added most of the papers.bib

Author: mridulk97

_bibliography/papers.bib

@@ -4,16 +4,15 @@
 @string{aps = {American Physical Society,}}
 
 @article{khurana2024hierarchical,
-  title={Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution},
-  author={Khurana, Mridul and Daw, Arka and Maruf, M and Uyeda, Josef C and Dahdul, Wasila and Charpentier, Caleb and Bak{\i}{\c{s}}, Yasin and Bart Jr, Henry L and Mabee, Paula M and Lapp, Hilmar and others},
-  publisher = {ECCV},
-  year={2024},
-  booktitle = {Proceedings of ECCV},
-  keywords = {Evolution, Diffusion Models, Hierarchical Conditioning, Generative AI, Computer Vision},
-  location = {Milan, Italy},
-  preview = {phylo_diffusion_architecture.jpg},
-  website = {https://imageomics.github.io/phylo-diffusion},
-  arxiv = {2408.00160v1}
+author = {Khurana, Mridul and Daw, Arka and Maruf, M. and Uyeda, Josef C. and Dahdul, Wasila and Charpentier, Caleb and Bakis, Yasin and Bart, Henry L. and Mabee, Paula M. and Lapp, Hilmar and Balhoff, James P. and Chao, Wei-Lun and Stewart, Charles and Berger-Wolf, Tanya and Karpatne, Anuj},
+title = {Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution},
+year = {2024},
+publisher = {ECCV},
+booktitle = {Proceedings of ECCV},
+keywords = {Evolution, Diffusion Models, Hierarchical Conditioning, Generative AI, Computer Vision},
+preview = {phylo_diffusion_architecture.jpg},
+website = {https://imageomics.github.io/phylo-diffusion},
+arxiv = {2408.00160v1},
 }
 
 @article{mehrab2024fish,
@@ -38,9 +37,9 @@ @article{sawhney2024motion
 @article{elhamod2023neuro,
   title={Neuro-Visualizer: An Auto-encoder-based Loss Landscape Visualization Method},
   author={Elhamod, Mohannad and Karpatne, Anuj},
-  journal={ICML 2024},
+  journal={ICML},
   arxiv = {2309.14601},
-  year={2023}
+  year={2024}
 }
 
 @article{maruf2023beyond,
@@ -62,7 +61,16 @@ @inproceedings{sawhney2023detecting
   title={Detecting and Tracking Hard-to-Detect Bacteria in Dense Porous Backgrounds},
   author={Sawhney, Medha and Karmarkar, Bhas and Leaman, Eric J and Daw, Arka and Karpatne, Anuj and Behkam, Bahareh},
   year={2023},
-  organization={CVPR Workshop on CV4Animals 2023}
+  booktitle={CVPR Workshop on CV4Animals 2023}
+}
+
+@article{daw2022mitigating,
+  title={Mitigating propagation failures in physics-informed neural networks using retain-resample-release (r3) sampling},
+  author={Daw, Arka and Bu, Jie and Wang, Sifan and Perdikaris, Paris and Karpatne, Anuj},
+  journal={arXiv preprint arXiv:2207.02338},
+  arxiv = {2207.02338},
+  booktitle= {ICML},
+  year={2023}
 }
 
