skip to main content

Title: Dense Transformer Networks for Brain Electron Microscopy Image Segmentation

The key idea of current deep learning methods for dense prediction is to apply a model on a regular patch centered on each pixel to make pixel-wise predictions. These methods are limited in the sense that the patches are determined by network architecture instead of learned from data. In this work, we propose the dense transformer networks, which can learn the shapes and sizes of patches from data. The dense transformer networks employ an encoder-decoder architecture, and a pair of dense transformer modules are inserted into each of the encoder and decoder paths. The novelty of this work is that we provide technical solutions for learning the shapes and sizes of patches from data and efficiently restoring the spatial correspondence required for dense prediction. The proposed dense transformer modules are differentiable, thus the entire network can be trained. We apply the proposed networks on biological image segmentation tasks and show superior performance is achieved in comparison to baseline methods.

Authors:
; ; ; ;
Award ID(s):
2028361
Publication Date:
NSF-PAR ID:
10148041
Journal Name:
Proceedings of the 28th International Joint Conference on Artificial Intelligence
Page Range or eLocation-ID:
2894 to 2900
Sponsoring Org:
National Science Foundation
More Like this
  1. The automatic classification of electrocardiogram (ECG) signals has played an important role in cardiovascular diseases diagnosis and prediction. Deep neural networks (DNNs), particularly Convolutional Neural Networks (CNNs), have excelled in a variety of intelligent tasks including biomedical and health informatics. Most the existing approaches either partition the ECG time series into a set of segments and apply 1D-CNNs or divide the ECG signal into a set of spectrogram images and apply 2D-CNNs. These studies, however, suffer from the limitation that temporal dependencies between 1D segments or 2D spectrograms are not considered during network construction. Furthermore, meta-data including gender and age has not been well studied in these researches. To address those limitations, we propose a multi-module Recurrent Convolutional Neural Networks (RCNNs) consisting of both CNNs to learn spatial representation and Recurrent Neural Networks (RNNs) to model the temporal relationship. Our multi-module RCNNs architecture is designed as an end-to-end deep framework with four modules: (i) timeseries module by 1D RCNNs which extracts spatio-temporal information of ECG time series; (ii) spectrogram module by 2D RCNNs which learns visual-temporal representation of ECG spectrogram ; (iii) metadata module which vectorizes age and gender information; (iv) fusion module which semantically fuses the information from threemore »above modules by a transformer encoder. Ten-fold cross validation was used to evaluate the approach on the MIT-BIH arrhythmia database (MIT-BIH) under different network configurations. The experimental results have proved that our proposed multi-module RCNNs with transformer encoder achieves the state-of-the-art with 99.14% F1 score and 98.29% accuracy.« less
  2. The key challenge in photorealistic style transfer is that an algorithm should faithfully transfer the style of a reference photo to a content photo while the generated image should look like one captured by a camera. Although several photorealistic style transfer algorithms have been proposed, they need to rely on post- and/or pre-processing to make the generated images look photorealistic. If we disable the additional processing, these algorithms would fail to produce plausible photorealistic stylization in terms of detail preservation and photorealism. In this work, we propose an effective solution to these issues. Our method consists of a construction step (C-step) to build a photorealistic stylization network and a pruning step (P-step) for acceleration. In the C-step, we propose a dense auto-encoder named PhotoNet based on a carefully designed pre-analysis. PhotoNet integrates a feature aggregation module (BFA) and instance normalized skip links (INSL). To generate faithful stylization, we introduce multiple style transfer modules in the decoder and INSLs. PhotoNet significantly outperforms existing algorithms in terms of both efficiency and effectiveness. In the P-step, we adopt a neural architecture search method to accelerate PhotoNet. We propose an automatic network pruning framework in the manner of teacher-student learning for photorealistic stylization. Themore »network architecture named PhotoNAS resulted from the search achieves significant acceleration over PhotoNet while keeping the stylization effects almost intact. We conduct extensive experiments on both image and video transfer. The results show that our method can produce favorable results while achieving 20-30 times acceleration in comparison with the existing state-of-the-art approaches. It is worth noting that the proposed algorithm accomplishes better performance without any pre- or post-processing.« less
