Publications

Highlights

(For a full list of publications and patents see below)

Self-Supervised Deep Learning for Model Correction in the Computational Crystallography Toolbox

The Computational Crystallography Toolbox (CCTBX) is open-source software that allows for processing of crystallographic data, including from serial femtosecond crystallography (SFX), for macromolecular structure determination. We describe the potential impact of using self-supervised deep learning to correct the scientific model in CCTBX and provide uncertainty quantification. We describe open questions in algorithm development to help spur advances through dialog between crystallographers and machine learning researchers.

Vidya Ganapati, Daniel Tchon, Aaron S. Brewster, Nicholas K. Sauter

ICML 2023 SynS & ML Workshop

| Link | PDF | Code |

Data-Driven Computational Imaging for Scientific Discovery

This work creates a novel method for data-driven reconstruction in computational imaging, when no ground truth training dataset is available. Light-emitting diode (LED) array microscopy, a modality that allows visualization of transparent objects in two and three dimensions with high resolution and field-of-view, is used as an illustrative example. Future directions are outlined for making this method applicable to large-scale scientific problems.

Andrew Olsen, Yolanda Hu, Vidya Ganapati

NeurIPS 2022 AI for Science Workshop

| Link | PDF | Code | Data |

A Self-Supervised Approach to Reconstruction in Sparse X-Ray Computed Tomography

Computed tomography allows for the elucidation of 3-dimensional internal structure by the attenuation of x-rays through an object at different rotations relative to the beam. However, the x-ray beam can damage the sample, necessitating the development of sparse x-ray tomography that only requires measurements at a low number of rotation angles. This work develops and validates a self-supervised probabilistic deep learning technique for object reconstruction in this sparse regime.

Rey Mendoza, Minh Nguyen, Judith Weng Zhu, Vincent Dumont, Talita Perciano, Juliane Mueller, Vidya Ganapati

NeurIPS 2022 Machine Learning and the Physical Sciences Workshop

| Link | PDF | Code |

Evaluating Research Grade Bioimpedance Hardware using Textile Electrodes for Long-term Fluid Status Monitoring

Human calf bioimpedance can be a useful for diagnostics and monitoring in conditions such as congestive heart failure. We prototype a fabric sock to mimic a printed circuit board and electronically connect to the calf; the sock consists of layers of conductive and insulating fabric connected by metallic snaps that act as vias.

Maggie Delano, Vidya Ganapati, Rezhwan Kamal, Bryan Le, Jackie Le, Rey Mendoza

Frontiers in Electronics (2022)

| Link | PDF |

HYPPO: A Surrogate-Based Multi-Level Parallelism Tool for Hyperparameter Optimization

What are the best hyperparameters (e.g. batch size, training rate, network depth) for a neural network? We would like to optimize these hyperparameters, but obtaining the derivatives for a gradient-based search is difficult. Thus, we estimate surrogate models of the underlying function relating the hyperparameters to figure of merit. Using forward function calls, we improve this surrogate function until our compute budget runs out. We validate HYPPO for different use cases, including sparse x-ray computed tomography.

Vincent Dumont, Casey Garner, Anuradha Trivedi, Chelsea Jones, Vidya Ganapati, Juliane Mueller, Talita Perciano, Mariam Kiran, Marc Day

2021 IEEE/ACM Workshop on Machine Learning in High Performance Computing Environments

| Link | PDF | Code |

See code documentation here.

Ultraefficient thermophotovoltaic power conversion by band-edge spectral filtering

Thermophotovoltaics (TPV) convert radiative heat to electricity with photovoltaics cells. This is a generalization of solar photovoltaics, which convert the radiation of the sun to electricity. TPV has the potential for high-efficiency electrical power generation from the combustion of fuel. TPV can also be used for converting waste heat or stored thermal energy to electricity. We achieved a record 28.8% efficiency of heat to electricity conversion by using photovoltaic cells with high back reflectivity.

