 31

Enhancing Whole Slide Pathology Foundation Models through Stain Normalization

Recent advancements in digital pathology have led to the development of numerous foundational models that utilize self-supervised learning on patches extracted from gigapixel whole slide images (WSIs). While this approach leverages vast amounts of unlabeled data, we have discovered a significant issue: features extracted from these self-supervised models tend to cluster by individual WSIs, a phenomenon we term WSI-specific feature collapse. This problem can potentially limit the model's generalization ability and performance on various downstream tasks. To address this issue, we introduce Stain Normalized Pathology Foundational Model, a novel foundational model trained on patches that have undergone stain normalization. Stain normalization helps reduce color variability arising from different laboratories and scanners, enabling the model to learn more consistent features. Stain Normalized Pathology Foundational Model is trained using 285,153,903 patches extracted from a total of 34,795 WSIs, combining data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project. Our experiments demonstrate that Stain Normalized Pathology Foundational Model significantly mitigates the feature collapse problem, indicating that the model has learned more generalized features rather than overfitting to individual WSI characteristics. We compared Stain Normalized Pathology Foundational Model with state-of-the-art models across six downstream task datasets, and our results show that Stain Normalized Pathology Foundational Model achieves excellent performance relative to the number of WSIs used and the model's parameter count. This suggests that the application of stain normalization has substantially improved the model's efficiency and generalization capabilities.

  • 5 authors
·
Aug 1, 2024

StainNet: A Special Staining Self-Supervised Vision Transformer for Computational Pathology

Foundation models trained with self-supervised learning (SSL) on large-scale histological images have significantly accelerated the development of computational pathology. These models can serve as backbones for region-of-interest (ROI) image analysis or patch-level feature extractors in whole-slide images (WSIs) based on multiple instance learning (MIL). Existing pathology foundation models (PFMs) are typically pre-trained on Hematoxylin-Eosin (H&E) stained pathology images. However, images with special stains, such as immunohistochemistry, are also frequently used in clinical practice. PFMs pre-trained mainly on H\&E-stained images may be limited in clinical applications involving special stains. To address this issue, we propose StainNet, a specialized foundation model for special stains based on the vision transformer (ViT) architecture. StainNet adopts a self-distillation SSL approach and is trained on over 1.4 million patch images cropping from 20,231 publicly available special staining WSIs in the HISTAI database. To evaluate StainNet, we conduct experiments on an in-house slide-level liver malignancy classification task and two public ROI-level datasets to demonstrate its strong ability. We also perform few-ratio learning and retrieval evaluations, and compare StainNet with recently larger PFMs to further highlight its strengths. We have released the StainNet model weights at: https://huggingface.co/JWonderLand/StainNet.

  • 9 authors
·
Dec 11

Adaptive Supervised PatchNCE Loss for Learning H&E-to-IHC Stain Translation with Inconsistent Groundtruth Image Pairs

Immunohistochemical (IHC) staining highlights the molecular information critical to diagnostics in tissue samples. However, compared to H&E staining, IHC staining can be much more expensive in terms of both labor and the laboratory equipment required. This motivates recent research that demonstrates that the correlations between the morphological information present in the H&E-stained slides and the molecular information in the IHC-stained slides can be used for H&E-to-IHC stain translation. However, due to a lack of pixel-perfect H&E-IHC groundtruth pairs, most existing methods have resorted to relying on expert annotations. To remedy this situation, we present a new loss function, Adaptive Supervised PatchNCE (ASP), to directly deal with the input to target inconsistencies in a proposed H&E-to-IHC image-to-image translation framework. The ASP loss is built upon a patch-based contrastive learning criterion, named Supervised PatchNCE (SP), and augments it further with weight scheduling to mitigate the negative impact of noisy supervision. Lastly, we introduce the Multi-IHC Stain Translation (MIST) dataset, which contains aligned H&E-IHC patches for 4 different IHC stains critical to breast cancer diagnosis. In our experiment, we demonstrate that our proposed method outperforms existing image-to-image translation methods for stain translation to multiple IHC stains. All of our code and datasets are available at https://github.com/lifangda01/AdaptiveSupervisedPatchNCE.

  • 4 authors
·
Mar 10, 2023

Hierarchical Spatial Algorithms for High-Resolution Image Quantization and Feature Extraction

This study introduces a modular framework for spatial image processing, integrating grayscale quantization, color and brightness enhancement, image sharpening, bidirectional transformation pipelines, and geometric feature extraction. A stepwise intensity transformation quantizes grayscale images into eight discrete levels, producing a posterization effect that simplifies representation while preserving structural detail. Color enhancement is achieved via histogram equalization in both RGB and YCrCb color spaces, with the latter improving contrast while maintaining chrominance fidelity. Brightness adjustment is implemented through HSV value-channel manipulation, and image sharpening is performed using a 3 * 3 convolution kernel to enhance high-frequency details. A bidirectional transformation pipeline that integrates unsharp masking, gamma correction, and noise amplification achieved accuracy levels of 76.10% and 74.80% for the forward and reverse processes, respectively. Geometric feature extraction employed Canny edge detection, Hough-based line estimation (e.g., 51.50{\deg} for billiard cue alignment), Harris corner detection, and morphological window localization. Cue isolation further yielded 81.87\% similarity against ground truth images. Experimental evaluation across diverse datasets demonstrates robust and deterministic performance, highlighting its potential for real-time image analysis and computer vision.

  • 1 authors
·
Oct 9

Towards Image Ambient Lighting Normalization

Lighting normalization is a crucial but underexplored restoration task with broad applications. However, existing works often simplify this task within the context of shadow removal, limiting the light sources to one and oversimplifying the scene, thus excluding complex self-shadows and restricting surface classes to smooth ones. Although promising, such simplifications hinder generalizability to more realistic settings encountered in daily use. In this paper, we propose a new challenging task termed Ambient Lighting Normalization (ALN), which enables the study of interactions between shadows, unifying image restoration and shadow removal in a broader context. To address the lack of appropriate datasets for ALN, we introduce the large-scale high-resolution dataset Ambient6K, comprising samples obtained from multiple light sources and including self-shadows resulting from complex geometries, which is the first of its kind. For benchmarking, we select various mainstream methods and rigorously evaluate them on Ambient6K. Additionally, we propose IFBlend, a novel strong baseline that maximizes Image-Frequency joint entropy to selectively restore local areas under different lighting conditions, without relying on shadow localization priors. Experiments show that IFBlend achieves SOTA scores on Ambient6K and exhibits competitive performance on conventional shadow removal benchmarks compared to shadow-specific models with mask priors. The dataset, benchmark, and code are available at https://github.com/fvasluianu97/IFBlend.

  • 5 authors
·
Mar 27, 2024

StainDiffuser: MultiTask Dual Diffusion Model for Virtual Staining

Hematoxylin and Eosin (H&E) staining is widely regarded as the standard in pathology for diagnosing diseases and tracking tumor recurrence. While H&E staining shows tissue structures, it lacks the ability to reveal specific proteins that are associated with disease severity and treatment response. Immunohistochemical (IHC) stains use antibodies to highlight the expression of these proteins on their respective cell types, improving diagnostic accuracy, and assisting with drug selection for treatment. Despite their value, IHC stains require additional time and resources, limiting their utilization in some clinical settings. Recent advances in deep learning have positioned Image-to-Image (I2I) translation as a computational, cost-effective alternative for IHC. I2I generates high fidelity stain transformations digitally, potentially replacing manual staining in IHC. Diffusion models, the current state of the art in image generation and conditional tasks, are particularly well suited for virtual IHC due to their ability to produce high quality images and resilience to mode collapse. However, these models require extensive and diverse datasets (often millions of samples) to achieve a robust performance, a challenge in virtual staining applications where only thousands of samples are typically available. Inspired by the success of multitask deep learning models in scenarios with limited data, we introduce STAINDIFFUSER, a novel multitask diffusion architecture tailored to virtual staining that achieves convergence with smaller datasets. STAINDIFFUSER simultaneously trains two diffusion processes: (a) generating cell specific IHC stains from H&E images and (b) performing H&E based cell segmentation, utilizing coarse segmentation labels exclusively during training. STAINDIFFUSER generates high-quality virtual stains for two markers, outperforming over twenty I2I baselines.