  3. Obeid, I. (Ed.)
    The Neural Engineering Data Consortium (NEDC) is developing the Temple University Digital Pathology Corpus (TUDP), an open source database of high-resolution images from scanned pathology samples [1], as part of its National Science Foundation-funded Major Research Instrumentation grant titled “MRI: High Performance Digital Pathology Using Big Data and Machine Learning” [2]. The long-term goal of this project is to release one million images. We have currently scanned over 100,000 images and are in the process of annotating breast tissue data for our first official corpus release, v1.0.0. This release contains 3,505 annotated images of breast tissue including 74 patients with cancerous diagnoses (out of a total of 296 patients). In this poster, we will present an analysis of this corpus and discuss the challenges we have faced in efficiently producing high quality annotations of breast tissue. It is well known that state of the art algorithms in machine learning require vast amounts of data. Fields such as speech recognition [3], image recognition [4] and text processing [5] are able to deliver impressive performance with complex deep learning models because they have developed large corpora to support training of extremely high-dimensional models (e.g., billions of parameters). Other fields that do notmore »have access to such data resources must rely on techniques in which existing models can be adapted to new datasets [6]. A preliminary version of this breast corpus release was tested in a pilot study using a baseline machine learning system, ResNet18 [7], that leverages several open-source Python tools. The pilot corpus was divided into three sets: train, development, and evaluation. Portions of these slides were manually annotated [1] using the nine labels in Table 1 [8] to identify five to ten examples of pathological features on each slide. Not every pathological feature is annotated, meaning excluded areas can include focuses particular to these labels that are not used for training. A summary of the number of patches within each label is given in Table 2. To maintain a balanced training set, 1,000 patches of each label were used to train the machine learning model. Throughout all sets, only annotated patches were involved in model development. The performance of this model in identifying all the patches in the evaluation set can be seen in the confusion matrix of classification accuracy in Table 3. The highest performing labels were background, 97% correct identification, and artifact, 76% correct identification. A correlation exists between labels with more than 6,000 development patches and accurate performance on the evaluation set. Additionally, these results indicated a need to further refine the annotation of invasive ductal carcinoma (“indc”), inflammation (“infl”), nonneoplastic features (“nneo”), normal (“norm”) and suspicious (“susp”). This pilot experiment motivated changes to the corpus that will be discussed in detail in this poster presentation. To increase the accuracy of the machine learning model, we modified how we addressed underperforming labels. One common source of error arose with how non-background labels were converted into patches. Large areas of background within other labels were isolated within a patch resulting in connective tissue misrepresenting a non-background label. In response, the annotation overlay margins were revised to exclude benign connective tissue in non-background labels. Corresponding patient reports and supporting immunohistochemical stains further guided annotation reviews. The microscopic diagnoses given by the primary pathologist in these reports detail the pathological findings within each tissue site, but not within each specific slide. The microscopic diagnoses informed revisions specifically targeting annotated regions classified as cancerous, ensuring that the labels “indc” and “dcis” were used only in situations where a micropathologist diagnosed it as such. Further differentiation of cancerous and precancerous labels, as well as the location of their focus on a slide, could be accomplished with supplemental immunohistochemically (IHC) stained slides. When distinguishing whether a focus is a nonneoplastic feature versus a cancerous growth, pathologists employ antigen targeting stains to the tissue in question to confirm the diagnosis. For example, a nonneoplastic feature of usual ductal hyperplasia will display diffuse staining for cytokeratin 5 (CK5) and no diffuse staining for estrogen receptor (ER), while a cancerous growth of ductal carcinoma in situ will have negative or focally positive staining for CK5 and diffuse staining for ER [9]. Many tissue samples contain cancerous and non-cancerous features with morphological overlaps that