Zunaid Omair, Gregg Scranton, Luis M. Pazos-Outón, T. Patrick Xiao, Myles A. Steiner, Vidya Ganapati, Per F. Peterson, John Holzrichter, Harry Atwater, Eli Yablonovitch

Proceedings of the National Academy of Sciences (2019)

| Link | PDF |

Illumination pattern design with deep learning for single-shot Fourier ptychographic microscopy

An experimental validation of the methods proposed and tested in simulation in Robey and Ganapati.

Yi Fei Cheng, Megan Strachan, Zachary Weiss, Moniher Deb, Dawn Carone, Vidya Ganapati

Optics Express (2019)

| Link | PDF |

Optimal physical preprocessing for example-based super-resolution

Computational imaging concerns the joint design of physical hardware with image post-processing algorithms. The data recorded by the image sensor may be garbled, but as long as it contains the necessary information, the final image can be reconstructed with image post-processing. The advantages of computational imaging are reduced hardware costs and the possible recovery of quantities difficult to image directly, such as depth and the phase of light. We optimize the end-to-end computational imaging pipeline with deep learning, in order to surpass existing imaging tradeoffs among speed, resolution, and field-of-view.

Alexander Robey, Vidya Ganapati

Optics Express (2018)

| Link | PDF |

Air Gaps as Intermediate Selective Reflectors to Reach Theoretical Efficiency Limits of Multibandgap Solar Cells

We proposed low-index intermediate “mirrors” to increase the efficiency of multi-bandgap solar cells. This theoretical result was validated with a 38.8% efficiency 4-bandgap solar cell developed at the National Renewable Energy Laboratory, setting the efficiency record for flat-plate solar cells.

Vidya Ganapati, Chi-Sing Ho, Eli Yablonovitch

IEEE Journal of Photovoltaics (2014)

| Link | PDF |

Light Trapping Textures Designed by Electromagnetic Optimization for Subwavelength Thick Solar Cells

Solar cells are routinely textured in order to increase light absorption and efficiency. The benefits of texturing are generally evaluated using ray optics approximations. These approximations fail when the solar cell thickness is on the order of the wavelength of light. We use inverse design and shape calculus to optimize surface textures for subwavelength-thick solar cells. We show that with optimized designs we can approach ray-optics limits for these thin cells.

Vidya Ganapati, Owen D. Miller, Eli Yablonovitch

IEEE Journal of Photovoltaics (2014)

| Link | PDF |

 

Patents

System and method for multiclass classification of images using a programmable light source
Vidya Ganapati, Eden Rephaeli
US Patent 11,229,353
| Link | PDF |

Optical implementation of machine learning for real time increased contrast via multiple wavelength illumination with tunable power
Eden Rephaeli, Vidya Ganapati, Daniele Piponi, Thomas Teisseyre
US Patent 10,878,264
| Link | PDF |

Tunable color-temperature white light source
Vidya Ganapati, Supriyo Sinha, Eden Rephaeli
US Patent 10,835,102
| Link | PDF |

Simultaneous visible and fluorescence endoscopic imaging
Vidya Ganapati, Eden Rephaeli, Daniele Piponi
US Patent 10,473,911
| Link | PDF |

System and method for 3D scene reconstruction with dual complementary pattern illumination
Vidya Ganapati, Eden Rephaeli
US Patent 10,410,365
| Link | PDF |

Parallel programmable array microscope
Victor M. Acosta, Vidya Ganapati
US Patent 9,535,242
| Link | PDF |

Full List of Publications

Self-Supervised Deep Learning for Model Correction in the Computational Crystallography Toolbox
Vidya Ganapati, Daniel Tchon, Aaron S. Brewster, Nicholas K. Sauter
ICML 2023 SynS & ML Workshop
| Link | PDF | Code |

Data-Driven Computational Imaging for Scientific Discovery
Andrew Olsen, Yolanda Hu, Vidya Ganapati
NeurIPS 2022 AI for Science Workshop
| Link | PDF | Code | Data |

A Self-Supervised Approach to Reconstruction in Sparse X-Ray Computed Tomography
Rey Mendoza, Minh Nguyen, Judith Weng Zhu, Vincent Dumont, Talita Perciano, Juliane Mueller, Vidya Ganapati
NeurIPS 2022 Machine Learning and the Physical Sciences Workshop
| Link | PDF | Code |

