Drug Discovery SMILES-to-Pharmacokinetics Diffusion Models with Deep Molecular Understanding

Autor: Hu, Bing, Layton, Anita, Chen, Helen

Artificial intelligence (AI) is increasingly used in every stage of drug development. One challenge facing drug discovery AI is that drug pharmacokinetic (PK) datasets are often collected independently from each other, often with limited overlap, cre

Externí odkaz: http://arxiv.org/abs/2408.07636

Jet modification via $\pi^0$-hadron correlations in Au$+$Au collisions at $\sqrt{s_{_{NN}}}=200$ GeV

Autor: PHENIX Collaboration, Abdulameer, N. J., Acharya, U., Adare, A., Afanasiev, S., Aidala, C., Ajitanand, N. N., Akiba, Y., Al-Bataineh, H., Alexander, J., Alfred, M., Aoki, K., Apadula, N., Aphecetche, L., Asai, J., Asano, H., Atomssa, E. T., Averbeck, R., Awes, T. C., Azmoun, B., Babintsev, V., Bai, M., Baksay, G., Baksay, L., Baldisseri, A., Bandara, N. S., Bannier, B., Barish, K. N., Barnes, P. D., Bassalleck, B., Basye, A. T., Bathe, S., Batsouli, S., Baublis, V., Baumann, C., Bazilevsky, A., Beaumier, M., Beckman, S., Belikov, S., Belmont, R., Bennett, R., Berdnikov, A., Berdnikov, Y., Bichon, L., Bickley, A. A., Blankenship, B., Blau, D. S., Boissevain, J. G., Bok, J. S., Borel, H., Borisov, V., Boyle, K., Brooks, M. L., Bryslawskyj, J., Buesching, H., Bumazhnov, V., Bunce, G., Butsyk, S., Camacho, C. M., Campbell, S., Chang, B. S., Chang, W. C., Charvet, J. L., Chen, C. -H., Chen, D., Chernichenko, S., Chiu, M., Chi, C. Y., Choi, I. J., Choi, J. B., Choudhury, R. K., Chujo, T., Chung, P., Churyn, A., Cianciolo, V., Citron, Z., Cole, B. A., Connors, M., Constantin, P., Corliss, R., Csanád, M., Csörgő, T., d'Enterria, D., Dahms, T., Dairaku, S., Danley, T. W., Das, K., Datta, A., Daugherity, M. S., David, G., DeBlasio, K., Dehmelt, K., Denisov, A., Deshpande, A., Desmond, E. J., Dietzsch, O., Dion, A., Diss, P. B., Donadelli, M., Doomra, V., Do, J. H., Drapier, O., Drees, A., Drees, K. A., Dubey, A. K., Durham, J. M., Durum, A., Dutta, D., Dzhordzhadze, V., Efremenko, Y. V., Ellinghaus, F., En'yo, H., Engelmore, T., Enokizono, A., Esha, R., Eyser, K. O., Fadem, B., Feege, N., Fields, D. E., Finger, Jr., M., Finger, M., Firak, D., Fitzgerald, D., Fleuret, F., Fokin, S. L., Fraenkel, Z., Frantz, J. E., Franz, A., Frawley, A. D., Fujiwara, K., Fukao, Y., Fusayasu, T., Gallus, P., Gal, C., Garg, P., Garishvili, I., Ge, H., Giordano, F., Glenn, A., Gong, H., Gonin, M., Gosset, J., Goto, Y., de Cassagnac, R. Granier, Grau, N., Greene, S. V., Perdekamp, M. Grosse, Gunji, T., Guo, T., Gustafsson, H. -Å., Hachiya, T., Henni, A. Hadj, Haggerty, J. S., Hahn, K. I., Hamagaki, H., Hamilton, H. F., Hanks, J., Han, R., Han, S. Y., Hartouni, E. P., Haruna, K., Hasegawa, S., Haseler, T. O. S., Hashimoto, K., Haslum, E., Hayano, R., Heffner, M., Hemmick, T. K., Hester, T., He, X., Hill, J. C., Hodges, A., Hohlmann, M., Hollis, R. S., Holzmann, W., Homma, K., Hong, B., Horaguchi, T., Hornback, D., Hoshino, T., Hotvedt, N., Huang, J., Ichihara, T., Ichimiya, R., Iinuma, H., Ikeda, Y., Imai, K., Imrek, J., Inaba, M., Iordanova, A., Isenhower, D., Ishihara, M., Isobe, T., Issah, M., Isupov, A., Ivanishchev, D., Jacak, B. V., Jezghani, M., Jiang, X., Jin, J., Ji, Z., Johnson, B. M., Joo, K. S., Jouan, D., Jumper, D. S., Kajihara, F., Kametani, S., Kamihara, N., Kamin, J., Kanda, S., Kang, J. H., Kapustinsky, J., Kawall, D., Kazantsev, A. V., Kempel, T., Key, J. A., Khachatryan, V., Khanzadeev, A., Kijima, K. M., Kikuchi, J., Kimelman, B., Kim, B. I., Kim, C., Kim, D. H., Kim, D. J., Kim, E., Kim, E. -J., Kim, G. W., Kim, M., Kim, S. H., Kinney, E., Kiriluk, K., Kiss, Á., Kistenev, E., Kitamura, R., Klatsky, J., Klay, J., Klein-Boesing, C., Kleinjan, D., Kline, P., Koblesky, T., Kochenda, L., Komkov, B., Konno, M., Koster, J., Kotov, D., Kovacs, L., Kozlov, A., Kravitz, A., Král, A., Kunde, G. J., Kurgyis, B., Kurita, K., Kurosawa, M., Kweon, M. J., Kwon, Y., Kyle, G. S., Lai, Y. S., Lajoie, J. G., Layton, D., Lebedev, A., Lee, D. M., Lee, K. B., Lee, S., Lee, S. H., Lee, T., Leitch, M. J., Leite, M. A. L., Lenzi, B., Liebing, P., Lim, S. H., Litvinenko, A., Liu, H., Liu, M. X., Liška, T., Li, X., Lokos, S., Loomis, D. A., Love, B., Lynch, D., Maguire, C. F., Makdisi, Y. I., Makek, M., Malakhov, A., Malik, M. D., Manion, A., Manko, V. I., Mannel, E., Mao, Y., Masui, H., Matathias, F., Mašek, L., McCumber, M., McGaughey, P. L., McGlinchey, D., McKinney, C., Means, N., Meles, A., Mendoza, M., Meredith, B., Miake, Y., Mignerey, A. C., Mikeš, P., Miki, K., Milov, A., Mishra, D. K., Mishra, M., Mitchell, J. T., Mitrankova, M., Mitrankov, Iu., Miyasaka, S., Mizuno, S., Mohanty, A. K., Montuenga, P., Moon, T., Morino, Y., Morreale, A., Morrison, D. P., Moukhanova, T. V., Mukhopadhyay, D., Mulilo, B., Murakami, T., Murata, J., Mwai, A., Nagamiya, S., Nagashima, K., Nagle, J. L., Naglis, M., Nagy, M. I., Nakagawa, I., Nakagomi, H., Nakamiya, Y., Nakamura, T., Nakano, K., Nattrass, C., Netrakanti, P. K., Newby, J., Nguyen, M., Niida, T., Nishimura, S., Nouicer, R., Novitzky, N., Novák, T., Nukazuka, G., Nyanin, A. S., O'Brien, E., Oda, S. X., Ogilvie, C. A., Okada, K., Oka, M., Onuki, Y., Koop, J. D. Orjuela, Orosz, M., Osborn, J. D., Oskarsson, A., Ouchida, M., Ozawa, K., Pak, R., Palounek, A. P. T., Pantuev, V., Papavassiliou, V., Park, J., Park, J. S., Park, S., Park, W. J., Patel, M., Pate, S. F., Pei, H., Peng, J. -C., Pereira, H., Perepelitsa, D. V., Perera, G. D. N., Peresedov, V., Peressounko, D. Yu., Perry, J., Petti, R., Pinkenburg, C., Pinson, R., Pisani, R. P., Potekhin, M., Purschke, M. L., Purwar, A. K., Qu, H., Rakotozafindrabe, A., Rak, J., Ramson, B. J., Ravinovich, I., Read, K. F., Rembeczki, S., Reygers, K., Reynolds, D., Riabov, V., Riabov, Y., Richford, D., Rinn, T., Roach, D., Roche, G., Rolnick, S. D., Rosati, M., Rosendahl, S. S. E., Rosnet, P., Rowan, Z., Rubin, J. G., Rukoyatkin, P., Ružička, P., Rykov, V. L., Sahlmueller, B., Saito, N., Sakaguchi, T., Sakai, S., Sakashita, K., Sako, H., Samsonov, V., Sarsour, M., Sato, S., Sato, T., Sawada, S., Schaefer, B., Schmoll, B. K., Sedgwick, K., Seele, J., Seidl, R., Semenov, A. Yu., Semenov, V., Sen, A., Seto, R., Sett, P., Sexton, A., Sharma, D., Shein, I., Shibata, T. -A., Shigaki, K., Shimomura, M., Shoji, K., Shukla, P., Sickles, A., Silva, C. L., Silvermyr, D., Silvestre, C., Sim, K. S., Singh, B. K., Singh, C. P., Singh, V., Slunečka, M., Smith, K. L., Snowball, M., Soldatov, A., Soltz, R. A., Sondheim, W. E., Sorensen, S. P., Sourikova, I. V., Staley, F., Stankus, P. W., Stenlund, E., Stepanov, M., Ster, A., Stoll, S. P., Sugitate, T., Suire, C., Sukhanov, A., Sumita, T., Sun, J., Sun, Z., Sziklai, J., Takagui, E. M., Taketani, A., Tanabe, R., Tanaka, Y., Tanida, K., Tannenbaum, M. J., Tarafdar, S., Taranenko, A., Tarján, P., Themann, H., Thomas, T. L., Tieulent, R., Timilsina, A., Todoroki, T., Togawa, M., Toia, A., Tomita, Y., Tomášek, L., Tomášek, M., Torii, H., Towell, C. L., Towell, R., Towell, R. S., Tram, V-N., Tserruya, I., Tsuchimoto, Y., Ujvari, B., Vale, C., Valle, H., van Hecke, H. W., Veicht, A., Velkovska, J., Vinogradov, A. A., Virius, M., Vrba, V., Vznuzdaev, E., Vértesi, R., Wang, X. R., Watanabe, Y., Watanabe, Y. S., Wei, F., Wessels, J., White, A. S., White, S. N., Winter, D., Wong, C. P., Woody, C. L., Wysocki, M., Xia, B., Xie, W., Xue, L., Yalcin, S., Yamaguchi, Y. L., Yamaura, K., Yang, R., Yanovich, A., Ying, J., Yokkaichi, S., Yoon, I., Yoo, J. H., Young, G. R., Younus, I., Yushmanov, I. E., Yu, H., Zajc, W. A., Zaudtke, O., Zelenski, A., Zhang, C., Zhou, S., Zolin, L., Zou, L.