  • 3 authors
·
Mar 17, 2024

Region Normalization for Image Inpainting

Feature Normalization (FN) is an important technique to help neural network training, which typically normalizes features across spatial dimensions. Most previous image inpainting methods apply FN in their networks without considering the impact of the corrupted regions of the input image on normalization, e.g. mean and variance shifts. In this work, we show that the mean and variance shifts caused by full-spatial FN limit the image inpainting network training and we propose a spatial region-wise normalization named Region Normalization (RN) to overcome the limitation. RN divides spatial pixels into different regions according to the input mask, and computes the mean and variance in each region for normalization. We develop two kinds of RN for our image inpainting network: (1) Basic RN (RN-B), which normalizes pixels from the corrupted and uncorrupted regions separately based on the original inpainting mask to solve the mean and variance shift problem; (2) Learnable RN (RN-L), which automatically detects potentially corrupted and uncorrupted regions for separate normalization, and performs global affine transformation to enhance their fusion. We apply RN-B in the early layers and RN-L in the latter layers of the network respectively. Experiments show that our method outperforms current state-of-the-art methods quantitatively and qualitatively. We further generalize RN to other inpainting networks and achieve consistent performance improvements. Our code is available at https://github.com/geekyutao/RN.

  • 8 authors
·
Nov 23, 2019

Image-to-Image Translation via Group-wise Deep Whitening-and-Coloring Transformation

Recently, unsupervised exemplar-based image-to-image translation, conditioned on a given exemplar without the paired data, has accomplished substantial advancements. In order to transfer the information from an exemplar to an input image, existing methods often use a normalization technique, e.g., adaptive instance normalization, that controls the channel-wise statistics of an input activation map at a particular layer, such as the mean and the variance. Meanwhile, style transfer approaches similar task to image translation by nature, demonstrated superior performance by using the higher-order statistics such as covariance among channels in representing a style. In detail, it works via whitening (given a zero-mean input feature, transforming its covariance matrix into the identity). followed by coloring (changing the covariance matrix of the whitened feature to those of the style feature). However, applying this approach in image translation is computationally intensive and error-prone due to the expensive time complexity and its non-trivial backpropagation. In response, this paper proposes an end-to-end approach tailored for image translation that efficiently approximates this transformation with our novel regularization methods. We further extend our approach to a group-wise form for memory and time efficiency as well as image quality. Extensive qualitative and quantitative experiments demonstrate that our proposed method is fast, both in training and inference, and highly effective in reflecting the style of an exemplar. Finally, our code is available at https://github.com/WonwoongCho/GDWCT.

  • 5 authors
·
Dec 24, 2018

Deep Line Art Video Colorization with a Few References

Coloring line art images based on the colors of reference images is an important stage in animation production, which is time-consuming and tedious. In this paper, we propose a deep architecture to automatically color line art videos with the same color style as the given reference images. Our framework consists of a color transform network and a temporal constraint network. The color transform network takes the target line art images as well as the line art and color images of one or more reference images as input, and generates corresponding target color images. To cope with larger differences between the target line art image and reference color images, our architecture utilizes non-local similarity matching to determine the region correspondences between the target image and the reference images, which are used to transform the local color information from the references to the target. To ensure global color style consistency, we further incorporate Adaptive Instance Normalization (AdaIN) with the transformation parameters obtained from a style embedding vector that describes the global color style of the references, extracted by an embedder. The temporal constraint network takes the reference images and the target image together in chronological order, and learns the spatiotemporal features through 3D convolution to ensure the temporal consistency of the target image and the reference image. Our model can achieve even better coloring results by fine-tuning the parameters with only a small amount of samples when dealing with an animation of a new style. To evaluate our method, we build a line art coloring dataset. Experiments show that our method achieves the best performance on line art video coloring compared to the state-of-the-art methods and other baselines.

  • 6 authors
·
Mar 24, 2020

ColorFlow: Retrieval-Augmented Image Sequence Colorization

Automatic black-and-white image sequence colorization while preserving character and object identity (ID) is a complex task with significant market demand, such as in cartoon or comic series colorization. Despite advancements in visual colorization using large-scale generative models like diffusion models, challenges with controllability and identity consistency persist, making current solutions unsuitable for industrial application.To address this, we propose ColorFlow, a three-stage diffusion-based framework tailored for image sequence colorization in industrial applications. Unlike existing methods that require per-ID finetuning or explicit ID embedding extraction, we propose a novel robust and generalizable Retrieval Augmented Colorization pipeline for colorizing images with relevant color references. Our pipeline also features a dual-branch design: one branch for color identity extraction and the other for colorization, leveraging the strengths of diffusion models. We utilize the self-attention mechanism in diffusion models for strong in-context learning and color identity matching. To evaluate our model, we introduce ColorFlow-Bench, a comprehensive benchmark for reference-based colorization. Results show that ColorFlow outperforms existing models across multiple metrics, setting a new standard in sequential image colorization and potentially benefiting the art industry. We release our codes and models on our project page: https://zhuang2002.github.io/ColorFlow/.

  • 7 authors
·
Dec 16, 2024 4

StableNormal: Reducing Diffusion Variance for Stable and Sharp Normal

This work addresses the challenge of high-quality surface normal estimation from monocular colored inputs (i.e., images and videos), a field which has recently been revolutionized by repurposing diffusion priors. However, previous attempts still struggle with stochastic inference, conflicting with the deterministic nature of the Image2Normal task, and costly ensembling step, which slows down the estimation process. Our method, StableNormal, mitigates the stochasticity of the diffusion process by reducing inference variance, thus producing "Stable-and-Sharp" normal estimates without any additional ensembling process. StableNormal works robustly under challenging imaging conditions, such as extreme lighting, blurring, and low quality. It is also robust against transparent and reflective surfaces, as well as cluttered scenes with numerous objects. Specifically, StableNormal employs a coarse-to-fine strategy, which starts with a one-step normal estimator (YOSO) to derive an initial normal guess, that is relatively coarse but reliable, then followed by a semantic-guided refinement process (SG-DRN) that refines the normals to recover geometric details. The effectiveness of StableNormal is demonstrated through competitive performance in standard datasets such as DIODE-indoor, iBims, ScannetV2 and NYUv2, and also in various downstream tasks, such as surface reconstruction and normal enhancement. These results evidence that StableNormal retains both the "stability" and "sharpness" for accurate normal estimation. StableNormal represents a baby attempt to repurpose diffusion priors for deterministic estimation. To democratize this, code and models have been publicly available in hf.co/Stable-X

  • 9 authors
·
Jun 24, 2024

On the Importance of Text Preprocessing for Multimodal Representation Learning and Pathology Report Generation

Vision-language models in pathology enable multimodal case retrieval and automated report generation. Many of the models developed so far, however, have been trained on pathology reports that include information which cannot be inferred from paired whole slide images (e.g., patient history), potentially leading to hallucinated sentences in generated reports. To this end, we investigate how the selection of information from pathology reports for vision-language modeling affects the quality of the multimodal representations and generated reports. More concretely, we compare a model trained on full reports against a model trained on preprocessed reports that only include sentences describing the cell and tissue appearances based on the H&E-stained slides. For the experiments, we built upon the BLIP-2 framework and used a cutaneous melanocytic lesion dataset of 42,433 H&E-stained whole slide images and 19,636 corresponding pathology reports. Model performance was assessed using image-to-text and text-to-image retrieval, as well as qualitative evaluation of the generated reports by an expert pathologist. Our results demonstrate that text preprocessing prevents hallucination in report generation. Despite the improvement in the quality of the generated reports, training the vision-language model on full reports showed better cross-modal retrieval performance.

