We use the Galaxy Morphology Posterior Estimation Network (GaMPEN) to estimate morphological parameters and associated uncertainties for ∼8 million galaxies in the Hyper Suprime-Cam Wide survey with
- Award ID(s):
- 1934757
- NSF-PAR ID:
- 10352446
- Date Published:
- Journal Name:
- Machine Learning: Science and Technology
- Volume:
- 3
- Issue:
- 1
- ISSN:
- 2632-2153
- Page Range / eLocation ID:
- 015007
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract z ≤ 0.75 andm ≤ 23. GaMPEN is a machine-learning framework that estimates Bayesian posteriors for a galaxy’s bulge-to-total light ratio (L B /L T ), effective radius (R e ), and flux (F ). By first training on simulations of galaxies and then applying transfer learning using real data, we trained GaMPEN with <1% of our data set. This two-step process will be critical for applying machine-learning algorithms to future large imaging surveys, such as the Rubin-Legacy Survey of Space and Time, the Nancy Grace Roman Space Telescope, and Euclid. By comparing our results to those obtained using light profile fitting, we demonstrate that GaMPEN’s predicted posterior distributions are well calibrated (≲5% deviation) and accurate. This represents a significant improvement over light profile fitting algorithms, which underestimate uncertainties by as much as ∼60%. For an overlapping subsample, we also compare the derived morphological parameters with values in two external catalogs and find that the results agree within the limits of uncertainties predicted by GaMPEN. This step also permits us to define an empirical relationship between the Sérsic index andL B /L T that can be used to convert between these two parameters. The catalog presented here represents a significant improvement in size (∼10×), depth (∼4 mag), and uncertainty quantification over previous state-of-the-art bulge+disk decomposition catalogs. With this work, we also release GaMPEN’s source code and trained models, which can be adapted to other data sets. -
Obeid, Iyad Selesnick (Ed.)Electroencephalography (EEG) is a popular clinical monitoring tool used for diagnosing brain-related disorders such as epilepsy [1]. As monitoring EEGs in a critical-care setting is an expensive and tedious task, there is a great interest in developing real-time EEG monitoring tools to improve patient care quality and efficiency [2]. However, clinicians require automatic seizure detection tools that provide decisions with at least 75% sensitivity and less than 1 false alarm (FA) per 24 hours [3]. Some commercial tools recently claim to reach such performance levels, including the Olympic Brainz Monitor [4] and Persyst 14 [5]. In this abstract, we describe our efforts to transform a high-performance offline seizure detection system [3] into a low latency real-time or online seizure detection system. An overview of the system is shown in Figure 1. The main difference between an online versus offline system is that an online system should always be causal and has minimum latency which is often defined by domain experts. The offline system, shown in Figure 2, uses two phases of deep learning models with postprocessing [3]. The channel-based long short term memory (LSTM) model (Phase 1 or P1) processes linear frequency cepstral coefficients (LFCC) [6] features from each EEG channel separately. We use the hypotheses generated by the P1 model and create additional features that carry information about the detected events and their confidence. The P2 model uses these additional features and the LFCC features to learn the temporal and spatial aspects of the EEG signals using a hybrid convolutional neural network (CNN) and LSTM model. Finally, Phase 3 aggregates the results from both P1 and P2 before applying a final postprocessing step. The online system implements Phase 1 by taking advantage of the Linux piping mechanism, multithreading techniques, and multi-core processors. To convert Phase 1 into an online system, we divide the system into five major modules: signal preprocessor, feature extractor, event decoder, postprocessor, and visualizer. The system reads 0.1-second frames from each EEG channel and sends them to the feature extractor and the visualizer. The feature extractor generates LFCC features in real time from the streaming EEG signal. Next, the system computes seizure and background probabilities using a channel-based LSTM model and applies a postprocessor to aggregate the detected events across channels. The system then displays the EEG signal and the decisions simultaneously using a visualization module. The online system uses C++, Python, TensorFlow, and PyQtGraph in its implementation. The online system accepts streamed EEG data sampled at 250 Hz as input. The system begins processing the EEG signal by applying a TCP montage [8]. Depending on the type of the montage, the EEG signal can have either 22 or 20 channels. To enable the online operation, we send 0.1-second (25 samples) length frames from each channel of the streamed EEG signal to the feature