Journal: Nat. Comput. Sci.

Volume 3, Issue 9

721 -- 0. The next seven years
722 -- 725John McCloskey, Mark Pelling, Carmine Galasso, Gemma Cremen, Emin Yahya Mentese, Max Hope, Thaisa Comelli, Tanvi Deshpande, Ramesh Guragain, Alejandro Barcena, Roberto Gentile. Reducing disaster risk for the poor in tomorrow's cities with computational science
726 -- 728Elisa Omodei. Using computational tools to monitor and improve access to quality food and water
729 -- 730Fernando Chirigati. Towards equitable education
731 -- 732Fernando Chirigati. Greener urban communities
733 -- 0Fernando Chirigati. From data to conservation laws
734 -- 0Kaitlin McCardle. Conversations that explain predictions
735 -- 736Paolo Santi. AI improves the design of urban communities
737 -- 738Benjamin Allen. Flipping the intuition for games on dynamic networks
739 -- 740Shina Caroline Lynn Kamerlin. Progress in using deep learning to treat cancer
741 -- 747Bassel Ghaddar, Martin J. Blaser, Subhajyoti De. Denoising sparse microbial signals from single-cell sequencing of mammalian host tissues
748 -- 762Yu Zheng 0010, Yuming Lin, Liang Zhao, Tinghai Wu, Depeng Jin, Yong Li 0008. Spatial planning of urban communities via deep reinforcement learning
763 -- 776Qi Su, Alex McAvoy, Joshua B. Plotkin. Strategy evolution on dynamic networks
777 -- 788Hanieh Mazloom-Farsibaf, Qiongjing Zou, Rebecca Hsieh, Gaudenz Danuser, Meghan K. Driscoll. Cellular harmonics for the morphology-invariant analysis of molecular organization at the cell surface
789 -- 804Xujun Zhang, Odin Zhang, Chao Shen, Wanglin Qu, Shicheng Chen, Hanqun Cao, Yu Kang 0002, Zhe Wang 0041, Ercheng Wang, Jintu Zhang, Yafeng Deng, Furui Liu, Tianyue Wang, Hongyan Du, Langcheng Wang, Peichen Pan, Guangyong Chen, Chang-Yu Hsieh, Tingjun Hou. Efficient and accurate large library ligand docking with KarmaDock
805 -- 0Xi Chen, Yuan Wang, Antonio Cappuccio, Wan-Sze Cheng, Frederique Ruf Zamojski, Venugopalan D. Nair, Clare M. Miller, Aliza B. Rubenstein, German Nudelman, Alicja Tadych, Chandra L. Theesfeld, Alexandria Vornholt, Mary-Catherine George, Felicia Ruffin, Michael Dagher, Daniel G. Chawla, Alessandra Soares-Schanoski, Rachel R. Spurbeck, Lishomwa C. Ndhlovu, Robert P. Sebra, Steven H. Kleinstein, Andrew G. Letizia, Irene Ramos, Vance G. Fowler, Christopher W. Woods, Elena Zaslavsky, Olga G. Troyanskaya, Stuart C. Sealfon. Author Correction: Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data

Volume 3, Issue 8

659 -- 0. The carbon footprint of computational research
660 -- 664Michelle N. Meyer, John Basl, David R. Choffnes, Christo Wilson, David M. J. Lazer. Enhancing the ethics of user-sourced online data collection and sharing
665 -- 0Jie Pan 0002. Optimal crystal structure solutions
666 -- 0Ananya Rastogi. Estimating cell growth rate
667 -- 668Liguo Wang 0002. Reference-guided search for open reading frames
669 -- 670Luer Zhong, Rhonda Bacher. Leveraging remeasured samples in biomedical studies
671 -- 672. Energy materials screening with defect graph neural networks
673 -- 674. An imaging-based approach to measure atmospheric turbulence
675 -- 686Matthew D. Witman, Anuj Goyal, Tadashi Ogitsu, Anthony H. McDaniel, Stephan Lany. Defect graph neural networks for materials discovery in high-temperature clean-energy applications
687 -- 699Yadong Wang, Darui Jin, Junzhang Chen, Xiangzhi Bai. Revelation of hidden 2D atmospheric turbulence strength fields from turbulence effects in infrared imaging
700 -- 708Ales Varabyou, Beril Erdogdu, Steven L. Salzberg, Mihaela Pertea. Investigating open reading frames in known and novel transcripts using ORFanage
709 -- 719Hanxuan Ye, Xianyang Zhang, Chen Wang 0001, Ellen L. Goode, Jun Chen. Batch-effect correction with sample remeasurement in highly confounded case-control studies
720 -- 0Liguo Wang 0002. Publisher Correction: Reference-guided search for open reading frames