  • 6 authors
·
Feb 26

Three-stage binarization of color document images based on discrete wavelet transform and generative adversarial networks

The efficient extraction of text information from the background in degraded color document images is an important challenge in the preservation of ancient manuscripts. The imperfect preservation of ancient manuscripts has led to different types of degradation over time, such as page yellowing, staining, and ink bleeding, seriously affecting the results of document image binarization. This work proposes an effective three-stage network method to image enhancement and binarization of degraded documents using generative adversarial networks (GANs). Specifically, in Stage-1, we first split the input images into multiple patches, and then split these patches into four single-channel patch images (gray, red, green, and blue). Then, three single-channel patch images (red, green, and blue) are processed by the discrete wavelet transform (DWT) with normalization. In Stage-2, we use four independent generators to separately train GAN models based on the four channels on the processed patch images to extract color foreground information. Finally, in Stage-3, we train two independent GAN models on the outputs of Stage-2 and the resized original input images (512x512) as the local and global predictions to obtain the final outputs. The experimental results show that the Avg-Score metrics of the proposed method are 77.64, 77.95, 79.05, 76.38, 75.34, and 77.00 on the (H)-DIBCO 2011, 2013, 2014, 2016, 2017, and 2018 datasets, which are at the state-of-the-art level. The implementation code for this work is available at https://github.com/abcpp12383/ThreeStageBinarization.

  • 6 authors
·
Nov 29, 2022

Style Injection in Diffusion: A Training-free Approach for Adapting Large-scale Diffusion Models for Style Transfer

Despite the impressive generative capabilities of diffusion models, existing diffusion model-based style transfer methods require inference-stage optimization (e.g. fine-tuning or textual inversion of style) which is time-consuming, or fails to leverage the generative ability of large-scale diffusion models. To address these issues, we introduce a novel artistic style transfer method based on a pre-trained large-scale diffusion model without any optimization. Specifically, we manipulate the features of self-attention layers as the way the cross-attention mechanism works; in the generation process, substituting the key and value of content with those of style image. This approach provides several desirable characteristics for style transfer including 1) preservation of content by transferring similar styles into similar image patches and 2) transfer of style based on similarity of local texture (e.g. edge) between content and style images. Furthermore, we introduce query preservation and attention temperature scaling to mitigate the issue of disruption of original content, and initial latent Adaptive Instance Normalization (AdaIN) to deal with the disharmonious color (failure to transfer the colors of style). Our experimental results demonstrate that our proposed method surpasses state-of-the-art methods in both conventional and diffusion-based style transfer baselines.

  • 3 authors
·
Dec 11, 2023

AdamP: Slowing Down the Slowdown for Momentum Optimizers on Scale-invariant Weights

Normalization techniques are a boon for modern deep learning. They let weights converge more quickly with often better generalization performances. It has been argued that the normalization-induced scale invariance among the weights provides an advantageous ground for gradient descent (GD) optimizers: the effective step sizes are automatically reduced over time, stabilizing the overall training procedure. It is often overlooked, however, that the additional introduction of momentum in GD optimizers results in a far more rapid reduction in effective step sizes for scale-invariant weights, a phenomenon that has not yet been studied and may have caused unwanted side effects in the current practice. This is a crucial issue because arguably the vast majority of modern deep neural networks consist of (1) momentum-based GD (e.g. SGD or Adam) and (2) scale-invariant parameters. In this paper, we verify that the widely-adopted combination of the two ingredients lead to the premature decay of effective step sizes and sub-optimal model performances. We propose a simple and effective remedy, SGDP and AdamP: get rid of the radial component, or the norm-increasing direction, at each optimizer step. Because of the scale invariance, this modification only alters the effective step sizes without changing the effective update directions, thus enjoying the original convergence properties of GD optimizers. Given the ubiquity of momentum GD and scale invariance in machine learning, we have evaluated our methods against the baselines on 13 benchmarks. They range from vision tasks like classification (e.g. ImageNet), retrieval (e.g. CUB and SOP), and detection (e.g. COCO) to language modelling (e.g. WikiText) and audio classification (e.g. DCASE) tasks. We verify that our solution brings about uniform gains in those benchmarks. Source code is available at https://github.com/clovaai/AdamP.

naver-ai NAVER AI Lab
·
Jun 15, 2020

Fine-Tuning and Training of DenseNet for Histopathology Image Representation Using TCGA Diagnostic Slides

Feature vectors provided by pre-trained deep artificial neural networks have become a dominant source for image representation in recent literature. Their contribution to the performance of image analysis can be improved through finetuning. As an ultimate solution, one might even train a deep network from scratch with the domain-relevant images, a highly desirable option which is generally impeded in pathology by lack of labeled images and the computational expense. In this study, we propose a new network, namely KimiaNet, that employs the topology of the DenseNet with four dense blocks, fine-tuned and trained with histopathology images in different configurations. We used more than 240,000 image patches with 1000x1000 pixels acquired at 20x magnification through our proposed "highcellularity mosaic" approach to enable the usage of weak labels of 7,126 whole slide images of formalin-fixed paraffin-embedded human pathology samples publicly available through the The Cancer Genome Atlas (TCGA) repository. We tested KimiaNet using three public datasets, namely TCGA, endometrial cancer images, and colorectal cancer images by evaluating the performance of search and classification when corresponding features of different networks are used for image representation. As well, we designed and trained multiple convolutional batch-normalized ReLU (CBR) networks. The results show that KimiaNet provides superior results compared to the original DenseNet and smaller CBR networks when used as feature extractor to represent histopathology images.

  • 22 authors
·
Jan 19, 2021

Paint Bucket Colorization Using Anime Character Color Design Sheets

Line art colorization plays a crucial role in hand-drawn animation production, where digital artists manually colorize segments using a paint bucket tool, guided by RGB values from character color design sheets. This process, often called paint bucket colorization, involves two main tasks: keyframe colorization, where colors are applied according to the character's color design sheet, and consecutive frame colorization, where these colors are replicated across adjacent frames. Current automated colorization methods primarily focus on reference-based and segment-matching approaches. However, reference-based methods often fail to accurately assign specific colors to each region, while matching-based methods are limited to consecutive frame colorization and struggle with issues like significant deformation and occlusion. In this work, we introduce inclusion matching, which allows the network to understand the inclusion relationships between segments, rather than relying solely on direct visual correspondences. By integrating this approach with segment parsing and color warping modules, our inclusion matching pipeline significantly improves performance in both keyframe colorization and consecutive frame colorization. To support our network's training, we have developed a unique dataset named PaintBucket-Character, which includes rendered line arts alongside their colorized versions and shading annotations for various 3D characters. To replicate industry animation data formats, we also created color design sheets for each character, with semantic information for each color and standard pose reference images. Experiments highlight the superiority of our method, demonstrating accurate and consistent colorization across both our proposed benchmarks and hand-drawn animations.