extractor and the visualizer. Feature extraction is performed sequentially on each channel. The signal preprocessor writes the sample frames into two streams to facilitate these modules. In the first stream, the feature extractor receives the signals using stdin. In parallel, as a second stream, the visualizer shares a user-defined file with the signal preprocessor. This user-defined file holds raw signal information as a buffer for the visualizer. The signal preprocessor writes into the file while the visualizer reads from it. Reading and writing into the same file poses a challenge. The visualizer can start reading while the signal preprocessor is writing into it. To resolve this issue, we utilize a file locking mechanism in the signal preprocessor and visualizer. Each of the processes temporarily locks the file, performs its operation, releases the lock, and tries to obtain the lock after a waiting period. The file locking mechanism ensures that only one process can access the file by prohibiting other processes from reading or writing while one process is modifying the file [9]. The feature extractor uses circular buffers to save 0.3 seconds or 75 samples from each channel for extracting 0.2-second or 50-sample long center-aligned windows. The module generates 8 absolute LFCC features where the zeroth cepstral coefficient is replaced by a temporal domain energy term. For extracting the rest of the features, three pipelines are used. The differential energy feature is calculated in a 0.9-second absolute feature window with a frame size of 0.1 seconds. The difference between the maximum and minimum temporal energy terms is calculated in this range. Then, the first derivative or the delta features are calculated using another 0.9-second window. Finally, the second derivative or delta-delta features are calculated using a 0.3-second window [6]. The differential energy for the delta-delta features is not included. In total, we extract 26 features from the raw sample windows which add 1.1 seconds of delay to the system. We used the Temple University Hospital Seizure Database (TUSZ) v1.2.1 for developing the online system [10]. The statistics for this dataset are shown in Table 1. A channel-based LSTM model was trained using the features derived from the train set using the online feature extractor module. A window-based normalization technique was applied to those features. In the offline model, we scale features by normalizing using the maximum absolute value of a channel [11] before applying a sliding window approach. Since the online system has access to a limited amount of data, we normalize based on the observed window. The model uses the feature vectors with a frame size of 1 second and a window size of 7 seconds. We evaluated the model using the offline P1 postprocessor to determine the efficacy of the delayed features and the window-based normalization technique. As shown by the results of experiments 1 and 4 in Table 2, these changes give us a comparable performance to the offline model. The online event decoder module utilizes this trained model for computing probabilities for the seizure and background classes. These posteriors are then postprocessed to remove spurious detections. The online postprocessor receives and saves 8 seconds of class posteriors in a buffer for further processing. It applies multiple heuristic filters (e.g., probability threshold) to make an overall decision by combining events across the channels. These filters evaluate the average confidence, the duration of a seizure, and the channels where the seizures were observed. The postprocessor delivers the label and confidence to the visualizer. The visualizer starts to display the signal as soon as it gets access to the signal file, as shown in Figure 1 using the “Signal File” and “Visualizer” blocks. Once the visualizer receives the label and confidence for the latest epoch from the postprocessor, it overlays the decision and color codes that epoch. The visualizer uses red for seizure with the label SEIZ and green for the background class with the label BCKG. Once the streaming finishes, the system saves three files: a signal file in which the sample frames are saved in the order they were streamed, a time segmented event (TSE) file with the overall decisions and confidences, and a hypotheses (HYP) file that saves the label and confidence for each epoch. The user can plot the signal and decisions using the signal and HYP files with only the visualizer by enabling appropriate options. For comparing the performance of different stages of development, we used the test set of TUSZ v1.2.1 database. It contains 1015 EEG records of varying duration. The any-overlap performance [12] of the overall system shown in Figure 2 is 40.29% sensitivity with 5.77 FAs per 24 hours. For comparison, the previous state-of-the-art model developed on this database performed at 30.71% sensitivity with 6.77 FAs per 24 hours [3]. The individual performances of the deep learning phases are as follows: Phase 1’s (P1) performance is 39.46% sensitivity and 11.62 FAs per 24 hours, and Phase 2 detects seizures with 41.16% sensitivity and 11.69 FAs per 24 hours. We trained an LSTM model with the delayed features and the window-based normalization technique for developing the online system. Using the offline decoder and postprocessor, the model performed at 36.23% sensitivity with 9.52 FAs per 24 hours. The trained model was then evaluated with the online modules. The current performance of the overall online system is 45.80% sensitivity with 28.14 FAs per 24 hours. Table 2 summarizes the performances of these systems. The performance of the online system deviates from the offline P1 model because the online postprocessor fails to combine the events as the seizure probability fluctuates during an event. The modules in the online system add a total of 11.1 seconds of delay for processing each second of the data, as shown in Figure 3. In practice, we also count the time for loading the model and starting the visualizer block. When we consider these facts, the system consumes 15 seconds to display the first hypothesis. The system detects seizure onsets with an average latency of 15 seconds. Implementing an automatic seizure detection model in real time is not trivial. We used a variety of techniques such as the file locking mechanism, multithreading, circular buffers, real-time event decoding, and signal-decision plotting to realize the system. A video demonstrating the system is available at: https://www.isip.piconepress.com/projects/nsf_pfi_tt/resources/videos/realtime_eeg_analysis/v2.5.1/video_2.5.1.mp4. The final conference submission will include a more detailed analysis of the online performance of each module. ACKNOWLEDGMENTS Research reported in this publication was most recently supported by the National Science Foundation Partnership for Innovation award number IIP-1827565 and the Pennsylvania Commonwealth Universal Research Enhancement Program (PA CURE). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the official views of any of these organizations. REFERENCES [1] A. Craik, Y. He, and J. L. Contreras-Vidal, “Deep learning for electroencephalogram (EEG) classification tasks: a review,” J. Neural Eng., vol. 16, no. 3, p. 031001, 2019. https://doi.org/10.1088/1741-2552/ab0ab5. [2] A. C. Bridi, T. Q. Louro, and R. C. L. Da Silva, “Clinical Alarms in intensive care: implications of alarm fatigue for the safety of patients,” Rev. Lat. Am. Enfermagem, vol. 22, no. 6, p. 1034, 2014. https://doi.org/10.1590/0104-1169.3488.2513. [3] M. Golmohammadi, V. Shah, I. Obeid, and J. Picone, “Deep Learning Approaches for Automatic Seizure Detection from Scalp Electroencephalograms,” 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, New York, USA: Springer, 2020, pp. 233–274. https://doi.org/10.1007/978-3-030-36844-9_8. [4] “CFM Olympic Brainz Monitor.” [Online]. Available: https://newborncare.natus.com/products-services/newborn-care-products/newborn-brain-injury/cfm-olympic-brainz-monitor. [Accessed: 17-Jul-2020]. [5] M. L. Scheuer, S. B. Wilson, A. Antony, G. Ghearing, A. Urban, and A. I. Bagic, “Seizure Detection: Interreader Agreement and Detection Algorithm Assessments Using a Large Dataset,” J. Clin. Neurophysiol., 2020. https://doi.org/10.1097/WNP.0000000000000709. [6] A. Harati, M. Golmohammadi, S. Lopez, I. Obeid, and J. Picone, “Improved EEG Event Classification Using Differential Energy,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium, 2015, pp. 1–4. https://doi.org/10.1109/SPMB.2015.7405421. [7] V. Shah, C. Campbell, I. Obeid, and J. Picone, “Improved Spatio-Temporal Modeling in Automated Seizure Detection using Channel-Dependent Posteriors,” Neurocomputing, 2021. [8] W. Tatum, A. Husain, S. Benbadis, and P. Kaplan, Handbook of EEG Interpretation. New York City, New York, USA: Demos Medical Publishing, 2007. [9] D. P. Bovet and C. Marco, Understanding the Linux Kernel, 3rd ed. O’Reilly Media, Inc., 2005. https://www.oreilly.com/library/view/understanding-the-linux/0596005652/. [10] V. Shah et al., “The Temple University Hospital Seizure Detection Corpus,” Front. Neuroinform., vol. 12, pp. 1–6, 2018. https://doi.org/10.3389/fninf.2018.00083. [11] F. Pedregosa et al., “Scikit-learn: Machine Learning in Python,” J. Mach. Learn. Res., vol. 12, pp. 2825–2830, 2011. https://dl.acm.org/doi/10.5555/1953048.2078195. [12] J. Gotman, D. Flanagan, J. Zhang, and B. Rosenblatt, “Automatic seizure detection in the newborn: Methods and initial evaluation,” Electroencephalogr. Clin. Neurophysiol., vol. 103, no. 3, pp. 356–362, 1997. https://doi.org/10.1016/S0013-4694(97)00003-9.more » « less
