Properties in material composition and crystal structures have been explored by density functional theory (DFT) calculations, using databases such as the Open Quantum Materials Database (OQMD). Databases like these have been used currently for the training of advanced machine learning and deep neural network models, the latter providing higher performance when predicting properties of materials. However, current alternatives have shown a deterioration in accuracy when increasing the number of layers in their architecture (over-fitting problem). As an alternative method to address this problem, we have implemented residual neural network architectures based on Merge and Run Networks, IRNet and UNet to improve performance while relaxing the observed network depth limitation. The evaluation of the proposed architectures include a 9:1 ratio to train and test as well as 10 fold cross validation. In the experiments we found that our proposed architectures based on IRNet and UNet are able to obtain a lower Mean Absolute Error (MAE) than current strategies. The full implementation (Python, Tensorflow and Keras) and the trained networks will be available online for community validation and advancing the state of the art from our findings.
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Extensible Structure-Informed Prediction of Formation Energy with improved accuracy and usability employing neural networks
In the present paper, we introduce a new neural network-based tool for the prediction of formation energies of atomic structures based on elemental and structural features of Voronoi-tessellated materials. We provide a concise overview of the connection between the machine learning and the true material–property relationship, how to improve the generalization accuracy by reducing overfitting, how new data can be incorporated into the model to tune it to a specific material system, and preliminary results on using models to preform local structure relaxations.
The present work resulted in three final models optimized for (1) highest test accuracy on the Open Quantum Materials Database (OQMD), (2) performance in the discovery of new materials, and (3) performance at a low computational cost. On a test set of 21,800 compounds randomly selected from OQMD, they achieve a mean absolute error (MAE) of 28, 40, and 42 meV/atom, respectively. The second model provides better predictions in a test case of interest not present in the OQMD, while the third reduces the computational cost by a factor of 8.
We collect our results in a new open-source tool called SIPFENN (Structure-Informed Prediction of Formation Energy using Neural Networks). SIPFENN not only improves the accuracy beyond existing models but also ships in a ready-to-use form with pre-trained neural networks and a GUI interface. By virtue of this, it can be included in DFT calculations routines at nearly no cost.
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- Award ID(s):
- 2050069
- NSF-PAR ID:
- 10318666
- Date Published:
- Journal Name:
- Computational materials science
- ISSN:
- 1879-0801
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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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 not 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.more » « less
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CuZrO 3 has been hypothesized to be a catalytic material with potential applications for CO 2 reduction. Unfortunately, this material has received limited attention in the literature, and to the best of our knowledge the exact crystal structure is still unknown. To address this challenge, we utilize several different structural prediction techniques in concert, including the Universal Structure Predictor: Evolutionary Xtallography (USPEX), the Materials Project Structure Predictor, and the Open Quantum Materials Database (OQMD). Leveraging these structural prediction techniques in conjunction with Density-Functional Theory (DFT) calculations, we determine a possible structure for CuZrO 3 , which resembles a “sandwich” morphology. Our calculations reveal that this new structure is significantly lower in energy than a previously hypothesized perovskite structure, albeit it still has a thermodynamic preference to decompose into CuO and ZrO 2 . In addition, we experimentally tried to synthesize CuZrO 3 based on literature reports and compared computational to experimental X-ray Diffraction (XRD) patterns confirming that the final product is a mixture of CuO and ZrO 2 . Finally, we conducted a computational surface energetics and CO 2 adsorption study on our discovered sandwich morphology, demonstrating that CO 2 can adsorb and activate on the material. However, these CO 2 adsorption results deviate from previously reported results further confirming that the CuZrO 3 is a metastable form and may not be experimentally accessible as a well-mixed oxide, since phase segregation to CuO and ZrO 2 is preferred. Taken together, our combined computational and experimental study provides evidence that the synthesis of CuZrO 3 is extremely difficult and if this oxide exists, it should have a sandwich-like morphology.more » « less
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null (Ed.)Abstract Deep neural networks (DNNs) have achieved state-of-the-art performance in many important domains, including medical diagnosis, security, and autonomous driving. In domains where safety is highly critical, an erroneous decision can result in serious consequences. While a perfect prediction accuracy is not always achievable, recent work on Bayesian deep networks shows that it is possible to know when DNNs are more likely to make mistakes. Knowing what DNNs do not know is desirable to increase the safety of deep learning technology in sensitive applications; Bayesian neural networks attempt to address this challenge. Traditional approaches are computationally intractable and do not scale well to large, complex neural network architectures. In this paper, we develop a theoretical framework to approximate Bayesian inference for DNNs by imposing a Bernoulli distribution on the model weights. This method called Monte Carlo DropConnect (MC-DropConnect) gives us a tool to represent the model uncertainty with little change in the overall model structure or computational cost. We extensively validate the proposed algorithm on multiple network architectures and datasets for classification and semantic segmentation tasks. We also propose new metrics to quantify uncertainty estimates. This enables an objective comparison between MC-DropConnect and prior approaches. Our empirical results demonstrate that the proposed framework yields significant improvement in both prediction accuracy and uncertainty estimation quality compared to the state of the art.more » « less
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Data driven generative deep learning models have recently emerged as one of the most promising approaches for new materials discovery. While generator models can generate millions of candidates, it is critical to train fast and accurate machine learning models to filter out stable, synthesizable materials with the desired properties. However, such efforts to build supervised regression or classification screening models have been severely hindered by the lack of unstable or unsynthesizable samples, which usually are not collected and deposited in materials databases such as ICSD and Materials Project (MP). At the same time, there is a significant amount of unlabelled data available in these databases. Here we propose a semi-supervised deep neural network (TSDNN) model for high-performance formation energy and synthesizability prediction, which is achieved via its unique teacher-student dual network architecture and its effective exploitation of the large amount of unlabeled data. For formation energy based stability screening, our semi-supervised classifier achieves an absolute 10.3% accuracy improvement compared to the baseline CGCNN regression model. For synthesizability prediction, our model significantly increases the baseline PU learning's true positive rate from 87.9% to 92.9% using 1/49 model parameters. To further prove the effectiveness of our models, we combined our TSDNN-energy and TSDNN-synthesizability models with our CubicGAN generator to discover novel stable cubic structures. Out of the 1000 recommended candidate samples by our models, 512 of them have negative formation energies as validated by our DFT formation energy calculations. Our experimental results show that our semi-supervised deep neural networks can significantly improve the screening accuracy in large-scale generative materials design. Our source code can be accessed at https://git/hub.com/usccolumbia/tsdnn.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1016/j.commatsci.2022.111254
