Weakly supervised latent variable inference of proximity bias in crispr gene knockouts from single-cell images
2025/11/19
Aditya Ravuri,
Kristina Ulicna,
Jana Osea,
Konstantin Donhauser ,
Jason Hartford,
(2025)
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Publications
Weakly supervised latent variable inference of proximity bias in crispr gene knockouts from single-cell images
2025/11/19
(2025)
Trajectory generation for ROI expansion in dental CBCT imaging: An out-of-FOV ROI annotation guided arc scan-based approach
2025/11/19
Ander Biguri,
Carola-Bibiane Schönlieb,
S M Ragib Shahriar Islam,
Claudio Landi,
Giovanni Di Domenico,
Pascal Grün,
Cristina Sarti,
Dritan Turhani,
Gernot Kronreif,
Wolfgang Birkfellner,
Sepideh Hatamikia,
Computational and Structural Biotechnology Journal (2025) 211-216
Linear combinations of Gaussian latents in generative models: interpolation and beyond
2025/11/18
Carl Henrik Ek,
Erik Bodin,
Alexandru I. Stere,
Dragos D Margineantu,
Henry Moss,
(2025)
Efficient Model-Based Reinforcement Learning Through Optimistic Thompson Sampling
2025/11/18
Carl Henrik Ek,
Jasmine Bayrooti,
Amanda Prorok,
(2025)
Beyond Quantification: Navigating Uncertainty in Professional AI Systems
2025/11/08
Jess Montgomery,
Neil D. Lawrence,
Diana Robinson,
Carl Henrik Ek,
Sylvie Delacroix,
Umang Bhatt,
Jacopo Domenicucci,
Gaël Varoquaux,
Vincent Fortuin,
Yulan He,
Tom Diethe,
Neill Campbell,
Mennatallah El-Assady,
Søren Hauberg,
Ivana Dusparic,
RSS: Data Science and Artificial Intelligence (2025)
Balancing objects and processes: advocating pluralism in biology: Comment on “Thoughts and thinkers: On the complementarity between objects and processes" by Chris Fields and Michael Levin
2025/11/06
Soumya Banerjee,
Physics of Life Reviews (2025) Pages 79-82
Online Reinforcement Learning for Autoformalization
2025/10/31
Soumya Banerjee,
Simon Sorg,
Wenda Li,
(2025)
Mortal Machines: On Life, Death, and Forgetting in Artificial Minds
2025/10/31
Soumya Banerjee,
Patrick Wagner,
(2025)
Investigating dynamics of Neural Cellular Automata applied to image data in diverse complex systems
2025/10/31
Soumya Banerjee,
Vaibhav Mahajan,
(2025)
Conjecture extraction for proof autoformalization
2025/10/31
Soumya Banerjee,
Simon Sorg,
Wenda Li,
(2025)
Bridging the Gap: How Goals Emerge from a Purposeless Universe
2025/10/31
Soumya Banerjee,
(2025)
Cosmicism and Artificial Intelligence: Beyond Human-Centric AI
2025/10/24
Soumya Banerjee,
(2025)
Evaluating Machine Learning Models for Prediction of Attention Deficit Hyperactivity Disorder among Autistic Individuals Using Genetic Data
2025/10/20
Soumya Banerjee,
Ryan Daniels,
Niran Okewole,
Christopher Bannon ,
Yuanjun Gu ,
Simon Baron-Cohen,
Varun Warrier,
Vincent-Raphael Bourque ,
European Neuropsychopharmacology (2025)
The relative intensity of bilateral and multilateral co-authorship with Russia since 1995
2025/10/09
Hongyu Zhou,
Tim C.E. Engels,
Ronald Rousseau,
(2025)
A remark on weighted average multiplicities in prime factorisation
2025/10/08
Challenger Mishra,
Daattavya Aggarwal,
Viktor Mirjanić,
(2025)
Synthetic Samsara: AI, Forgetting, and the Simulation of Cycles
2025/09/30
Soumya Banerjee,
Patrick Wagner,
(2025)
Investigating dynamics of Neural Cellular Automata in complex systems
2025/09/30
Soumya Banerjee,
Vaibhav Mahajan,
(2025)
The Changing Geography of Medical Research
2025/09/29
Hongyu Zhou,
Prashant Garg,
Thiemo Fetzer,
(2025)
When Planes Fly Better than Birds: Should AIs Think like Humans?