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Abstract In a novel approach employing implicit likelihood inference (ILI), also known as likelihood-free inference, we calibrate the parameters of cosmological hydrodynamic simulations against observations, which has previously been unfeasible due to the high computational cost of these simulations. For computational efficiency, we train neural networks as emulators on ∼1000 cosmological simulations from the CAMELS project to estimate simulated observables, taking as input the cosmological and astrophysical parameters, and use these emulators as surrogates for the cosmological simulations. Using the cosmic star formation rate density (SFRD) and, separately, the stellar mass functions (SMFs) at different redshifts, we perform ILI on selected cosmological and astrophysical parameters (Ω
m ,σ 8, stellar wind feedback, and kinetic black hole feedback) and obtain full six-dimensional posterior distributions. In the performance test, the ILI from the emulated SFRD (SMFs) can recover the target observables with a relative error of 0.17% (0.4%). We find that degeneracies exist between the parameters inferred from the emulated SFRD, confirmed with new full cosmological simulations. We also find that the SMFs can break the degeneracy in the SFRD, which indicates that the SMFs provide complementary constraints for the parameters. Further, we find that a parameter combination inferred from an observationally inferred SFRD reproduces the target observed SFRD very well, whereas, in the case of the SMFs, the inferred and observed SMFs show significant discrepancies that indicate potential limitations of the current galaxy formation modeling and calibration framework, and/or systematic differences and inconsistencies between observations of the SMFs. -
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Abstract As the next generation of large galaxy surveys come online, it is becoming increasingly important to develop and understand the machine-learning tools that analyze big astronomical data. Neural networks are powerful and capable of probing deep patterns in data, but they must be trained carefully on large and representative data sets. We present a new “hump” of the Cosmology and Astrophysics with MachinE Learning Simulations (CAMELS) project: CAMELS-SAM, encompassing one thousand dark-matter-only simulations of (100
h −1cMpc)3with different cosmological parameters (Ωm andσ 8) and run through the Santa Cruz semi-analytic model for galaxy formation over a broad range of astrophysical parameters. As a proof of concept for the power of this vast suite of simulated galaxies in a large volume and broad parameter space, we probe the power of simple clustering summary statistics to marginalize over astrophysics and constrain cosmology using neural networks. We use the two-point correlation, count-in-cells, and void probability functions, and we probe nonlinear and linear scales across 0.68 <R <27h −1cMpc. We find our neural networks can both marginalize over the uncertainties in astrophysics to constrain cosmology to 3%–8% error across various types of galaxy selections, while simultaneously learning about the SC-SAM astrophysical parameters. This work encompasses vital first steps toward creating algorithms able to marginalize over the uncertainties in our galaxy formation models and measure the underlying cosmology of our Universe. CAMELS-SAM has been publicly released alongside the rest of CAMELS, and it offers great potential to many applications of machine learning in astrophysics:https://camels-sam.readthedocs.io . -
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Abstract We introduce a novel machine-learning framework for estimating the Bayesian posteriors of morphological parameters for arbitrarily large numbers of galaxies. The Galaxy Morphology Posterior Estimation Network (GaMPEN) estimates values and uncertainties for a galaxy’s bulge-to-total-light ratio (
L B /L T ), effective radius (R e ), and flux (F ). To estimate posteriors, GaMPEN uses the Monte Carlo Dropout technique and incorporates the full covariance matrix between the output parameters in its loss function. GaMPEN also uses a spatial transformer network (STN) to automatically crop input galaxy frames to an optimal size before determining their morphology. This will allow it to be applied to new data without prior knowledge of galaxy size. Training and testing GaMPEN on galaxies simulated to matchz < 0.25 galaxies in Hyper Suprime-Cam Wideg -band images, we demonstrate that GaMPEN achieves typical errors of 0.1 inL B /L T , 0.″17 (∼7%) inR e , and 6.3 × 104nJy (∼1%) inF . GaMPEN's predicted uncertainties are well calibrated and accurate (<5% deviation)—for regions of the parameter space with high residuals, GaMPEN correctly predicts correspondingly large uncertainties. We also demonstrate that we can apply categorical labels (i.e., classifications such ashighly bulge dominated ) to predictions in regions with high residuals and verify that those labels are ≳97% accurate. To the best of our knowledge, GaMPEN is the first machine-learning framework for determining joint posterior distributions of multiple morphological parameters and is also the first application of an STN to optical imaging in astronomy.
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- https://doi.org/10.1088/2632-2153/ac3843
