AI-driven 3D Spatial Transcriptomics

Authors: Almagro-Pérez, Cristina, Song, Andrew H., Weishaupt, Luca, Kim, Ahrong, Jaume, Guillaume, Williamson, Drew F. K., Hemker, Konstantin, Lu, Ming Y., Singh, Kritika, Chen, Bowen, Le, Long Phi, Baras, Alexander S., Jiang, Sizun, Bashashati, Ali, Liu, Jonathan T. C., Mahmood, Faisal

Subject Terms: Computer Science - Computer Vision and Pattern Recognition, Statistics - Applications

Access URL: http://arxiv.org/abs/2502.17761

Molecular-driven Foundation Model for Oncologic Pathology

Authors: Vaidya, Anurag, Zhang, Andrew, Jaume, Guillaume, Song, Andrew H., Ding, Tong, Wagner, Sophia J., Lu, Ming Y., Doucet, Paul, Robertson, Harry, Almagro-Perez, Cristina, Chen, Richard J., ElHarouni, Dina, Ayoub, Georges, Bossi, Connor, Ligon, Keith L., Gerber, Georg, Le, Long Phi, Mahmood, Faisal

Subject Terms: Computer Science - Computer Vision and Pattern Recognition, Computer Science - Artificial Intelligence

Access URL: http://arxiv.org/abs/2501.16652

Multimodal Whole Slide Foundation Model for Pathology

Authors: Ding, Tong, Wagner, Sophia J., Song, Andrew H., Chen, Richard J., Lu, Ming Y., Zhang, Andrew, Vaidya, Anurag J., Jaume, Guillaume, Shaban, Muhammad, Kim, Ahrong, Williamson, Drew F. K., Chen, Bowen, Almagro-Perez, Cristina, Doucet, Paul, Sahai, Sharifa, Chen, Chengkuan, Komura, Daisuke, Kawabe, Akihiro, Ishikawa, Shumpei, Gerber, Georg, Peng, Tingying, Le, Long Phi, Mahmood, Faisal

Subject Terms: Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Artificial Intelligence, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Statistics - Applications

Access URL: http://arxiv.org/abs/2411.19666

Embed and Emulate: Contrastive representations for simulation-based inference

Authors: Jiang, Ruoxi, Lu, Peter Y., Willett, Rebecca

Subject Terms: Computer Science - Machine Learning, Statistics - Machine Learning

Access URL: http://arxiv.org/abs/2409.18402

HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis

Authors: Jaume, Guillaume, Doucet, Paul, Song, Andrew H., Lu, Ming Y., Almagro-Pérez, Cristina, Wagner, Sophia J., Vaidya, Anurag J., Chen, Richard J., Williamson, Drew F. K., Kim, Ahrong, Mahmood, Faisal

Subject Terms: Computer Science - Computer Vision and Pattern Recognition

Access URL: http://arxiv.org/abs/2406.16192

Using graph neural networks to reconstruct charged pion showers in the CMS High Granularity Calorimeter