Volume 3, Issue 7

571 -- 0. Of data and transparency
572 -- 574Da Yan 0001, Adam D. Smith, Cheng-Chien Chen. Structure prediction and materials design with generative neural networks
575 -- 0Jie Pan 0002. Physics-inspired model for online content dynamics
576 -- 0Fernando Chirigati. A language model for medical predictive tasks
577 -- 0Kaitlin McCardle. Shedding light on microbiome-drug interactions
578 -- 579James P. Bagrow. Using fast and slow data to unfold city dynamics
580 -- 581Chris C. R. Smith. Machine learning speeds up genetic structure analysis
582 -- 583Zheyang Zhang, Jialiang Huang. Cellular deconvolution with continuous transitions
584 -- 585Pawel F. Przytycki. Uncovering the genetic circuits that drive diseases
586 -- 587. A software resource for large graph processing and analysis
588 -- 600Luca Pappalardo, Ed Manley, Vedran Sekara, Laura Alessandretti. Future directions in human mobility science
601 -- 610Alex Chohlas-Wood, Madison Coots, Sharad Goel, Julian Nyarko. Designing equitable algorithms
611 -- 620Yanyan Xu, Luis E. Olmos, David Mateo, Alberto Hernando, Xiaokang Yang, Marta C. González. Urban dynamics through the lens of human mobility
621 -- 629Albert Dominguez Mantes, Daniel Mas Montserrat, Carlos D. Bustamante, Xavier Giró i Nieto, Alexander G. Ioannidis. Neural ADMIXTURE for rapid genomic clustering
630 -- 643Liyang Song, Xiwei Sun, Ting Qi, Jian Yang 0005. Mixed model-based deconvolution of cell-state abundances (MeDuSA) along a one-dimensional trajectory
644 -- 657Xi Chen, Yuan Wang, Antonio Cappuccio, Wan-Sze Cheng, Frederique Ruf Zamojski, Venugopalan D. Nair, Clare M. Miller, Aliza B. Rubenstein, German Nudelman, Alicja Tadych, Chandra L. Theesfeld, Alexandria Vornholt, Mary-Catherine George, Felicia Ruffin, Michael Dagher, Daniel G. Chawla, Alessandra Soares-Schanoski, Rachel R. Spurbeck, Lishomwa C. Ndhlovu, Robert P. Sebra, Steven H. Kleinstein, Andrew G. Letizia, Irene Ramos, Vance G. Fowler, Christopher W. Woods, Elena Zaslavsky, Olga G. Troyanskaya, Stuart C. Sealfon. Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data
658 -- 0Gengjie Jia, Yu Li, Xue Zhong, Kanix Wang, Milton Pividori, Rabab Alomairy, Aniello Esposito, Hatem Ltaief, Chikashi Terao, Masato Akiyama, Koichi Matsuda, David E. Keyes, Hae Kyung Im, Takashi Gojobori, Yoichiro Kamatani, Michiaki Kubo, Nancy J. Cox, James A. Evans, Xin Gao 0001, Andrey Rzhetsky. Author Correction: The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci

Volume 3, Issue 6

455 -- 456. A computational quest for a sustainable world
457 -- 460Sophia Chen. Are quantum computers really energy efficient?
461 -- 463Edmundo Molina-Perez. Harnessing the power of decision-support tools to trigger climate action
464 -- 466Kaitlin McCardle. Collaborations drive energy storage research
467 -- 469Kaitlin McCardle. People, places, and the planet
470 -- 472Kaitlin McCardle. Little by little, a bird builds its nest
473 -- 475Jie Pan 0002. Towards a welcoming climate for LGBTQ people
476 -- 0Ananya Rastogi. Particle picking in tomograms
477 -- 0Fernando Chirigati. Experts go deeper
478 -- 0Kaitlin McCardle. Building molecules across the periodic table
479 -- 0Jie Pan 0002. Treating quantum states as human faces
480 -- 481Marco Bernardi. Computing electron dynamics in momentum space
482 -- 483. A single-cell transcriptomic meta-analysis platform for inflammatory bowel disease
484 -- 485. Why bigger quantum neural networks do better
486 -- 494Matthew MacLeod, Prado Domercq, Sam Harrison, Antonia Praetorius. Computational models to confront the complex pollution footprint of plastic in the environment
495 -- 503Jakub Kubecka, Yosef Knattrup, Morten Engsvang, Andreas Buchgraitz Jensen, Daniel Ayoubi, Haide Wu, Ove Christiansen, Jonas Elm. Current and future machine learning approaches for modeling atmospheric cluster formation
504 -- 513Ke R. Yang, Gregory W. Kyro, Victor S. Batista. The landscape of computational approaches for artificial photosynthesis
514 -- 521Loïc Lannelongue, Hans-Erik G. Aronson, Alex Bateman, Ewan Birney, Talia Caplan, Martin Juckes, Johanna R. McEntyre, Andrew D. Morris, Gerry Reilly, Michael Inouye. GREENER principles for environmentally sustainable computational science
522 -- 531Hu Nie, Peilu Lin, Yu Zhang, Yihong Wan, Jiesheng Li, Chengqian Yin, Lei Zhang. Single-cell meta-analysis of inflammatory bowel disease with scIBD
532 -- 541Zhenfa Zheng, Yongliang Shi, Jin-Jian Zhou, Oleg V. Prezhdo, Qijing Zheng, Jin Zhao. Ab initio real-time quantum dynamics of charge carriers in momentum space
542 -- 551Martin Larocca, Nathan Ju, Diego García-Martín, Patrick J. Coles, Marco Cerezo. Theory of overparametrization in quantum neural networks
552 -- 568Luca Cappelletti, Tommaso Fontana, Elena Casiraghi, Vida Ravanmehr, Tiffany J. Callahan, Carlos Cano, Marcin P. Joachimiak, Christopher J. Mungall, Peter N. Robinson, Justin T. Reese, Giorgio Valentini. GRAPE for fast and scalable graph processing and random-walk-based embedding
569 -- 0He Li, Zechen Tang, Xiaoxun Gong, Nianlong Zou, Wenhui Duan, Yong Xu. Author Correction: Deep-learning electronic-structure calculation of magnetic superstructures

Volume 3, Issue 5

361 -- 0. Experimental validation, anyone?
362 -- 364Nicholas David, Wenhao Sun, Connor W. Coley. The promise and pitfalls of AI for molecular and materials synthesis
365 -- 0Ananya Rastogi. Exploring robust pattern formation
366 -- 367Ava P. Amini, Kevin K. Yang. From noise to protein with image models
368 -- 369Alberto Corigliano. Discovering kirigami patterns
370 -- 371. A machine learning-based model for the quantification of mental conflict
372 -- 373. A graph neural network for predicting the adsorption energy of molecules on metal surfaces
374 -- 381Guido Caldarelli, Elsa Arcaute, Marc Barthelemy, Michael Batty, Carlos Gershenson, Dirk Helbing, Stefano Mancuso, Yamir Moreno, José J. Ramasco, Céline Rozenblat, Ángel Sánchez, José Luis Fernández-Villacañas. The role of complexity for digital twins of cities
382 -- 392Jin Sub Lee, Jisun Kim, Philip M. Kim. Score-based generative modeling for de novo protein design
393 -- 402Jacob Saldinger, Matt Raymond, Paolo Elvati, Angela Violi. Domain-agnostic predictions of nanoscale interactions in proteins and nanoparticles
403 -- 417Gengjie Jia, Yu Li, Xue Zhong, Kanix Wang, Milton Pividori, Rabab Alomairy, Aniello Esposito, Hatem Ltaief, Chikashi Terao, Masato Akiyama, Koichi Matsuda, David E. Keyes, Hae Kyung Im, Takashi Gojobori, Yoichiro Kamatani, Michiaki Kubo, Nancy J. Cox, James A. Evans, Xin Gao, Andrey Rzhetsky. The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci
418 -- 432Yuki Konaka, Honda Naoki. Decoding reward-curiosity conflict in decision-making from irrational behaviors
433 -- 442Sergio Pablo-García, Santiago Morandi, Rodrigo A. Vargas-Hernández, Kjell Jorner, Zarko Ivkovic, Núria López, Alán Aspuru-Guzik. Fast evaluation of the adsorption energy of organic molecules on metals via graph neural networks
443 -- 454Levi H. Dudte, Gary P. T. Choi, Kaitlyn P. Becker, L. Mahadevan. An additive framework for kirigami design

Volume 3, Issue 4

277 -- 278. Computationally probing moiré magnets
279 -- 0Fernando Chirigati. Moving toward safer driverless vehicles
280 -- 0Jie Pan 0002. Transfer learning for metal-organic frameworks
281 -- 0Kaitlin McCardle. Learning properties of metal complexes
282 -- 284David Soriano. Uncovering magnetic interactions in moiré magnets
285 -- 286Ali Rahnavard. Omics correlation for efficient network construction
287 -- 288. A deep-learning method for studying magnetic superstructures
289 -- 290. A machine learning algorithm for studying how molecules self-assemble and function
291 -- 300Sharon Hammes-Schiffer. Exploring proton-coupled electron transfer at multiple scales
301 -- 313Maalavika Pillai, Emilia Hojel, Mohit Kumar Jolly, Yogesh Goyal. Unraveling non-genetic heterogeneity in cancer with dynamical models and computational tools
314 -- 320Baishun Yang, Yang Li, Hongjun Xiang, Haiqing Lin, Bing Huang. Moiré magnetic exchange interactions in twisted magnets
321 -- 327He Li, Zechen Tang, Xiaoxun Gong, Nianlong Zou, Wenhui Duan, Yong Xu. Deep-learning electronic-structure calculation of magnetic superstructures
328 -- 333Alec F. White, Chenghan Li, Xing Zhang, Garnet Kin-Lic Chan. Quantum harmonic free energies for biomolecules and nanomaterials
334 -- 345Hendrik Jung, Roberto Covino, A. Arjun, Christian Leitold, Christoph Dellago, Peter G. Bolhuis, Gerhard Hummer. Machine-guided path sampling to discover mechanisms of molecular self-organization
346 -- 359Martin Becker 0003, Huda Nassar, Camilo Espinosa, Ina A. Stelzer, Dorien Feyaerts, Eloïse Berson, Neda Hajiakhoond Bidoki, Alan L. Chang, Geetha Saarunya, Anthony Culos, Davide De Francesco, Ramin Fallahzadeh, Qun Liu, Yeasul Kim, Ivana Maric, Samson Mataraso, Seyedeh Neelufar Payrovnaziri, Thanaphong Phongpreecha, Neal G. Ravindra, Natalie Stanley, Sayane Shome, Yuqi Tan, Melan Thuraiappah, Maria Xenochristou, Lei Xue, Gary M. Shaw, David K. Stevenson, Martin S. Angst, Brice Gaudilliere, Nima Aghaeepour. Large-scale correlation network construction for unraveling the coordination of complex biological systems

Volume 3, Issue 3

185 -- 186. Guiding element mixing
187 -- 188Kaitlin McCardle. Understanding cancer drivers and passengers
189 -- 0Kaitlin McCardle. Accounting for quantum effects in catalysis
190 -- 191Simon L. Batzner. Biasing energy surfaces towards the unknown
192 -- 193. Revealing trajectories of the mind via non-linear manifolds of brain activity
194 -- 195. Oscillations and avalanches coexist in brain networks close to criticality
196 -- 197. A single-cell-resolution mathematical model of the CA1 human hippocampus
198 -- 209Dierk Raabe, Jaber Rezaei Mianroodi, Jörg Neugebauer. Accelerating the design of compositionally complex materials via physics-informed artificial intelligence
210 -- 220Xie Zhang, Jun Kang, Suhuai Wei. Defect modeling and control in structurally and compositionally complex materials
221 -- 229Alberto Ferrari, Fritz Körmann, Mark Asta, Jörg Neugebauer. Simulating short-range order in compositionally complex materials
230 -- 239Maksim Kulichenko, Kipton Barros, Nicholas Lubbers, Ying Wai Li, Richard A. Messerly, Sergei Tretiak, Justin S. Smith, Benjamin T. Nebgen. Uncertainty-driven dynamics for active learning of interatomic potentials
240 -- 253Erica L. Busch, Jessie Huang, Andrew Benz, Tom Wallenstein, Guillaume Lajoie, Guy Wolf, Smita Krishnaswamy, Nicholas B. Turk-Browne. Multi-view manifold learning of human brain-state trajectories
254 -- 263Fabrizio Lombardi, Selver Pepic, Oren Shriki, Gasper Tkacik, Daniele De Martino. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain
264 -- 276Daniela Gandolfi, Jonathan Mapelli, Sergio M. G. Solinas, Paul Triebkorn, Egidio D'Angelo, Viktor K. Jirsa, Michele Migliore. Full-scale scaffold model of the human hippocampus CA1 area