cause variability between annotators. The informative fields IHC slides provide could play an integral role in machine model pathology diagnostics. Following the revisions made on all the annotations, a second experiment was run using ResNet18. Compared to the pilot study, an increase of model prediction accuracy was seen for the labels indc, infl, nneo, norm, and null. This increase is correlated with an increase in annotated area and annotation accuracy. Model performance in identifying the suspicious label decreased by 25% due to the decrease of 57% in the total annotated area described by this label. A summary of the model performance is given in Table 4, which shows the new prediction accuracy and the absolute change in error rate compared to Table 3. The breast tissue subset we are developing includes 3,505 annotated breast pathology slides from 296 patients. The average size of a scanned SVS file is 363 MB. The annotations are stored in an XML format. A CSV version of the annotation file is also available which provides a flat, or simple, annotation that is easy for machine learning researchers to access and interface to their systems. Each patient is identified by an anonymized medical reference number. Within each patient’s directory, one or more sessions are identified, also anonymized to the first of the month in which the sample was taken. These sessions are broken into groupings of tissue taken on that date (in this case, breast tissue). A deidentified patient report stored as a flat text file is also available. Within these slides there are a total of 16,971 total annotated regions with an average of 4.84 annotations per slide. Among those annotations, 8,035 are non-cancerous (normal, background, null, and artifact,) 6,222 are carcinogenic signs (inflammation, nonneoplastic and suspicious,) and 2,714 are cancerous labels (ductal carcinoma in situ and invasive ductal carcinoma in situ.) The individual patients are split up into three sets: train, development, and evaluation. Of the 74 cancerous patients, 20 were allotted for both the development and evaluation sets, while the remain 34 were allotted for train. The remaining 222 patients were split up to preserve the overall distribution of labels within the corpus. This was done in hope of creating control sets for comparable studies. Overall, the development and evaluation sets each have 80 patients, while the training set has 136 patients. In a related component of this project, slides from the Fox Chase Cancer Center (FCCC) Biosample Repository (https://www.foxchase.org/research/facilities/genetic-research-facilities/biosample-repository -facility) are being digitized in addition to slides provided by Temple University Hospital. This data includes 18 different types of tissue including approximately 38.5% urinary tissue and 16.5% gynecological tissue. These slides and the metadata provided with them are already anonymized and include diagnoses in a spreadsheet with sample and patient ID. We plan to release over 13,000 unannotated slides from the FCCC Corpus simultaneously with v1.0.0 of TUDP. Details of this release will also be discussed in this poster. Few digitally annotated databases of pathology samples like TUDP exist due to the extensive data collection and processing required. The breast corpus subset should be released by November 2021. By December 2021 we should also release the unannotated FCCC data. We are currently annotating urinary tract data as well. We expect to release about 5,600 processed TUH slides in this subset. We have an additional 53,000 unprocessed TUH slides digitized. Corpora of this size will stimulate the development of a new generation of deep learning technology. In clinical settings where resources are limited, an assistive diagnoses model could support pathologists’ workload and even help prioritize suspected cancerous cases. ACKNOWLEDGMENTS This material is supported by the National Science Foundation under grants nos. CNS-1726188 and 1925494. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. REFERENCES [1] N. Shawki et al., “The Temple University Digital Pathology Corpus,” in Signal Processing in Medicine and Biology: Emerging Trends in Research and Applications, 1st ed., I. Obeid, I. Selesnick, and J. Picone, Eds. New York City, New York, USA: Springer, 2020, pp. 67 104. https://www.springer.com/gp/book/9783030368432. [2] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning.” Major Research Instrumentation (MRI), Division of Computer and Network Systems, Award No. 1726188, January 1, 2018 – December 31, 2021. https://www. isip.piconepress.com/projects/nsf_dpath/. [3] A. Gulati et al., “Conformer: Convolution-augmented Transformer for Speech Recognition,” in Proceedings of the Annual Conference of the International Speech Communication Association (INTERSPEECH), 2020, pp. 5036-5040. https://doi.org/10.21437/interspeech.2020-3015. [4] C.