  • 6 authors
·
Oct 25, 2024

PixCell: A generative foundation model for digital histopathology images

The digitization of histology slides has revolutionized pathology, providing massive datasets for cancer diagnosis and research. Contrastive self-supervised and vision-language models have been shown to effectively mine large pathology datasets to learn discriminative representations. On the other hand, generative models, capable of synthesizing realistic and diverse images, present a compelling solution to address unique problems in pathology that involve synthesizing images; overcoming annotated data scarcity, enabling privacy-preserving data sharing, and performing inherently generative tasks, such as virtual staining. We introduce PixCell, the first diffusion-based generative foundation model for histopathology. We train PixCell on PanCan-30M, a vast, diverse dataset derived from 69,184 H\&E-stained whole slide images covering various cancer types. We employ a progressive training strategy and a self-supervision-based conditioning that allows us to scale up training without any annotated data. PixCell generates diverse and high-quality images across multiple cancer types, which we find can be used in place of real data to train a self-supervised discriminative model. Synthetic images shared between institutions are subject to fewer regulatory barriers than would be the case with real clinical images. Furthermore, we showcase the ability to precisely control image generation using a small set of annotated images, which can be used for both data augmentation and educational purposes. Testing on a cell segmentation task, a mask-guided PixCell enables targeted data augmentation, improving downstream performance. Finally, we demonstrate PixCell's ability to use H\&E structural staining to infer results from molecular marker studies; we use this capability to infer IHC staining from H\&E images. Our trained models are publicly released to accelerate research in computational pathology.

Tissue Cross-Section and Pen Marking Segmentation in Whole Slide Images

Tissue segmentation is a routine preprocessing step to reduce the computational cost of whole slide image (WSI) analysis by excluding background regions. Traditional image processing techniques are commonly used for tissue segmentation, but often require manual adjustments to parameter values for atypical cases, fail to exclude all slide and scanning artifacts from the background, and are unable to segment adipose tissue. Pen marking artifacts in particular can be a potential source of bias for subsequent analyses if not removed. In addition, several applications require the separation of individual cross-sections, which can be challenging due to tissue fragmentation and adjacent positioning. To address these problems, we develop a convolutional neural network for tissue and pen marking segmentation using a dataset of 200 H&E stained WSIs. For separating tissue cross-sections, we propose a novel post-processing method based on clustering predicted centroid locations of the cross-sections in a 2D histogram. On an independent test set, the model achieved a mean Dice score of 0.981pm0.033 for tissue segmentation and a mean Dice score of 0.912pm0.090 for pen marking segmentation. The mean absolute difference between the number of annotated and separated cross-sections was 0.075pm0.350. Our results demonstrate that the proposed model can accurately segment H&E stained tissue cross-sections and pen markings in WSIs while being robust to many common slide and scanning artifacts. The model with trained model parameters and post-processing method are made publicly available as a Python package called SlideSegmenter.

  • 3 authors
·
Jan 24, 2024

Single Image BRDF Parameter Estimation with a Conditional Adversarial Network

Creating plausible surfaces is an essential component in achieving a high degree of realism in rendering. To relieve artists, who create these surfaces in a time-consuming, manual process, automated retrieval of the spatially-varying Bidirectional Reflectance Distribution Function (SVBRDF) from a single mobile phone image is desirable. By leveraging a deep neural network, this casual capturing method can be achieved. The trained network can estimate per pixel normal, base color, metallic and roughness parameters from the Disney BRDF. The input image is taken with a mobile phone lit by the camera flash. The network is trained to compensate for environment lighting and thus learned to reduce artifacts introduced by other light sources. These losses contain a multi-scale discriminator with an additional perceptual loss, a rendering loss using a differentiable renderer, and a parameter loss. Besides the local precision, this loss formulation generates material texture maps which are globally more consistent. The network is set up as a generator network trained in an adversarial fashion to ensure that only plausible maps are produced. The estimated parameters not only reproduce the material faithfully in rendering but capture the style of hand-authored materials due to the more global loss terms compared to previous works without requiring additional post-processing. Both the resolution and the quality is improved.

  • 2 authors
·
Oct 11, 2019

iColoriT: Towards Propagating Local Hint to the Right Region in Interactive Colorization by Leveraging Vision Transformer

Point-interactive image colorization aims to colorize grayscale images when a user provides the colors for specific locations. It is essential for point-interactive colorization methods to appropriately propagate user-provided colors (i.e., user hints) in the entire image to obtain a reasonably colorized image with minimal user effort. However, existing approaches often produce partially colorized results due to the inefficient design of stacking convolutional layers to propagate hints to distant relevant regions. To address this problem, we present iColoriT, a novel point-interactive colorization Vision Transformer capable of propagating user hints to relevant regions, leveraging the global receptive field of Transformers. The self-attention mechanism of Transformers enables iColoriT to selectively colorize relevant regions with only a few local hints. Our approach colorizes images in real-time by utilizing pixel shuffling, an efficient upsampling technique that replaces the decoder architecture. Also, in order to mitigate the artifacts caused by pixel shuffling with large upsampling ratios, we present the local stabilizing layer. Extensive quantitative and qualitative results demonstrate that our approach highly outperforms existing methods for point-interactive colorization, producing accurately colorized images with a user's minimal effort. Official codes are available at https://pmh9960.github.io/research/iColoriT

  • 4 authors
·
Jul 14, 2022

Contribution-based Low-Rank Adaptation with Pre-training Model for Real Image Restoration

Recently, pre-trained model and efficient parameter tuning have achieved remarkable success in natural language processing and high-level computer vision with the aid of masked modeling and prompt tuning. In low-level computer vision, however, there have been limited investigations on pre-trained models and even efficient fine-tuning strategy has not yet been explored despite its importance and benefit in various real-world tasks such as alleviating memory inflation issue when integrating new tasks on AI edge devices. Here, we propose a novel efficient parameter tuning approach dubbed contribution-based low-rank adaptation (CoLoRA) for multiple image restorations along with effective pre-training method with random order degradations (PROD). Unlike prior arts that tune all network parameters, our CoLoRA effectively fine-tunes small amount of parameters by leveraging LoRA (low-rank adaptation) for each new vision task with our contribution-based method to adaptively determine layer by layer capacity for that task to yield comparable performance to full tuning. Furthermore, our PROD strategy allows to extend the capability of pre-trained models with improved performance as well as robustness to bridge synthetic pre-training and real-world fine-tuning. Our CoLoRA with PROD has demonstrated its superior performance in various image restoration tasks across diverse degradation types on both synthetic and real-world datasets for known and novel tasks.

  • 3 authors
·
Aug 2, 2024

Layer Normalization

Training state-of-the-art, deep neural networks is computationally expensive. One way to reduce the training time is to normalize the activities of the neurons. A recently introduced technique called batch normalization uses the distribution of the summed input to a neuron over a mini-batch of training cases to compute a mean and variance which are then used to normalize the summed input to that neuron on each training case. This significantly reduces the training time in feed-forward neural networks. However, the effect of batch normalization is dependent on the mini-batch size and it is not obvious how to apply it to recurrent neural networks. In this paper, we transpose batch normalization into layer normalization by computing the mean and variance used for normalization from all of the summed inputs to the neurons in a layer on a single training case. Like batch normalization, we also give each neuron its own adaptive bias and gain which are applied after the normalization but before the non-linearity. Unlike batch normalization, layer normalization performs exactly the same computation at training and test times. It is also straightforward to apply to recurrent neural networks by computing the normalization statistics separately at each time step. Layer normalization is very effective at stabilizing the hidden state dynamics in recurrent networks. Empirically, we show that layer normalization can substantially reduce the training time compared with previously published techniques.

  • 3 authors
·
Jul 21, 2016

UMat: Uncertainty-Aware Single Image High Resolution Material Capture

We propose a learning-based method to recover normals, specularity, and roughness from a single diffuse image of a material, using microgeometry appearance as our primary cue. Previous methods that work on single images tend to produce over-smooth outputs with artifacts, operate at limited resolution, or train one model per class with little room for generalization. Previous methods that work on single images tend to produce over-smooth outputs with artifacts, operate at limited resolution, or train one model per class with little room for generalization. In contrast, in this work, we propose a novel capture approach that leverages a generative network with attention and a U-Net discriminator, which shows outstanding performance integrating global information at reduced computational complexity. We showcase the performance of our method with a real dataset of digitized textile materials and show that a commodity flatbed scanner can produce the type of diffuse illumination required as input to our method. Additionally, because the problem might be illposed -more than a single diffuse image might be needed to disambiguate the specular reflection- or because the training dataset is not representative enough of the real distribution, we propose a novel framework to quantify the model's confidence about its prediction at test time. Our method is the first one to deal with the problem of modeling uncertainty in material digitization, increasing the trustworthiness of the process and enabling more intelligent strategies for dataset creation, as we demonstrate with an active learning experiment.