Volume 3, Issue 2

115 -- 0. Why can't we predict earthquakes?
116 -- 117Fernando Chirigati. Advancing the science of synthesis
118 -- 0Fernando Chirigati. A successful few drive urban scaling
119 -- 0Kaitlin McCardle. Advancing organic reaction discovery
120 -- 0Jie Pan 0002. Effective phase analyzer learned from stock images
121 -- 0Ananya Rastogi. When and where the climate threshold will be reached
122 -- 123Yang Jiao. Evolving wave networks for materials design
124 -- 125Yunan Luo. Sensing the shape of functional proteins with topology
126 -- 127Sandeep Choubey. Gene regulation meets Bayesian non-parametrics
128 -- 138Sunkyu Yu. Evolving scattering networks for engineering disorder
139 -- 148Julia Westermayr, Joe Gilkes, Rhyan Barrett, Reinhard Johann Maurer. High-throughput property-driven generative design of functional organic molecules
149 -- 163Yuchi Qiu, Guo-Wei Wei 0001. Persistent spectral theory-guided protein engineering
164 -- 173Tal Einav, Adrian Creanga, Sarah F. Andrews, Adrian B. McDermott, Masaru Kanekiyo. Harnessing low dimensionality to visualize the antibody-virus landscape for influenza
174 -- 183Zeliha Kilic, Max Schweiger, Camille Moyer, Douglas Shepherd, Steve Pressé. Gene expression model inference from snapshot RNA data using Bayesian non-parametrics

Volume 3, Issue 12

993 -- 0. Formats for reporting primary research
994 -- 997Gaomou Xu, Tao Wang. Fewer false positives in electrocatalytic nitrogen reduction by synergizing theory and experiment
998 -- 1000Tsz Wai Ko, Shyue Ping Ong. Recent advances and outstanding challenges for machine learning interatomic potentials
1001 -- 1002Ananya Rastogi. From inception to current challenges in bioinformatics
1003 -- 0Jie Pan 0002. Towards programmed protein generation
1004 -- 0Kaitlin McCardle. Shedding light on GNN affinity predictions
1005 -- 0Fernando Chirigati. One algorithm to play them all
1006 -- 0Ananya Rastogi. Drawing statistically valid conclusions with ML
1007 -- 1008Nguyen-Quoc-Khanh Le. Predicting emerging drug interactions using GNNs
1009 -- 1010Mie Andersen. Machine learning speeds up search for surface structure
1011 -- 1012David J. Wen, Christina V. Theodoris. Interpretable model of CRISPR-Cas9 enzymatic reactions
1013 -- 1014Lachlan Whitehead. Moving towards a generalized denoising network for microscopy
1015 -- 1022Yang Jeong Park, Hyungi Kim, Jeonghee Jo, Sungroh Yoon. Deep contrastive learning of molecular conformation for efficient property prediction
1023 -- 1033Yongqi Zhang, Quanming Yao, Ling Yue, Xian Wu, Ziheng Zhang, Zhenxi Lin, Yefeng Zheng 0001. Emerging drug interaction prediction enabled by a flow-based graph neural network with biomedical network
1034 -- 1044Xiaochen Du, James K. Damewood, Jaclyn R. Lunger, Reisel Millan, Bilge Yildiz, Lin Li, Rafael Gómez-Bombarelli. Machine-learning-accelerated simulations to enable automatic surface reconstruction
1045 -- 1055Chenru Duan, Yuanqi Du, Haojun Jia, Heather J. Kulik. Accurate transition state generation with an object-aware equivariant elementary reaction diffusion model
1056 -- 1066Zijun Zhang, Adam R. Lamson, Michael J. Shelley, Olga G. Troyanskaya. Interpretable neural architecture search and transfer learning for understanding CRISPR-Cas9 off-target enzymatic reactions
1067 -- 1080Xinyang Li, Xiaowan Hu, Xingye Chen, Jiaqi Fan, Zhifeng Zhao, Jiamin Wu, Haoqian Wang, Qionghai Dai. Spatial redundancy transformer for self-supervised fluorescence image denoising