Evaluating Research Grade Bioimpedance Hardware using Textile Electrodes for Long-term Fluid Status Monitoring
Maggie Delano, Vidya Ganapati, Rezhwan Kamal, Bryan Le, Jackie Le, Rey Mendoza
Frontiers in Electronics (2022)
| Link | PDF |

HYPPO: A Surrogate-Based Multi-Level Parallelism Tool for Hyperparameter Optimization
Vincent Dumont, Casey Garner, Anuradha Trivedi, Chelsea Jones, Vidya Ganapati, Juliane Mueller, Talita Perciano, Mariam Kiran, Marc Day
2021 IEEE/ACM Workshop on Machine Learning in High Performance Computing Environments
| Link | PDF | Code |

Ultraefficient thermophotovoltaic power conversion by band-edge spectral filtering
Zunaid Omair, Gregg Scranton, Luis M. Pazos-Outón, T. Patrick Xiao, Myles A. Steiner, Vidya Ganapati, Per F. Peterson, John Holzrichter, Harry Atwater, Eli Yablonovitch
Proceedings of the National Academy of Sciences (2019)
| Link | PDF |

Deep Learned Optical Multiplexing for Multi-Focal Plane Microscopy
Yi Fei Cheng, Ziad Sabry, Megan Strachan, Skyler Cornell, Jake Chanenson, Eva-Maria S. Collins, Vidya Ganapati
arXiv:1907.01528 (2019)
| Link | PDF |

Illumination pattern design with deep learning for single-shot Fourier ptychographic microscopy
Yi Fei Cheng, Megan Strachan, Zachary Weiss, Moniher Deb, Dawn Carone, Vidya Ganapati
Optics Express (2019)
| Link | PDF |

Optimal physical preprocessing for example-based super-resolution
Alexander Robey, Vidya Ganapati
Optics Express (2018)
| Link | PDF |

Ultra-Efficient Thermophotovoltaics Exploiting Spectral Filtering by the Photovoltaic Band-Edge
Vidya Ganapati, T. Patrick Xiao, Eli Yablonovitch
arXiv:1611.03544 (2016)
| Link | PDF |

The Voltage Boost Enabled by Luminescence Extraction in Solar Cells
Vidya Ganapati, Myles A. Steiner, Eli Yablonovitch
IEEE Journal of Photovoltaics (2016)
| Link | PDF |

Air Gaps as Intermediate Selective Reflectors to Reach Theoretical Efficiency Limits of Multibandgap Solar Cells
Vidya Ganapati, Chi-Sing Ho, Eli Yablonovitch
IEEE Journal of Photovoltaics (2014)
| Link | PDF |

Single spherical mirror optic for extreme ultraviolet lithography enabled by inverse lithography technology
Gregg Scranton, Samarth Bhargava, Vidya Ganapati, Eli Yablonovitch
Optics Express (2014)
| Link | PDF |

Light Trapping Textures Designed by Electromagnetic Optimization for Subwavelength Thick Solar Cells
Vidya Ganapati, Owen D. Miller, Eli Yablonovitch
IEEE Journal of Photovoltaics (2014)
| Link | PDF |

Seeding of Silicon Wire Growth by Out-Diffused Metal Precipitates
Vidya Ganapati, David P. Fenning, Mariana I. Bertoni, Chito E. Kendrick, Alexandria E. Fecych, Joan M. Redwing, Tonio Buonassisi
Small (2011)
| Link | PDF |

Infrared birefringence imaging of residual stress and bulk defects in multicrystalline silicon
Vidya Ganapati, Stephan Schoenfelder, Sergio Castellanos, Sebastian Oener, Ringo Koepge, Aaron Sampson, Matthew A. Marcus, Barry Lai, Humphrey Morhenn, Giso Hahn, Joerg Bagdahn, Tonio Buonassisi
Journal of Applied Physics (2010)
| Link | PDF |