Publikováno v: Phys. Rev. C 110, 044901 (2024)

High-momentum two-particle correlations are a useful tool for studying jet-quenching effects in the quark-gluon plasma. Angular correlations between neutral-pion triggers and charged hadrons with transverse momenta in the range 4--12~GeV/$c$ and 0.5-

Externí odkaz: http://arxiv.org/abs/2406.08301

Synthesis and characterization of space-time light sheets: A tutorial

Autor: Romer, Miguel A., Hall, Layton A., Abouraddy, Ayman F.

Space-time wave packets (STWPs) are a new class of pulsed optical beams with many unique and intriguing attributes, including propagation invariance and tunable group velocity in linear optical media. STWPs are a form of spatiotemporally structured l

Externí odkaz: http://arxiv.org/abs/2405.14102

Synthetic Data from Diffusion Models Improve Drug Discovery Prediction

Autor: Hu, Bing, Saragadam, Ashish, Layton, Anita, Chen, Helen

Artificial intelligence (AI) is increasingly used in every stage of drug development. Continuing breakthroughs in AI-based methods for drug discovery require the creation, improvement, and refinement of drug discovery data. We posit a new data challe

Externí odkaz: http://arxiv.org/abs/2405.03799

The Ramshaw-Mesina Hybrid Algorithm applied to the Navier Stokes Equations

Autor: Çibik, Aytekin, Siddiqua, Farjana, Layton, William

In 1991, Ramshaw and Mesina proposed a novel synthesis of penalty methods and artificial compression methods. When the two were balanced they found the combination was 3-4 orders more accurate than either alone. This report begins the study of their

Externí odkaz: http://arxiv.org/abs/2404.11755