Volume 3, Issue 11

907 -- 0. Code sharing in the spotlight
908 -- 911Yash Raj Shrestha, Georg von Krogh, Stefan Feuerriegel. Building open-source AI
912 -- 0Fernando Chirigati. Memory and computation together at last
913 -- 0Jie Pan 0002. A full-stack platform for spiking deep learning
914 -- 0Ananya Rastogi. Impact of spillovers on technological changes
915 -- 0Kaitlin McCardle. Predicting electronic structure calculation results
916 -- 917T. Matthew Evans. Investigating the elegance of empty space
918 -- 919Conrard Giresse Tetsassi Feugmo. Accurately predicting molecular spectra with deep learning
920 -- 921. A software framework for end-to-end genomic sequence analysis with deep learning
922 -- 933Agnieszka Ilnicka, Gisbert Schneider. Designing molecules with autoencoder networks
934 -- 945Sean D. Griesemer, Yi Xia, Chris Wolverton. Accelerating the prediction of stable materials with machine learning
946 -- 956Adam R. Klie, David Laub, James V. Talwar, Hayden Stites, Tobias Jores, Joe J. Solvason, Emma K. Farley, Hannah Carter. Predictive analyses of regulatory sequences with EUGENe
957 -- 964Zihan Zou, Yujin Zhang, Lijun Liang, Mingzhi Wei, Jiancai Leng, Jun Jiang, Yi Luo 0003, Wei Hu. A deep learning model for predicting selected organic molecular spectra
965 -- 974Xingyi Guan, Joseph P. Heindel, Taehee Ko, Chao Yang, Teresa Head-Gordon. Using machine learning to go beyond potential energy surface benchmarking for chemical reactivity
975 -- 992Lindsay Riley, Peter Cheng, Tatiana Segura. Identification and analysis of 3D pores in packed particulate materials

Volume 3, Issue 10

807 -- 0. Ada Lovelace, a role model for the ages
808 -- 809Ananya Rastogi. Moving towards better communication
810 -- 812Ananya Rastogi. Tackling environmental challenges, one molecule at a time
813 -- 814Ananya Rastogi. Laying the foundations of programming and system design
815 -- 0Kaitlin McCardle. Drug discovery with limited resources
816 -- 0Jie Pan 0002. Adding charge to neural network potentials
817 -- 0Ananya Rastogi. The waiting game
818 -- 0Fernando Chirigati. Alerting for imminent earthquakes
819 -- 820Zhaorong Fu, Jueming Bao, Jianwei Wang. Programmability empowering quantum boson sampling
821 -- 822Ganna Gryn'ova. Crafting molecular architectures with guided diffusion
823 -- 824Brennan Klein. A consolidated framework for quantifying interaction dynamics
825 -- 826. Measuring three-dimensional organization on cell surfaces with cellular harmonics
827 -- 828. AI-powered structure-based drug design inspired by the lock-and-key model
829 -- 830. Efficient prediction of relative ligand binding affinity in drug discovery
831 -- 832. STAligner enables the integration and alignment of multiple spatial transcriptomics datasets
833 -- 838Thilo Hagendorff, Sarah Fabi, Michal Kosinski. Human-like intuitive behavior and reasoning biases emerged in large language models but disappeared in ChatGPT
839 -- 848Shang Yu, Zhi-Peng Zhong, Yuhua Fang, Raj B. Patel, Qing-Peng Li, Wei Liu, Zhenghao Li, Liang Xu, Steven Sagona-Stophel, Ewan Mer, Sarah E. Thomas, Yu Meng, Zhi-peng Li, Yuan-Ze Yang, Zhaoan Wang, Nai-Jie Guo, Wen-Hao Zhang, Geoffrey K. Tranmer, Ying Dong, Yi-Tao Wang, Jian-Shun Tang, Chuan-feng Li, Ian A. Walmsley, Guang-Can Guo. A universal programmable Gaussian boson sampler for drug discovery
849 -- 859Odin Zhang, Tianyue Wang, Gaoqi Weng, Dejun Jiang 0002, Ning Wang, Xiaorui Wang, Huifeng Zhao, Jialu Wu, Ercheng Wang, Guangyong Chen, Yafeng Deng, Peichen Pan, Yu Kang 0002, Chang-Yu Hsieh, Tingjun Hou. Learning on topological surface and geometric structure for 3D molecular generation
860 -- 872Jie Yu, Zhaojun Li, Geng Chen, Xiangtai Kong, Jie Hu, Dingyan Wang, Duanhua Cao, Yanbei Li, Ruifeng Huo, Gang Wang, Xiaohong Liu, Hualiang Jiang, Xutong Li, Xiaomin Luo, Mingyue Zheng. Computing the relative binding affinity of ligands based on a pairwise binding comparison network
873 -- 882Tomer Weiss 0002, Eduardo Mayo Yanes, Sabyasachi Chakraborty, Luca Cosmo, Alex M. Bronstein, Renana Gershoni-Poranne. Guided diffusion for inverse molecular design
883 -- 893Oliver M. Cliff, Annie G. Bryant, Joseph T. Lizier, Naotsugu Tsuchiya, Ben D. Fulcher. Unifying pairwise interactions in complex dynamics
894 -- 906Xiang Zhou, Kangning Dong, Shihua Zhang. Integrating spatial transcriptomics data across different conditions, technologies and developmental stages