  • 4 authors
·
May 25, 2023

Red Blood Cell Segmentation with Overlapping Cell Separation and Classification on Imbalanced Dataset

Automated red blood cell (RBC) classification on blood smear images helps hematologists to analyze RBC lab results in a reduced time and cost. However, overlapping cells can cause incorrect predicted results, and so they have to be separated into multiple single RBCs before classifying. To classify multiple classes with deep learning, imbalance problems are common in medical imaging because normal samples are always higher than rare disease samples. This paper presents a new method to segment and classify RBCs from blood smear images, specifically to tackle cell overlapping and data imbalance problems. Focusing on overlapping cell separation, our segmentation process first estimates ellipses to represent RBCs. The method detects the concave points and then finds the ellipses using directed ellipse fitting. The accuracy from 20 blood smear images was 0.889. Classification requires balanced training datasets. However, some RBC types are rare. The imbalance ratio of this dataset was 34.538 for 12 RBC classes from 20,875 individual RBC samples. The use of machine learning for RBC classification with an imbalanced dataset is hence more challenging than many other applications. We analyzed techniques to deal with this problem. The best accuracy and F1-score were 0.921 and 0.8679, respectively, using EfficientNet-B1 with augmentation. Experimental results showed that the weight balancing technique with augmentation had the potential to deal with imbalance problems by improving the F1-score on minority classes, while data augmentation significantly improved the overall classification performance.

  • 5 authors
·
Dec 2, 2020

Color Matching Using Hypernetwork-Based Kolmogorov-Arnold Networks

We present cmKAN, a versatile framework for color matching. Given an input image with colors from a source color distribution, our method effectively and accurately maps these colors to match a target color distribution in both supervised and unsupervised settings. Our framework leverages the spline capabilities of Kolmogorov-Arnold Networks (KANs) to model the color matching between source and target distributions. Specifically, we developed a hypernetwork that generates spatially varying weight maps to control the nonlinear splines of a KAN, enabling accurate color matching. As part of this work, we introduce a first large-scale dataset of paired images captured by two distinct cameras and evaluate the efficacy of our and existing methods in matching colors. We evaluated our approach across various color-matching tasks, including: (1) raw-to-raw mapping, where the source color distribution is in one camera's raw color space and the target in another camera's raw space; (2) raw-to-sRGB mapping, where the source color distribution is in a camera's raw space and the target is in the display sRGB space, emulating the color rendering of a camera ISP; and (3) sRGB-to-sRGB mapping, where the goal is to transfer colors from a source sRGB space (e.g., produced by a source camera ISP) to a target sRGB space (e.g., from a different camera ISP). The results show that our method outperforms existing approaches by 37.3% on average for supervised and unsupervised cases while remaining lightweight compared to other methods. The codes, dataset, and pre-trained models are available at: https://github.com/gosha20777/cmKAN

  • 7 authors
·
Mar 14

Autonomous labeling of surgical resection margins using a foundation model

Assessing resection margins is central to pathological specimen evaluation and has profound implications for patient outcomes. Current practice employs physical inking, which is applied variably, and cautery artifacts can obscure the true margin on histological sections. We present a virtual inking network (VIN) that autonomously localizes the surgical cut surface on whole-slide images, reducing reliance on inks and standardizing margin-focused review. VIN uses a frozen foundation model as the feature extractor and a compact two-layer multilayer perceptron trained for patch-level classification of cautery-consistent features. The dataset comprised 120 hematoxylin and eosin (H&E) stained slides from 12 human tonsil tissue blocks, resulting in ~2 TB of uncompressed raw image data, where a board-certified pathologist provided boundary annotations. In blind testing with 20 slides from previously unseen blocks, VIN produced coherent margin overlays that qualitatively aligned with expert annotations across serial sections. Quantitatively, region-level accuracy was ~73.3% across the test set, with errors largely confined to limited areas that did not disrupt continuity of the whole-slide margin map. These results indicate that VIN captures cautery-related histomorphology and can provide a reproducible, ink-free margin delineation suitable for integration into routine digital pathology workflows and for downstream measurement of margin distances.

  • 12 authors
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Nov 27

ColorizeDiffusion v2: Enhancing Reference-based Sketch Colorization Through Separating Utilities

Reference-based sketch colorization methods have garnered significant attention due to their potential applications in the animation production industry. However, most existing methods are trained with image triplets of sketch, reference, and ground truth that are semantically and spatially well-aligned, while real-world references and sketches often exhibit substantial misalignment. This mismatch in data distribution between training and inference leads to overfitting, consequently resulting in spatial artifacts and significant degradation in overall colorization quality, limiting potential applications of current methods for general purposes. To address this limitation, we conduct an in-depth analysis of the carrier, defined as the latent representation facilitating information transfer from reference to sketch. Based on this analysis, we propose a novel workflow that dynamically adapts the carrier to optimize distinct aspects of colorization. Specifically, for spatially misaligned artifacts, we introduce a split cross-attention mechanism with spatial masks, enabling region-specific reference injection within the diffusion process. To mitigate semantic neglect of sketches, we employ dedicated background and style encoders to transfer detailed reference information in the latent feature space, achieving enhanced spatial control and richer detail synthesis. Furthermore, we propose character-mask merging and background bleaching as preprocessing steps to improve foreground-background integration and background generation. Extensive qualitative and quantitative evaluations, including a user study, demonstrate the superior performance of our proposed method compared to existing approaches. An ablation study further validates the efficacy of each proposed component.

  • 6 authors
·
Apr 9

Object Remover Performance Evaluation Methods using Class-wise Object Removal Images

Object removal refers to the process of erasing designated objects from an image while preserving the overall appearance, and it is one area where image inpainting is widely used in real-world applications. The performance of an object remover is quantitatively evaluated by measuring the quality of object removal results, similar to how the performance of an image inpainter is gauged. Current works reporting quantitative performance evaluations utilize original images as references. In this letter, to validate the current evaluation methods cannot properly evaluate the performance of an object remover, we create a dataset with object removal ground truth and compare the evaluations made by the current methods using original images to those utilizing object removal ground truth images. The disparities between two evaluation sets validate that the current methods are not suitable for measuring the performance of an object remover. Additionally, we propose new evaluation methods tailored to gauge the performance of an object remover. The proposed methods evaluate the performance through class-wise object removal results and utilize images without the target class objects as a comparison set. We confirm that the proposed methods can make judgments consistent with human evaluators in the COCO dataset, and that they can produce measurements aligning with those using object removal ground truth in the self-acquired dataset.