Authors: Aamir, M., Adamov, G., Adams, T., Adloff, C., Afanasiev, S., Agrawal, C., Ahmad, A., Ahmed, H. A., Akbar, S., Akchurin, N., Akgul, B., Akgun, B., Akpinar, R. O., Aktas, E., Kadhim, A. Al, Alexakhin, V., Alimena, J., Alison, J., Alpana, A., Alshehri, W., Dominguez, P. Alvarez, Alyari, M., Amendola, C., Amir, R. B., Andersen, S. B., Andreev, Y., Antoszczuk, P. D., Aras, U., Ardila, L., Aspell, P., Avila, M., Awad, I., Aydilek, O., Azimi, Z., Pretel, A. Aznar, Bach, O. A., Bainbridge, R., Bakshi, A., Bam, B., Banerjee, S., Barney, D., Bayraktar, O., Beaudette, F., Beaujean, F., Becheva, E., Behera, P. K., Belloni, A., Bergauer, T., Besancon, M., Bylund, O. Bessidskaia, Bhatt, L., Bhattacharya, S., Bhowmil, D., Blekman, F., Blinov, P., Bloch, P., Bodek, A., Boger, a., Bonnemaison, A., Bouyjou, F., Brennan, L., Brondolin, E., Brusamolino, A., Bubanja, I., Perraguin, A. Buchot, Bunin, P., Misura, A. Burazin, Butler-nalin, A., Cakir, A., Callier, S., Campbell, S., Candemir, Y. B., Canderan, K., Cankocak, K., Cappati, A., Caregari, S., Carron, S., Carty, C., Cauchois, A., Ceard, L., Cerci, S., Chang, P. J., Chatterjee, R. M., Chatterjee, S., Chattopadhyay, P., Chatzistavrou, T., Chaudhary, M. S., Chen, J. A., Chen, J., Chen, Y., Cheng, K., Cheung, H., Chhikara, J., Chiron, A., Chiusi, M., Chokheli, D., Chudasama, R., Clement, E., Mendez, S. Coco, Coko, D., Coskun, K., Couderc, F., Crossman, B., Cui, Z., Cuisset, T., Cummings, G., Curtis, E. M., D'Alfonso, M., Döhler-Ball, J., Dadazhanova, O., Damgov, J., Das, I., Gupta, S. Das, Dauncey, P., Mendes, A. David Tinoco, Davies, G., Davignon, O., de Barbaro, P., De La Taille, C., De Silva, M., De Wit, A., Debbins, P., Defranchis, M. M., Delagnes, E., Devouge, P., Di Guglielmo, G., Diehl, L., Dilsiz, K., Dincer, G. G., Dittmann, J., Dragicevic, M., Du, D., Dubinchik, B., Dugad, S., Dulucq, F., Dumanoglu, I., Duran, B., Dutta, S., Dutta, V., Dychkant, A., Dünser, M., Edberg, T., Ehle, I. T., Berni, A. El, Elias, F., Eno, S. C., Erdogan, E. N., Erkmen, B., Ershov, Y., Ertorer, E. Y., Extier, S., Eychenne, L., Fedar, Y. E., Fedi, G., De Almeida, J. P. Figueiredo De Sá Sousa, Alves, B. A. Fontana Santos, Frahm, E., Francis, K., Freeman, J., French, T., Gaede, F., Gandhi, P. K., Ganjour, S., Garcia-Bellido, A., Gastaldi, F., Gazi, L., Gecse, Z., Gerwig, H., Gevin, O., Ghosh, S., Gill, K., Gingu, C., Gleyzer, S., Godinovic, N., Goettlicher, P., Goff, R., Gok, M., Golunov, A., Gonultas, B., Martínez, J. D. González, Gorbounov, N., Gouskos, L., Gray, A., Gray, L., Grieco, C., Groenroos, S., Groner, D., Gruber, A., Grummer, A., Grönroos, S., Guerrero, D., Guilloux, F., Guler, Y., Gungordu, A. D., Guo, J., Guo, K., Guler, E. Gurpinar, Gutti, H. K., Guvenli, A. A., Gülmez, E., Hacisahinoglu, B., Halkin, Y., Machado, G. Hamilton Ilha, Hare, H. S., Hatakeyama, K., Heering, A. H., Hegde, V., Heintz, U., Hinton, N., Hinzmann, A., Hirschauer, J., Hitlin, D., Hoff, J., Hos, İ., Hou, B., Hou, X., Howard, A., Howe, C., Hsieh, H., Hsu, T., Hua, H., Hummer, F., Imran, M., Incandela, J., Iren, E., Isildak, B., Jackson, P. S., Jackson, W. J., Jain, S., Jana, P., Jaroslavceva, J., Jena, S., Jige, A., Jordano, P. P., Joshi, U., Kaadze, K., Kachanov, V., Kafizov, A., Kalipoliti, L., Tharayil, A. Kallil, Kaluzinska, O., Kamble, S., Kaminskiy, A., Kanemura, M., Kanso, H., Kao, Y., Kapic, A., Kapsiak, C., Karjavine, V., Karmakar, S., Karneyeu, A., Kaya, M., Topaksu, A. Kayis, Kaynak, B., Kazhykarim, Y., Khan, F. A., Khudiakov, A., Kieseler, J., Kim, R. S., Klijnsma, T., Kloiber, E. G., Klute, M., Kocak, Z., Kodali, K. R., Koetz, K., Kolberg, T., Kolcu, O. B., Komaragiri, J. R., Komm, M., Kopsalis, I., Krause, H. A., Krawczyk, M. A., Vinayakam, T. R. Krishnaswamy, Kristiansen, K., Kristic, A., Krohn, M., Kronheim, B., Krüger, K., Kudtarkar, C., Kulis, S., Kumar, M., Kumar, N., Kumar, S., Verma, R. Kumar, Kunori, S., Kunts, A., Kuo, C., Kurenkov, A., Kuryatkov, V., Kyre, S., Ladenson, J., Lamichhane, K., Landsberg, G., Langford, J., Laudrain, A., Laughlin, R., Lawhorn, J., Dortz, O. Le, Lee, S. W., Lektauers, A., Lelas, D., Leon, M., Levchuk, L., Li, A. J., Li, J., Li, Y., Liang, Z., Liao, H., Lin, K., Lin, W., Lin, Z., Lincoln, D., Linssen, L., Litomin, A., Liu, G., Liu, Y., Lobanov, A., Lohezic, V., Loiseau, T., Lu, C., Lu, R., Lu, S. Y., Lukens, P., Mackenzie, M., Magnan, A., Magniette, F., Mahjoub, A., Mahon, D., Majumder, G., Makarenko, V., Malakhov, A., Malgeri, L., Mallios, S., Mandloi, C., Mankel, A., Mannelli, M., Mans, J., Mantilla, C., Martinez, G., Massa, C., Masterson, P., Matthewman, M., Matveev, V., Mayekar, S., Mazlov, I., Mehta, A., Mestvirishvili, A., Miao, Y., Milella, G., Mirza, I. R., Mitra, P., Moccia, S., Mohanty, G. B., Monti, F., Moortgat, F., Murthy, S., Music, J., Musienko, Y., Nabili, S., Nelson, J. W., Nema, A., Neutelings, I., Niedziela, J., Nikitenko, A., Noonan, D., Noy, M., Nurdan, K., Obraztsov, S., Ochando, C., Ogul, H., Olsson, J., Onel, Y., Ozkorucuklu, S., Paganis, E., Palit, P., Pan, R., Pandey, S., Pantaleo, F., Papageorgakis, C., Paramesvaran, S., Paranjpe, M. M., Parolia, S., Parsons, A. G., Parygin, P., Pastika, J., Paulini, M., Paus, C., Castillo, K. Peñaló, Pedro, K., Pekic, V., Peltola, T., Peng, B., Perego, A., Perini, D., Petrilli, A., Pham, H., Podem, S. K., Popov, V., Portales, L., Potok, O., Pradeep, P. B., Pramanik, R., Prosper, H., Prvan, M., Qasim, S. R., Qu, H., Quast, T., Trivio, A. Quiroga, Rabour, L., Raicevic, N., Rao, M. A., Rapacz, K., Redjeb, W., Reinecke, M., Revering, M., Roberts, A., Rohlf, J., Rosado, P., Rose, A., Rothman, S., Rout, P. K., Rovere, M., Roy, A., Rubinov, P., Rumerio, P., Rusack, R., Rygaard, L., Ryjov, V., Sadivnycha, S., Sahin, M. Ö., Sakarya, U., Salerno, R., Saradhy, R., Saraf, M., Sarbandi, K., Sarkisla, M. A., Satyshev, I., Saud, N., Sauvan, J., Schindler, G., Schmidt, A., Schmidt, I., Schmitt, M. H., Sculac, A., Sculac, T., Sedelnikov, A., Seez, C., Sefkow, F., Selivanova, D., Selvaggi, M., Sergeychik, V., Sert, H., Shahid, M., Sharma, P., Sharma, R., Sharma, S., Shelake, M., Shenai, A., Shih, C. W., Shinde, R., Shmygol, D., Shukla, R., Sicking, E., Silva, P., Simsek, C., Simsek, E., Sirasva, B. K., Sirois, Y., Song, S., Song, Y., Soudais, G., Sriram, S., Jacques, R. R. St, Leiton, A. G. Stahl, Steen, A., Stein, J., Strait, J., Strobbe, N., Su, X., Sukhov, E., Suleiman, A., Cerci, D. Sunar, Suryadevara, P., Swain, K., Syal, C., Tali, B., Tanay, K., Tang, W., Tanvir, A., Tao, J., Tarabini, A., Tatli, T., Taylor, R., Taysi, Z. C., Teafoe, G., Tee, C. Z., Terrill, W., Thienpont, D., Thomas, P. E., Thomas, R., Titov, M., Todd, C., Todd, E., Toms, M., Tosun, A., Troska, J., Tsai, L., Tsamalaidze, Z., Tsionou, D., Tsipolitis, G., Tsirigoti, M., Tu, R., Polat, S. N. Tural, Undleeb, S., Usai, E., Uslan, E., Ustinov, V., Uzunian, A., Vernazza, E., Viahin, O., Viazlo, O., Vichoudis, P., Vijay, A., Virdee, T., Voirin, E., Vojinovic, M., Vámi, T. Á., Wade, A., Walter, D., Wang, C., Wang, F., Wang, J., Wang, K., Wang, X., Wang, Y., Wang, Z., Wanlin, E., Wayne, M., Wetzel, J., Whitbeck, A., Wickwire, R., Wilmot, D., Wilson, J., Wu, H., Xiao, M., Yang, J., Yazici, B., Ye, Y., Yerli, B., Yetkin, T., Yi, R., Yohay, R., Yu, T., Yuan, C., Yuan, X., Yuksel, O., YushmanoV, I., Yusuff, I., Zabi, A., Zareckis, D., Zehetner, P., Zghiche, A., Zhang, C., Zhang, D., Zhang, H., Zhang, J., Zhang, Z., Zhao, X., Zhong, J., Zhou, Y., Zorbilmez, Ç.