-J. Wu et al., “Machine Learning at Facebook: Understanding Inference at the Edge,” in Proceedings of the IEEE International Symposium on High Performance Computer Architecture (HPCA), 2019, pp. 331–344. https://ieeexplore.ieee.org/document/8675201. [5] I. Caswell and B. Liang, “Recent Advances in Google Translate,” Google AI Blog: The latest from Google Research, 2020. [Online]. Available: https://ai.googleblog.com/2020/06/recent-advances-in-google-translate.html. [Accessed: 01-Aug-2021]. [6] V. Khalkhali, N. Shawki, V. Shah, M. Golmohammadi, I. Obeid, and J. Picone, “Low Latency Real-Time Seizure Detection Using Transfer Deep Learning,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2021, pp. 1 7. https://www.isip. piconepress.com/publications/conference_proceedings/2021/ieee_spmb/eeg_transfer_learning/. [7] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning,” Philadelphia, Pennsylvania, USA, 2020. https://www.isip.piconepress.com/publications/reports/2020/nsf/mri_dpath/. [8] I. Hunt, S. Husain, J. Simons, I. Obeid, and J. Picone, “Recent Advances in the Temple University Digital Pathology Corpus,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2019, pp. 1–4. https://ieeexplore.ieee.org/document/9037859. [9] A. P. Martinez, C. Cohen, K. Z. Hanley, and X. (Bill) Li, “Estrogen Receptor and Cytokeratin 5 Are Reliable Markers to Separate Usual Ductal Hyperplasia From Atypical Ductal Hyperplasia and Low-Grade Ductal Carcinoma In Situ,” Arch. Pathol. Lab. Med., vol. 140, no. 7, pp. 686–689, Apr. 2016. https://doi.org/10.5858/arpa.2015-0238-OA.« less
  4. Deep-learning (DL)-based object detection algorithms can greatly benefit the community at large in fighting fires, advancing climate intelligence, and reducing health complications caused by hazardous smoke particles. Existing DL-based techniques, which are mostly based on convolutional networks, have proven to be effective in wildfire detection. However, there is still room for improvement. First, existing methods tend to have some commercial aspects, with limited publicly available data and models. In addition, studies aiming at the detection of wildfires at the incipient stage are rare. Smoke columns at this stage tend to be small, shallow, and often far from view, with low visibility. This makes finding and labeling enough data to train an efficient deep learning model very challenging. Finally, the inherent locality of convolution operators limits their ability to model long-range correlations between objects in an image. Recently, encoder–decoder transformers have emerged as interesting solutions beyond natural language processing to help capture global dependencies via self- and inter-attention mechanisms. We propose Nemo: a set of evolving, free, and open-source datasets, processed in standard COCO format, and wildfire smoke and fine-grained smoke density detectors, for use by the research community. We adapt Facebook’s DEtection TRansformer (DETR) to wildfire detection, which results inmore »a much simpler technique, where the detection does not rely on convolution filters and anchors. Nemo is the first open-source benchmark for wildfire smoke density detection and Transformer-based wildfire smoke detection tailored to the early incipient stage. Two popular object detection algorithms (Faster R-CNN and RetinaNet) are used as alternatives and baselines for extensive evaluation. Our results confirm the superior performance of the transformer-based method in wildfire smoke detection across different object sizes. Moreover, we tested our model with 95 video sequences of wildfire starts from the public HPWREN database. Our model detected 97.9% of the fires in the incipient stage and 80% within 5 min from the start. On average, our model detected wildfire smoke within 3.6 min from the start, outperforming the baselines.« less
  5. Recent papers in neural machine translation have proposed the strict use of attention mechanisms over previous stan- dards such as recurrent and convolutional neural networks (RNNs and CNNs). We propose that by running traditionally stacked encoding branches from encoder-decoder attention- focused architectures in parallel, that even more sequential operations can be removed from the model and thereby de- crease training time. In particular, we modify the recently published attention-based architecture called Transformer by Google, by replacing sequential attention modules with par- allel ones, reducing the amount of training time and substan- tially improving BLEU scores at the same time. Experiments over the English to German and English to French translation tasks show that our model establishes a new state of the art.