2025/09/16
Soumya Banerjee,
(2025)
Wu-Wei in the Machine: Open-Ended Learning in Goal-Free Generative Agent Societies
2025/08/31
Soumya Banerjee,
(2025)
Towards a taxonomy of life-like systems: An information theoretic view of life
2025/08/31
Soumya Banerjee,
(2025)
Re-Envisioning Superintelligence using Generative AI and Science Fiction
2025/08/31
Soumya Banerjee,
(2025)
From AGI to ASI: Mapping the Societal and Systemic Impact of Superintelligence
2025/08/31
Soumya Banerjee,
(2025)
Moving beyond word error rate to evaluate automatic speech recognition in clinical samples: Lessons from research into schizophrenia-spectrum disorders
2025/08/25
Shrankhla Pandey,
Sarah Morgan,
Sandra Anna Just,
Brita Elvevåg,
Ivan Nenchev,
Anna-Lena Bröcker,
Christiane Montag,
Psychiatry Research (2025)
DOI: 10.1016/j.psychres.2025.116690
How long does the human civilization need to last in order to observe another advanced intelligence in the Universe?
2025/07/31
Soumya Banerjee,
,
Journal of the British Interplanetary Society (2025) 230-237
Transformers as Unrolled Inference in Probabilistic Laplacian Eigenmaps: An Interpretation and Potential Improvements
2025/07/28
Aditya Ravuri,
Neil D. Lawrence,
(2025)
Graph Convolutional Neural Networks to Model the Brain for Insomnia
2025/07/02
Sam Nallaperuma,
Kevin Monteiro ,
Martina Mason,
Steve Niederer,
(2025)
Bridging the Gap with Retrieval-Augmented Generation: Making Prosthetic Device User Manuals Available in Marginalised Languages
2025/06/30
Soumya Banerjee,
Vikranth Harthikote Nagaraja,
Laurence Kenney,
Abhishek Dasgupta,
Lesley Davidson,
Ikechukwu Ogbonna,
(2025)
Prompt Variability Effects On LLM Code Generation
2025/06/11
Radzim Sendyka,
Diana Robinson,
Neil D. Lawrence,
Andrei Paleyes,
Christian Cabrera,
(2025)
Smooth Model Compression without Fine-Tunin
2025/05/31
Ander Biguri,
Carola-Bibiane Schönlieb,
Christina Runkel,
Natacha Kuete Meli,
Jovita Lukasik,
Michael Moeller,
(2025)
Protein Language Model Zero-Shot Fitness Predictions are Improved by Inference-only Dropout
2025/05/31
Aditya Ravuri,
Neil D. Lawrence,
(2025)
LLM Performance for Code Generation on Noisy Tasks
2025/05/29
Diana Robinson,
Neil D. Lawrence,
Radzim Sendyka,
Christian Cabrera,
Andrei Paleyes,
(2025)
The Human Visual System Can Inspire New Interaction Paradigms for LLMs
2025/05/05
Diana Robinson,
Neil D. Lawrence,
(2025)
Framework conditions and funding for AI in science Mutual learning exercise on national policies for AI in science : first thematic report
2025/04/30
(2025)
DOI: 10.2777/7211107
Arab Spring's Impact on Science through the Lens of Scholarly Attention, Funding, and Migration
2025/04/25
Hongyu Zhou,
Yasaman Asgari,
Özgür Kadir Özer,
Rezvaneh Rezapour,
Mary Ellen Sloane,
Alexandre Bovet,
(2025)
DeepSynBa: A deep learning method to improve drug combination predictions using full dose-response matrices and contextual features of cell lines and cancer indications Free
2025/04/21
Carl Henrik Ek,
Marta Milo,
Haoting Zhang,
Halil ibrahim Kuru,
A. Ercument Cicek,
Oznur Tastan,
Magnus Rattray,
Cancer Research (2025)
DOI: 10.1158/1538-7445.AM2025-3646
Benchmarking learned algorithms for computed tomography image reconstruction tasks
2025/03/31
Ander Biguri,
Carola-Bibiane Schönlieb,
Maximilian B. Kiss,
Zakhar Shumaylov,
Ferdia Sherry,
K. Joost Batenburg,
Felix Lucka,
Applied Mathematics for Modern Challenges (2025) 1-43
Noisier2Inverse: Self-Supervised Learning for Image Reconstruction with Correlated Noise
2025/03/25
Ander Biguri,
Nadja Gruber,
Johannes Schwab,
Markus Haltmeier,
Clemens Dlaska,
Gyeongha Hwang,
(2025)
I apologize for my actions”: Emergent Properties and Technical Challenges of Generative Agents
2025/03/20
Soumya Banerjee,
N’yoma Diamond,
(2025)
cymyc: Calabi-Yau Metrics, Yukawas, and Curvature
2025/03/05
Challenger Mishra,