  • 4 authors
·
Apr 17, 2024

MagicColor: Multi-Instance Sketch Colorization

We present MagicColor, a diffusion-based framework for multi-instance sketch colorization. The production of multi-instance 2D line art colorization adheres to an industry-standard workflow, which consists of three crucial stages: the design of line art characters, the coloring of individual objects, and the refinement process. The artists are required to repeat the process of coloring each instance one by one, which is inaccurate and inefficient. Meanwhile, current generative methods fail to solve this task due to the challenge of multi-instance pair data collection. To tackle these challenges, we incorporate three technical designs to ensure precise character detail transcription and achieve multi-instance sketch colorization in a single forward. Specifically, we first propose the self-play training strategy to solve the lack of training data. Then we introduce an instance guider to feed the color of the instance. To achieve accurate color matching, we present fine-grained color matching with edge loss to enhance visual quality. Equipped with the proposed modules, MagicColor enables automatically transforming sketches into vividly-colored images with accurate consistency and multi-instance control. Experiments on our collected datasets show that our model outperforms existing methods regarding chromatic precision. Specifically, our model critically automates the colorization process with zero manual adjustments, so novice users can produce stylistically consistent artwork by providing reference instances and the original line art. Our code and additional details are available at https://yinhan-zhang.github.io/color

  • 5 authors
·
Mar 21

A Survey on All-in-One Image Restoration: Taxonomy, Evaluation and Future Trends

Image restoration (IR) seeks to recover high-quality images from degraded observations caused by a wide range of factors, including noise, blur, compression, and adverse weather. While traditional IR methods have made notable progress by targeting individual degradation types, their specialization often comes at the cost of generalization, leaving them ill-equipped to handle the multifaceted distortions encountered in real-world applications. In response to this challenge, the all-in-one image restoration (AiOIR) paradigm has recently emerged, offering a unified framework that adeptly addresses multiple degradation types. These innovative models enhance the convenience and versatility by adaptively learning degradation-specific features while simultaneously leveraging shared knowledge across diverse corruptions. In this survey, we provide the first in-depth and systematic overview of AiOIR, delivering a structured taxonomy that categorizes existing methods by architectural designs, learning paradigms, and their core innovations. We systematically categorize current approaches and assess the challenges these models encounter, outlining research directions to propel this rapidly evolving field. To facilitate the evaluation of existing methods, we also consolidate widely-used datasets, evaluation protocols, and implementation practices, and compare and summarize the most advanced open-source models. As the first comprehensive review dedicated to AiOIR, this paper aims to map the conceptual landscape, synthesize prevailing techniques, and ignite further exploration toward more intelligent, unified, and adaptable visual restoration systems. A curated code repository is available at https://github.com/Harbinzzy/All-in-One-Image-Restoration-Survey.

  • 5 authors
·
Oct 19, 2024

What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization

Summarization models often generate text that is poorly calibrated to quality metrics because they are trained to maximize the likelihood of a single reference (MLE). To address this, recent work has added a calibration step, which exposes a model to its own ranked outputs to improve relevance or, in a separate line of work, contrasts positive and negative sets to improve faithfulness. While effective, much of this work has focused on how to generate and optimize these sets. Less is known about why one setup is more effective than another. In this work, we uncover the underlying characteristics of effective sets. For each training instance, we form a large, diverse pool of candidates and systematically vary the subsets used for calibration fine-tuning. Each selection strategy targets distinct aspects of the sets, such as lexical diversity or the size of the gap between positive and negatives. On three diverse scientific long-form summarization datasets (spanning biomedical, clinical, and chemical domains), we find, among others, that faithfulness calibration is optimal when the negative sets are extractive and more likely to be generated, whereas for relevance calibration, the metric margin between candidates should be maximized and surprise--the disagreement between model and metric defined candidate rankings--minimized. Code to create, select, and optimize calibration sets is available at https://github.com/griff4692/calibrating-summaries

  • 10 authors
·
May 12, 2023 1

Troublemaker Learning for Low-Light Image Enhancement

Low-light image enhancement (LLIE) restores the color and brightness of underexposed images. Supervised methods suffer from high costs in collecting low/normal-light image pairs. Unsupervised methods invest substantial effort in crafting complex loss functions. We address these two challenges through the proposed TroubleMaker Learning (TML) strategy, which employs normal-light images as inputs for training. TML is simple: we first dim the input and then increase its brightness. TML is based on two core components. First, the troublemaker model (TM) constructs pseudo low-light images from normal images to relieve the cost of pairwise data. Second, the predicting model (PM) enhances the brightness of pseudo low-light images. Additionally, we incorporate an enhancing model (EM) to further improve the visual performance of PM outputs. Moreover, in LLIE tasks, characterizing global element correlations is important because more information on the same object can be captured. CNN cannot achieve this well, and self-attention has high time complexity. Accordingly, we propose Global Dynamic Convolution (GDC) with O(n) time complexity, which essentially imitates the partial calculation process of self-attention to formulate elementwise correlations. Based on the GDC module, we build the UGDC model. Extensive quantitative and qualitative experiments demonstrate that UGDC trained with TML can achieve competitive performance against state-of-the-art approaches on public datasets. The code is available at https://github.com/Rainbowman0/TML_LLIE.

  • 8 authors
·
Feb 6, 2024

DocRes: A Generalist Model Toward Unifying Document Image Restoration Tasks

Document image restoration is a crucial aspect of Document AI systems, as the quality of document images significantly influences the overall performance. Prevailing methods address distinct restoration tasks independently, leading to intricate systems and the incapability to harness the potential synergies of multi-task learning. To overcome this challenge, we propose DocRes, a generalist model that unifies five document image restoration tasks including dewarping, deshadowing, appearance enhancement, deblurring, and binarization. To instruct DocRes to perform various restoration tasks, we propose a novel visual prompt approach called Dynamic Task-Specific Prompt (DTSPrompt). The DTSPrompt for different tasks comprises distinct prior features, which are additional characteristics extracted from the input image. Beyond its role as a cue for task-specific execution, DTSPrompt can also serve as supplementary information to enhance the model's performance. Moreover, DTSPrompt is more flexible than prior visual prompt approaches as it can be seamlessly applied and adapted to inputs with high and variable resolutions. Experimental results demonstrate that DocRes achieves competitive or superior performance compared to existing state-of-the-art task-specific models. This underscores the potential of DocRes across a broader spectrum of document image restoration tasks. The source code is publicly available at https://github.com/ZZZHANG-jx/DocRes

  • 5 authors
·
May 7, 2024

Free-Lunch Color-Texture Disentanglement for Stylized Image Generation

Recent advances in Text-to-Image (T2I) diffusion models have transformed image generation, enabling significant progress in stylized generation using only a few style reference images. However, current diffusion-based methods struggle with fine-grained style customization due to challenges in controlling multiple style attributes, such as color and texture. This paper introduces the first tuning-free approach to achieve free-lunch color-texture disentanglement in stylized T2I generation, addressing the need for independently controlled style elements for the Disentangled Stylized Image Generation (DisIG) problem. Our approach leverages the Image-Prompt Additivity property in the CLIP image embedding space to develop techniques for separating and extracting Color-Texture Embeddings (CTE) from individual color and texture reference images. To ensure that the color palette of the generated image aligns closely with the color reference, we apply a whitening and coloring transformation to enhance color consistency. Additionally, to prevent texture loss due to the signal-leak bias inherent in diffusion training, we introduce a noise term that preserves textural fidelity during the Regularized Whitening and Coloring Transformation (RegWCT). Through these methods, our Style Attributes Disentanglement approach (SADis) delivers a more precise and customizable solution for stylized image generation. Experiments on images from the WikiArt and StyleDrop datasets demonstrate that, both qualitatively and quantitatively, SADis surpasses state-of-the-art stylization methods in the DisIG task.Code will be released at https://deepffff.github.io/sadis.github.io/.

  • 7 authors
·
Mar 18

Detecting Recolored Image by Spatial Correlation

Image forensics, aiming to ensure the authenticity of the image, has made great progress in dealing with common image manipulation such as copy-move, splicing, and inpainting in the past decades. However, only a few researchers pay attention to an emerging editing technique called image recoloring, which can manipulate the color values of an image to give it a new style. To prevent it from being used maliciously, the previous approaches address the conventional recoloring from the perspective of inter-channel correlation and illumination consistency. In this paper, we try to explore a solution from the perspective of the spatial correlation, which exhibits the generic detection capability for both conventional and deep learning-based recoloring. Through theoretical and numerical analysis, we find that the recoloring operation will inevitably destroy the spatial correlation between pixels, implying a new prior of statistical discriminability. Based on such fact, we generate a set of spatial correlation features and learn the informative representation from the set via a convolutional neural network. To train our network, we use three recoloring methods to generate a large-scale and high-quality data set. Extensive experimental results in two recoloring scenes demonstrate that the spatial correlation features are highly discriminative. Our method achieves the state-of-the-art detection accuracy on multiple benchmark datasets and exhibits well generalization for unknown types of recoloring methods.