Source: JINST 19 (2024) P11025

Subject Terms: Physics - Instrumentation and Detectors, High Energy Physics - Experiment, Physics - Data Analysis, Statistics and Probability

Access URL: http://arxiv.org/abs/2406.11937

Revealing the Microscopic Mechanism of Elementary Vortex Pinning in Superconductors

Authors: Chen, C., Liu, Y., Chen, Y., Hu, Y. N., Zhang, T. Z., Li, D., Wang, X., Wang, C. X., Lu, Z. Y. W., Zhang, Y. H., Zhang, Q. L., Dong, X. L., Wang, R., Feng, D. L., Zhang, T.

Source: Phys. Rev. X 14, 041039 (2024)

Subject Terms: Condensed Matter - Superconductivity, Condensed Matter - Materials Science, Physics - Applied Physics

Access URL: http://arxiv.org/abs/2403.17671

Artificial Intelligence for Digital and Computational Pathology

Authors: Song, Andrew H., Jaume, Guillaume, Williamson, Drew F. K., Lu, Ming Y., Vaidya, Anurag, Miller, Tiffany R., Mahmood, Faisal

Source: Nature Reviews Bioengineering 2023

Subject Terms: Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Artificial Intelligence, Computer Science - Computer Vision and Pattern Recognition, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2401.06148

A Foundational Multimodal Vision Language AI Assistant for Human Pathology

Authors: Lu, Ming Y., Chen, Bowen, Williamson, Drew F. K., Chen, Richard J., Ikamura, Kenji, Gerber, Georg, Liang, Ivy, Le, Long Phi, Ding, Tong, Parwani, Anil V, Mahmood, Faisal

Subject Terms: Computer Science - Computer Vision and Pattern Recognition, Computer Science - Artificial Intelligence

Access URL: http://arxiv.org/abs/2312.07814

Multimodal Foundation Models for Material Property Prediction and Discovery

Authors: Moro, Viggo, Loh, Charlotte, Dangovski, Rumen, Ghorashi, Ali, Ma, Andrew, Chen, Zhuo, Kim, Samuel, Lu, Peter Y., Christensen, Thomas, Soljačić, Marin

Source: Newton, Volume 1, Issue 1, 100016 (2025) Newton, Volume 1, Issue 1, 100016 (2025) Newton, Volume 1, Issue 1, 100016 (2025)

Subject Terms: Computer Science - Machine Learning, Condensed Matter - Materials Science

Access URL: http://arxiv.org/abs/2312.00111

A General-Purpose Self-Supervised Model for Computational Pathology

Authors: Chen, Richard J., Ding, Tong, Lu, Ming Y., Williamson, Drew F. K., Jaume, Guillaume, Chen, Bowen, Zhang, Andrew, Shao, Daniel, Song, Andrew H., Shaban, Muhammad, Williams, Mane, Vaidya, Anurag, Sahai, Sharifa, Oldenburg, Lukas, Weishaupt, Luca L., Wang, Judy J., Williams, Walt, Le, Long Phi, Gerber, Georg, Mahmood, Faisal