 @article{bu2023let,
@@ -96,6 +104,161 @@ @article{elhamod2022cophy
 }
 
 
+@incollection{daw2022physics,
+  title={Physics-guided architecture (PGA) of LSTM models for uncertainty quantification in lake temperature modeling},
+  author={Daw, Arka and Thomas, R Quinn and Carey, Cayelan C and Read, Jordan S and Appling, Alison P and Karpatne, Anuj},
+  booktitle={Knowledge Guided Machine Learning},
+  pages={399--416},
+  year={2022},
+  publisher={Chapman and Hall/CRC}
+}
+
+@article{
+  author = {Elhamod, Mohannad and Diamond, Kelly M. and Maga, A. Murat and Bakis, Yasin and Bart, Henry L. and Mabee, Paula and Dahdul, Wasila and Leipzig, Jeremy and Greenberg, Jane and Avants, Brian and Karpatne, Anuj},
+  title = {Hierarchy-guided Neural Networks for Species Classification},
+  journal={Methods in Ecology and Evolution},
+  volume={13},
+  number={3},
+  pages={1--23},
+  year={642--652},
+}
+
+@article{bu2021learning,
+  title={Learning compact representations of neural networks using discriminative masking (DAM)},
+  author={Bu, Jie and Daw, Arka and Maruf, M and Karpatne, Anuj},
+  journal={Advances in Neural Information Processing Systems},
+  volume={34},
+  pages={3491--3503},
+  year={2021}
+}
+
+@inproceedings{papakis2021graph,
+  title={A graph convolutional neural network based approach for traffic monitoring using augmented detections with optical flow},
+  author={Papakis, Ioannis and Sarkar, Abhijit and Karpatne, Anuj},
+  booktitle={2021 IEEE International Intelligent Transportation Systems Conference (ITSC)},
+  pages={2980--2986},
+  year={2021},
+  organization={IEEE}
+}
+
+@inproceedings{yu2021physics,
+  title={Physics-guided ai for large-scale spatiotemporal data},
+  author={Yu, Rose and Perdikaris, Paris and Karpatne, Anuj},
+  booktitle={Proceedings of the 27th ACM SIGKDD Conference on Knowledge Discovery \& Data Mining},
+  pages={4088--4089},
+  year={2021}
+}
+
+@inproceedings{daw2021pid,
+  title={PID-GAN: A GAN Framework based on a Physics-informed Discriminator for Uncertainty Quantification with Physics},
+  author={Daw, Arka and Maruf, M and Karpatne, Anuj},
+  booktitle={Proceedings of the 27th ACM SIGKDD Conference on Knowledge Discovery \& Data Mining},
+  pages={237--247},
+  year={2021}
+}
+
+@inproceedings{elhamod2021biology,
+  title={Biology-guided neural network for species classification},
+  author={Elhamod, M and Maruf, MA and Mandke, PK and Karpatne, A},
+  booktitle={INTEGRATIVE AND COMPARATIVE BIOLOGY},
+  volume={61},
+  pages={E228--E229},
+  year={2021},
+  organization={OXFORD UNIV PRESS INC JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA}
+}
+
+@inproceedings{maruf2021biology,
+  title={Biology-guided neural network for fish trait discovery},
+  author={Maruf, MA and Elhamod, M and Mandke, PK and Karpatne, A},
+  booktitle={INTEGRATIVE AND COMPARATIVE BIOLOGY},
+  volume={61},
+  pages={E577--E578},
+  year={2021},
+  organization={OXFORD UNIV PRESS INC JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA}
+}
+
+@inbook{doi:10.1137/1.9781611976700.76,
+author = {Jie Bu and Anuj Karpatne},
+title = {Quadratic Residual Networks: A New Class of Neural Networks for Solving Forward and Inverse Problems in Physics Involving PDEs},
+booktitle = {Proceedings of the 2021 SIAM International Conference on Data Mining (SDM)},
+chapter = {},
+pages = {675-683},
+doi = {10.1137/1.9781611976700.76},
+URL = {https://epubs.siam.org/doi/abs/10.1137/1.9781611976700.76},
+eprint = {https://epubs.siam.org/doi/pdf/10.1137/1.9781611976700.76},
+}
+
+
+@inbook{doi:10.1137/1.9781611976700.31,
+author = {M. Maruf and Anuj Karpatne},
+title = {Maximizing Cohesion and Separation in Graph Representation Learning: A Distance-aware Negative Sampling Approach},
+booktitle = {Proceedings of the 2021 SIAM International Conference on Data Mining (SDM)},
+chapter = {},
+pages = {271-279},
+doi = {10.1137/1.9781611976700.31},
+URL = {https://epubs.siam.org/doi/abs/10.1137/1.9781611976700.31},
+eprint = {https://epubs.siam.org/doi/pdf/10.1137/1.9781611976700.31},
+}
+
+
+@article{doi:10.1089/big.2020.0071,
+author = {Muralidhar, Nikhil and Bu, Jie and Cao, Ze and He, Long and Ramakrishnan, Naren and Tafti, Danesh and Karpatne, Anuj},
+title = {Physics-Guided Deep Learning for Drag Force Prediction in Dense Fluid-Particulate Systems},
+journal = {Big Data},
+volume = {8},
+number = {5},
+pages = {431-449},
+year = {2020},
+doi = {10.1089/big.2020.0071},
+note ={PMID: 33090021},
+URL = {https://doi.org/10.1089/big.2020.0071},
+eprint = {https://doi.org/10.1089/big.2020.0071},
+}
+
+@article{papakis2020gcnnmatch,
+  title={Gcnnmatch: Graph convolutional neural networks for multi-object tracking via sinkhorn normalization},
+  author={Papakis, Ioannis and Sarkar, Abhijit and Karpatne, Anuj},
+  journal={arXiv preprint arXiv:2010.00067},
+  year={2020}
+}
+
+
+@inbook{doi:10.1137/1.9781611976236.63,
+author = {Nikhil Muralidhar and Jie Bu and Ze Cao and Long He and Naren Ramakrishnan and Danesh Tafti and Anuj Karpatne},
+title = {PhyNet: Physics Guided Neural Networks for Particle Drag Force Prediction in Assembly},
+booktitle = {Proceedings of the 2020 SIAM International Conference on Data Mining (SDM)},
+chapter = {},
+pages = {559-567},
+doi = {10.1137/1.9781611976236.63},
+URL = {https://epubs.siam.org/doi/abs/10.1137/1.9781611976236.63},
+eprint = {https://epubs.siam.org/doi/pdf/10.1137/1.9781611976236.63},
+}
+
+@inbook{doi:10.1137/1.9781611976236.60,
+author = {Arka Daw and R. Quinn Thomas and Cayelan C. Carey and Jordan S. Read and Alison P. Appling and Anuj Karpatne},
+title = {Physics-Guided Architecture (PGA) of Neural Networks for Quantifying Uncertainty in Lake Temperature Modeling},
+booktitle = {Proceedings of the 2020 SIAM International Conference on Data Mining (SDM)},
+chapter = {},
+pages = {532-540},
+doi = {10.1137/1.9781611976236.60},
+URL = {https://epubs.siam.org/doi/abs/10.1137/1.9781611976236.60},
+eprint = {https://epubs.siam.org/doi/pdf/10.1137/1.9781611976236.60},
+}
+
+@article{muralidhar2019physics,
+  title={Physics-guided design and learning of neural networks for predicting drag force on particle suspensions in moving fluids},
+  author={Muralidhar, Nikhil and Bu, Jie and Cao, Ze and He, Long and Ramakrishnan, Naren and Tafti, Danesh and Karpatne, Anuj},
+  journal={arXiv preprint arXiv:1911.04240},
+  year={2019}
+}
+
+@inproceedings{daw2019physics,
+  title={Physics-aware architecture of neural networks for uncertainty quantification: Application in lake temperature modeling},
+  author={Daw, Arka and Karpatne, Anuj},
+  year={2019},
+  organization={SIGKDD}
+}
+