  • 5 authors
·
Apr 22, 2022

On residual network depth

Deep residual architectures, such as ResNet and the Transformer, have enabled models of unprecedented depth, yet a formal understanding of why depth is so effective remains an open question. A popular intuition, following Veit et al. (2016), is that these residual networks behave like ensembles of many shallower models. Our key finding is an explicit analytical formula that verifies this ensemble perspective, proving that increasing network depth is mathematically equivalent to expanding the size of this implicit ensemble. Furthermore, our expansion reveals a hierarchical ensemble structure in which the combinatorial growth of computation paths leads to an explosion in the output signal, explaining the historical necessity of normalization layers in training deep models. This insight offers a first principles explanation for the historical dependence on normalization layers and sheds new light on a family of successful normalization-free techniques like SkipInit and Fixup. However, while these previous approaches infer scaling factors through optimizer analysis or a heuristic analogy to Batch Normalization, our work offers the first explanation derived directly from the network's inherent functional structure. Specifically, our Residual Expansion Theorem reveals that scaling each residual module provides a principled solution to taming the combinatorial explosion inherent to these architectures. We further show that this scaling acts as a capacity controls that also implicitly regularizes the model's complexity.

  • 2 authors
·
Oct 3

VacancySBERT: the approach for representation of titles and skills for semantic similarity search in the recruitment domain

The paper focuses on deep learning semantic search algorithms applied in the HR domain. The aim of the article is developing a novel approach to training a Siamese network to link the skills mentioned in the job ad with the title. It has been shown that the title normalization process can be based either on classification or similarity comparison approaches. While classification algorithms strive to classify a sample into predefined set of categories, similarity search algorithms take a more flexible approach, since they are designed to find samples that are similar to a given query sample, without requiring pre-defined classes and labels. In this article semantic similarity search to find candidates for title normalization has been used. A pre-trained language model has been adapted while teaching it to match titles and skills based on co-occurrence information. For the purpose of this research fifty billion title-descriptions pairs had been collected for training the model and thirty three thousand title-description-normalized title triplets, where normalized job title was picked up manually by job ad creator for testing purposes. As baselines FastText, BERT, SentenceBert and JobBert have been used. As a metric of the accuracy of the designed algorithm is Recall in top one, five and ten model's suggestions. It has been shown that the novel training objective lets it achieve significant improvement in comparison to other generic and specific text encoders. Two settings with treating titles as standalone strings, and with included skills as additional features during inference have been used and the results have been compared in this article. Improvements by 10% and 21.5% have been achieved using VacancySBERT and VacancySBERT (with skills) respectively. The benchmark has been developed as open-source to foster further research in the area.

  • 3 authors
·
Jul 31, 2023

Reducing Domain Gap with Diffusion-Based Domain Adaptation for Cell Counting

Generating realistic synthetic microscopy images is critical for training deep learning models in label-scarce environments, such as cell counting with many cells per image. However, traditional domain adaptation methods often struggle to bridge the domain gap when synthetic images lack the complex textures and visual patterns of real samples. In this work, we adapt the Inversion-Based Style Transfer (InST) framework originally designed for artistic style transfer to biomedical microscopy images. Our method combines latent-space Adaptive Instance Normalization with stochastic inversion in a diffusion model to transfer the style from real fluorescence microscopy images to synthetic ones, while weakly preserving content structure. We evaluate the effectiveness of our InST-based synthetic dataset for downstream cell counting by pre-training and fine-tuning EfficientNet-B0 models on various data sources, including real data, hard-coded synthetic data, and the public Cell200-s dataset. Models trained with our InST-synthesized images achieve up to 37\% lower Mean Absolute Error (MAE) compared to models trained on hard-coded synthetic data, and a 52\% reduction in MAE compared to models trained on Cell200-s (from 53.70 to 25.95 MAE). Notably, our approach also outperforms models trained on real data alone (25.95 vs. 27.74 MAE). Further improvements are achieved when combining InST-synthesized data with lightweight domain adaptation techniques such as DACS with CutMix. These findings demonstrate that InST-based style transfer most effectively reduces the domain gap between synthetic and real microscopy data. Our approach offers a scalable path for enhancing cell counting performance while minimizing manual labeling effort. The source code and resources are publicly available at: https://github.com/MohammadDehghan/InST-Microscopy.

  • 2 authors
·
Dec 12

NoiSER: Noise is All You Need for Low-Light Image Enhancement

In this paper, we present an embarrassingly simple yet effective solution to a seemingly impossible mission, low-light image enhancement (LLIE) without access to any task-related data. The proposed solution, Noise SElf-Regression (NoiSER), simply learns a convolutional neural network equipped with a instance-normalization layer by taking a random noise image, N(0,sigma^2) for each pixel, as both input and output for each training pair, and then the low-light image is fed to the learned network for predicting the normal-light image. Technically, an intuitive explanation for its effectiveness is as follows: 1) the self-regression reconstructs the contrast between adjacent pixels of the input image, 2) the instance-normalization layers may naturally remediate the overall magnitude/lighting of the input image, and 3) the N(0,sigma^2) assumption for each pixel enforces the output image to follow the well-known gray-world hypothesis Gary-world_Hypothesis when the image size is big enough, namely, the averages of three RGB components of an image converge to the same value. Compared to existing SOTA LLIE methods with access to different task-related data, NoiSER is surprisingly highly competitive in enhancement quality, yet with a much smaller model size, and much lower training and inference cost. With only sim 1K parameters, NoiSER realizes about 1 minute for training and 1.2 ms for inference with 600x400 resolution on RTX 2080 Ti. As a bonus, NoiSER possesses automated over-exposure suppression ability and shows excellent performance on over-exposed photos.

  • 6 authors
·
Nov 9, 2022

Micro-Batch Training with Batch-Channel Normalization and Weight Standardization

Batch Normalization (BN) has become an out-of-box technique to improve deep network training. However, its effectiveness is limited for micro-batch training, i.e., each GPU typically has only 1-2 images for training, which is inevitable for many computer vision tasks, e.g., object detection and semantic segmentation, constrained by memory consumption. To address this issue, we propose Weight Standardization (WS) and Batch-Channel Normalization (BCN) to bring two success factors of BN into micro-batch training: 1) the smoothing effects on the loss landscape and 2) the ability to avoid harmful elimination singularities along the training trajectory. WS standardizes the weights in convolutional layers to smooth the loss landscape by reducing the Lipschitz constants of the loss and the gradients; BCN combines batch and channel normalizations and leverages estimated statistics of the activations in convolutional layers to keep networks away from elimination singularities. We validate WS and BCN on comprehensive computer vision tasks, including image classification, object detection, instance segmentation, video recognition and semantic segmentation. All experimental results consistently show that WS and BCN improve micro-batch training significantly. Moreover, using WS and BCN with micro-batch training is even able to match or outperform the performances of BN with large-batch training.