Volume 3, Issue 1

1 -- 0. Cover runners-up of 2022
2 -- 0Fernando Chirigati. Leveraging the power of crowds
3 -- 0Ananya Rastogi. Deep learning to estimate brain age
4 -- 0Kaitlin McCardle. Uncovering contaminants via machine learning
5 -- 0Jie Pan 0002. Large language model for molecular chemistry
6 -- 7Stefan Vuckovic. Using AI to navigate through the DFA zoo
8 -- 9Yang Yang 0067, Zewen K. Tuong, Di Yu. Dimensionality reduction under scrutiny
10 -- 11. Towards a purely physics-based computational binding affinity estimation
12 -- 24Mingjian Wen, Evan Walter Clark Spotte-Smith, Samuel M. Blau, Matthew J. McDermott, Aditi S. Krishnapriyan, Kristin A. Persson. Chemical reaction networks and opportunities for machine learning
25 -- 37Alexander Miessen, Pauline J. Ollitrault, Francesco Tacchino, Ivano Tavernelli. Quantum algorithms for quantum dynamics
38 -- 47Chenru Duan, Aditya Nandy, Ralf Meyer, Naveen Arunachalam, Heather J. Kulik. A transferable recommender approach for selecting the best density functional approximations in chemical discovery
48 -- 58Yiwei Liu, Cheng Zhang, Zhonghua Liu, Donald G. Truhlar, Ying Wang, Xiao He 0004. Supervised learning of a chemistry functional with damped dispersion
59 -- 70Vivek Govind Kumar, Adithya Polasa, Shilpi Agrawal, Thallapuranam K. Suresh Kumar, Mahmoud Moradi. Binding affinity estimation from restrained umbrella sampling simulations
71 -- 85Tze Hui Koh, William E. Bishop, Takashi Kawashima, Brian B. Jeon, Ranjani Srinivasan, Yu Mu, Ziqiang Wei, Sandra J. Kuhlman, Misha B. Ahrens, Steven M. Chase, Byron M. Yu. Dimensionality reduction of calcium-imaged neuronal population activity
86 -- 100Eric D. Sun, Rong Ma, James Zou 0001. Dynamic visualization of high-dimensional data
101 -- 114R. Patrick Xian, Vincent Stimper, Marios Zacharias, Maciej Dendzik, Shuo Dong, Samuel Beaulieu, Bernhard Schölkopf, Martin Wolf, Laurenz Rettig, Christian Carbogno, Stefan Bauer, Ralph Ernstorfer. A machine learning route between band mapping and band structure