Subject Terms: Computer Science - Computer Vision and Pattern Recognition, Computer Science - Artificial Intelligence, Quantitative Biology - Tissues and Organs

Access URL: http://arxiv.org/abs/2308.15474

Towards a Visual-Language Foundation Model for Computational Pathology

Authors: Lu, Ming Y., Chen, Bowen, Williamson, Drew F. K., Chen, Richard J., Liang, Ivy, Ding, Tong, Jaume, Guillaume, Odintsov, Igor, Zhang, Andrew, Le, Long Phi, Gerber, Georg, Parwani, Anil V, Mahmood, Faisal

Subject Terms: Computer Science - Computer Vision and Pattern Recognition, Computer Science - Artificial Intelligence

Access URL: http://arxiv.org/abs/2307.12914

Visual Language Pretrained Multiple Instance Zero-Shot Transfer for Histopathology Images

Authors: Lu, Ming Y., Chen, Bowen, Zhang, Andrew, Williamson, Drew F. K., Chen, Richard J., Ding, Tong, Le, Long Phi, Chuang, Yung-Sung, Mahmood, Faisal

Subject Terms: Computer Science - Computer Vision and Pattern Recognition

Access URL: http://arxiv.org/abs/2306.07831

Training neural operators to preserve invariant measures of chaotic attractors

Authors: Jiang, Ruoxi, Lu, Peter Y., Orlova, Elena, Willett, Rebecca

Subject Terms: Computer Science - Machine Learning, Mathematics - Dynamical Systems

Access URL: http://arxiv.org/abs/2306.01187

Deep Stochastic Mechanics

Authors: Orlova, Elena, Ustimenko, Aleksei, Jiang, Ruoxi, Lu, Peter Y., Willett, Rebecca

Source: Proceedings of the 41st International Conference on Machine Learning, 235, 2024, 38779-38814; https://proceedings.mlr.press/v235/orlova24a.html

Subject Terms: Computer Science - Machine Learning, Quantum Physics, Statistics - Machine Learning

Access URL: http://arxiv.org/abs/2305.19685

Modeling meteorite craters by impacting melted tin on sand

Authors: Huang, H. Y., Tsai, P. R., Lu, C. Y., Hau, H., Chen, Y. L., Ling, Z. T., Wu, Y. R., Hong, Tzay-Ming

Subject Terms: Astrophysics - Earth and Planetary Astrophysics, Physics - Fluid Dynamics, Physics - Geophysics

Access URL: http://arxiv.org/abs/2303.18016

Model Stitching: Looking For Functional Similarity Between Representations

Authors: Hernandez, Adriano, Dangovski, Rumen, Lu, Peter Y., Soljacic, Marin

Subject Terms: Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2303.11277

Q-Flow: Generative Modeling for Differential Equations of Open Quantum Dynamics with Normalizing Flows

Authors: Dugan, Owen, Lu, Peter Y., Dangovski, Rumen, Luo, Di, Soljačić, Marin

Subject Terms: Quantum Physics, Condensed Matter - Disordered Systems and Neural Networks, Condensed Matter - Quantum Gases, Computer Science - Machine Learning, Physics - Computational Physics

Access URL: http://arxiv.org/abs/2302.12235

X-ray morphology due to charge-exchange emissions used to study the global structure around Mars

Authors: Liang, G. Y., Sun, T. R., Lu, H. Y., Zhu, X. L., Wu, Y., Li, S. B., Wei, H. G., Yuan, D. W., Cui, W., Ma, X. W., Zhao, G.

Subject Terms: Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics

Access URL: http://arxiv.org/abs/2212.09909

The real demonstration of High-Quality Carbon Nano-Tubes (CNTs) as the electrical connection for the potential application in a vertical 3D integrated technology

Authors: Lu, P.-Y., Li, Y.-R., Yen, C.-M., Hung, H.-T., Kao, C.-R., Pu, W.-C., Chen, C.-C. A., Lee, M.-H., Liao, M.-H.

Source: 2020 IEEE 70th Electronic Components and Technology Conference (ECTC) Electronic Components and Technology Conference (ECTC), 2020 IEEE 70th. :1573-1578 Jun, 2020

Relation: 2020 IEEE 70th Electronic Components and Technology Conference (ECTC)