  • 5 authors
·
Mar 25, 2019

Bridging the Gap Between Computational Photography and Visual Recognition

What is the current state-of-the-art for image restoration and enhancement applied to degraded images acquired under less than ideal circumstances? Can the application of such algorithms as a pre-processing step to improve image interpretability for manual analysis or automatic visual recognition to classify scene content? While there have been important advances in the area of computational photography to restore or enhance the visual quality of an image, the capabilities of such techniques have not always translated in a useful way to visual recognition tasks. Consequently, there is a pressing need for the development of algorithms that are designed for the joint problem of improving visual appearance and recognition, which will be an enabling factor for the deployment of visual recognition tools in many real-world scenarios. To address this, we introduce the UG^2 dataset as a large-scale benchmark composed of video imagery captured under challenging conditions, and two enhancement tasks designed to test algorithmic impact on visual quality and automatic object recognition. Furthermore, we propose a set of metrics to evaluate the joint improvement of such tasks as well as individual algorithmic advances, including a novel psychophysics-based evaluation regime for human assessment and a realistic set of quantitative measures for object recognition performance. We introduce six new algorithms for image restoration or enhancement, which were created as part of the IARPA sponsored UG^2 Challenge workshop held at CVPR 2018. Under the proposed evaluation regime, we present an in-depth analysis of these algorithms and a host of deep learning-based and classic baseline approaches. From the observed results, it is evident that we are in the early days of building a bridge between computational photography and visual recognition, leaving many opportunities for innovation in this area.

  • 24 authors
·
Jan 27, 2019

PLUTO: Pathology-Universal Transformer

Pathology is the study of microscopic inspection of tissue, and a pathology diagnosis is often the medical gold standard to diagnose disease. Pathology images provide a unique challenge for computer-vision-based analysis: a single pathology Whole Slide Image (WSI) is gigapixel-sized and often contains hundreds of thousands to millions of objects of interest across multiple resolutions. In this work, we propose PathoLogy Universal TransfOrmer (PLUTO): a light-weight pathology FM that is pre-trained on a diverse dataset of 195 million image tiles collected from multiple sites and extracts meaningful representations across multiple WSI scales that enable a large variety of downstream pathology tasks. In particular, we design task-specific adaptation heads that utilize PLUTO's output embeddings for tasks which span pathology scales ranging from subcellular to slide-scale, including instance segmentation, tile classification, and slide-level prediction. We compare PLUTO's performance to other state-of-the-art methods on a diverse set of external and internal benchmarks covering multiple biologically relevant tasks, tissue types, resolutions, stains, and scanners. We find that PLUTO matches or outperforms existing task-specific baselines and pathology-specific foundation models, some of which use orders-of-magnitude larger datasets and model sizes when compared to PLUTO. Our findings present a path towards a universal embedding to power pathology image analysis, and motivate further exploration around pathology foundation models in terms of data diversity, architectural improvements, sample efficiency, and practical deployability in real-world applications.

  • 33 authors
·
May 13, 2024

SeaS: Few-shot Industrial Anomaly Image Generation with Separation and Sharing Fine-tuning

We introduce SeaS, a unified industrial generative model for automatically creating diverse anomalies, authentic normal products, and precise anomaly masks. While extensive research exists, most efforts either focus on specific tasks, i.e., anomalies or normal products only, or require separate models for each anomaly type. Consequently, prior methods either offer limited generative capability or depend on a vast array of anomaly-specific models. We demonstrate that U-Net's differentiated learning ability captures the distinct visual traits of slightly-varied normal products and diverse anomalies, enabling us to construct a unified model for all tasks. Specifically, we first introduce an Unbalanced Abnormal (UA) Text Prompt, comprising one normal token and multiple anomaly tokens. More importantly, our Decoupled Anomaly Alignment (DA) loss decouples anomaly attributes and binds them to distinct anomaly tokens of UA, enabling SeaS to create unseen anomalies by recombining these attributes. Furthermore, our Normal-image Alignment (NA) loss aligns the normal token to normal patterns, making generated normal products globally consistent and locally varied. Finally, SeaS produces accurate anomaly masks by fusing discriminative U-Net features with high-resolution VAE features. SeaS sets a new benchmark for industrial generation, significantly enhancing downstream applications, with average improvements of +8.66% pixel-level AP for synthesis-based AD approaches, +1.10% image-level AP for unsupervised AD methods, and +12.79% IoU for supervised segmentation models. Code is available at https://github.com/HUST-SLOW/SeaS{https://github.com/HUST-SLOW/SeaS}.

  • 6 authors
·
Oct 19, 2024

CoLoR-Filter: Conditional Loss Reduction Filtering for Targeted Language Model Pre-training

Selecting high-quality data for pre-training is crucial in shaping the downstream task performance of language models. A major challenge lies in identifying this optimal subset, a problem generally considered intractable, thus necessitating scalable and effective heuristics. In this work, we propose a data selection method, CoLoR-Filter (Conditional Loss Reduction Filtering), which leverages an empirical Bayes-inspired approach to derive a simple and computationally efficient selection criterion based on the relative loss values of two auxiliary models. In addition to the modeling rationale, we evaluate CoLoR-Filter empirically on two language modeling tasks: (1) selecting data from C4 for domain adaptation to evaluation on Books and (2) selecting data from C4 for a suite of downstream multiple-choice question answering tasks. We demonstrate favorable scaling both as we subselect more aggressively and using small auxiliary models to select data for large target models. As one headline result, CoLoR-Filter data selected using a pair of 150m parameter auxiliary models can train a 1.2b parameter target model to match a 1.2b parameter model trained on 25b randomly selected tokens with 25x less data for Books and 11x less data for the downstream tasks. Code: https://github.com/davidbrandfonbrener/color-filter-olmo Filtered data: https://huggingface.co/datasets/davidbrandfonbrener/color-filtered-c4

  • 5 authors
·
Jun 15, 2024 1

Partial Correlations in Compositional Data Analysis

Partial correlations quantify linear association between two variables adjusting for the influence of the remaining variables. They form the backbone for graphical models and are readily obtained from the inverse of the covariance matrix. For compositional data, the covariance structure is specified from log ratios of variables, so unless we try to "open" the data via a normalization, this implies changes in the definition and interpretation of partial correlations. In the present work, we elucidate how results derived by Aitchison (1986) lead to a natural definition of partial correlation that has a number of advantages over current measures of association. For this, we show that the residuals of log-ratios between a variable with a reference, when adjusting for all remaining variables including the reference, are reference-independent. Since the reference itself can be controlled for, correlations between residuals are defined for the variables directly without the necessity to recur to ratios except when specifying which variables are partialled out. Thus, perhaps surprisingly, partial correlations do not have the problems commonly found with measures of pairwise association on compositional data. They are well-defined between two variables, are properly scaled, and allow for negative association. By design, they are subcompositionally incoherent, but they share this property with conventional partial correlations (where results change when adjusting for the influence of fewer variables). We discuss the equivalence with normalization-based approaches whenever the normalizing variables are controlled for. We also discuss the partial variances and correlations we obtain from a previously studied data set of Roman glass cups.

  • 1 authors
·
Apr 20, 2019

Enhancing Image Rescaling using Dual Latent Variables in Invertible Neural Network

Normalizing flow models have been used successfully for generative image super-resolution (SR) by approximating complex distribution of natural images to simple tractable distribution in latent space through Invertible Neural Networks (INN). These models can generate multiple realistic SR images from one low-resolution (LR) input using randomly sampled points in the latent space, simulating the ill-posed nature of image upscaling where multiple high-resolution (HR) images correspond to the same LR. Lately, the invertible process in INN has also been used successfully by bidirectional image rescaling models like IRN and HCFlow for joint optimization of downscaling and inverse upscaling, resulting in significant improvements in upscaled image quality. While they are optimized for image downscaling too, the ill-posed nature of image downscaling, where one HR image could be downsized to multiple LR images depending on different interpolation kernels and resampling methods, is not considered. A new downscaling latent variable, in addition to the original one representing uncertainties in image upscaling, is introduced to model variations in the image downscaling process. This dual latent variable enhancement is applicable to different image rescaling models and it is shown in extensive experiments that it can improve image upscaling accuracy consistently without sacrificing image quality in downscaled LR images. It is also shown to be effective in enhancing other INN-based models for image restoration applications like image hiding.

  • 4 authors
·
Jul 24, 2022