Justin Tan,
Giorgi Butbaia,
Damián Mayorga Peña,
Per Berglund,
Tristan Hübsch,
Vishnu Jejjala,
Journal of High Energy Physics (2025)
Gene-level alignment of single-cell trajectories
2024/12/16
Dinithi Sumanaweera,
C. Suo,
A.M. Cujba,
D. Muraro,
E. Dann,
K. Polanski,
A.S. Steemers,
W. Lee,
A.J. Oliver,
J.E. Park,
K.B. Meyer,
Nature Methods (2024) 1-14
Towards One Model for Classical Dimensionality Reduction: A Probabilistic Perspective on UMAP and t-SNE
2024/12/12
Aditya Ravuri,
Neil D. Lawrence,
(2024)
DOI: 10.48550/arXiv.2405.17412
Building Trustworthy AI: The Role of Patient and Public Involvement in Healthcare AI Development
2024/11/30
Soumya Banerjee,
(2024) 329-331
DOI: 10.1609/aaaiss.v4i1.31811
The BACON system for equation discovery from scientific data: Transforming classical artificial intelligence with modern machine learning approaches
2024/10/31
Soumya Banerjee,
J. Miller,
(2024)
GRANOLA: Adaptive Normalization for Graph Neural Networks
2024/10/31
Moshe Eliasof,
B. Bevilacqua,
C.B. Schonlieb,
H Maron,
(2024)
DOI: 10.48550/arXiv.2404.13344
Disrupted functional brain network associated with presence of hallucinations in Parkinsons Disease
2024/10/30
Sarah Morgan,
M. Montagnese,
M. Mehta,
D. Ffytche ,
M. Firbank,
R.A. Lawson,
J.P. Taylor,
E.T. Bullmore,
(2024)
DOI: 10.1101/2024.09.30.24314594
DiGRAF: Diffeomorphic Graph-Adaptive Activation Function
2024/10/30
Moshe Eliasof,
K.S.I. Mantri,
X. Wang,
C.B. Schonlieb,
B. Riberiro,
B. Bevilacqua,
(2024)
DOI: 10.48550/arXiv.2407.02013
cymyc -- Calabi-Yau Metrics, Yukawas, and Curvature
2024/10/25
Justin Tan,
Challenger Mishra,
P. Berglund,
G. Butbaia,
T. Hubsch,
V. Jejjala,
D.M. Pena,
(2024)
Fast neural network inverse model to maximize throughput in ultra-wideband WDM systems
2024/10/21
Sam Nallaperuma,
Z. Gan,
M. Shevchenko,
S.J. Savory,
Optics Express (2024) 38642-38654
DOI: 10.1364/OE.536632
Calabi-Yau metrics through Grassmannian learning and Donaldson's algorithm
2024/10/15
Carl Henrik Ek,
Oisin Kim,
Challenger Mishra,
(2024)
DOI: 10.48550/arXiv.2410.11284
A study of why we need to reassess full reference image quality assessment with medical images
2024/09/24
Ander Biguri,
A. Breger,
M.S. Landman,
I. Selby,
N. Amberg,
E. Brunner,
J. Grohl,
S. Hatamikia,
L. Ning,
C. Karner,
S. Dittmer,
(2024)
DOI: 10.48550/arXiv.2405.19097
Molecular and micro-architectural mapping of gray matter alterations in psychosis
2024/09/12
Isaac Sebenius,
Sarah Morgan,
N. Garcia-San-Martin,
R.A. Bethlehem,
A. Mihalik,
J. Seidlitz,
C. Aleman-Morillo,
L. Dorfschmidt,
G. Shafiei,
V. Ortiz-Garcia de la Foz,
K. Merritt,
A. David,
Molecular Psychiatry (2024) 1-10
DOI: 10.1038/s41380-024-02724-0
Resilient Graph Neural Networks: A Coupled Dynamical Systems Approach
2024/09/11
Moshe Eliasof,
D. Murarib,
F. Sherrya,
C.B. Schonlieb,
(2024)
DOI: 10.48550/arXiv.2311.06942
Learned denoising with simulated and experimental low-dose CT data
2024/08/15
Ander Biguri,
M.B. Kiss,
C.B. Schonlieb,
K.J. Batenburg,
F. Lucka,
(2024)
DOI: 10.48550/arXiv.2408.08115
Advancing the frontiers of deep learning for low-dose 3D cone-beam computed tomography (CT) reconstruction
2024/08/15
Ander Biguri,
S. Mukherjee,
(2024) 81-82
DOI: 10.1109/ICASSPW62465.2024.10626185
BERT's Conceptual Cartography: Mapping the Landscapes of Meaning
2024/08/13
Ryan Daniels,
N. Haket,
(2024)
DOI: 10.48550/arXiv.2408.07190
Precision String Phenomenology
2024/07/18
Challenger Mishra,
Justin Tan,
P. Berglund,
G. Butbaia,
T. Hubsch,
V. Jejjala,
D.M. Pena,
(2024)
DOI: 10.48550/arXiv.2407.13836
The GeometricKernels Package: Heat and Mat\'ern Kernels for Geometric Learning on Manifolds, Meshes, and Graphs
2024/07/10
Aditya Ravuri,
P. Mostowsky,
V. Dutordoir,
I. Azangulov,
N. Jaquier,
M.J. Hutchinson,
L. Rozo,
A. Terenin,
V. Borovitskiy,
(2024)
DOI: 10.48550/arXiv.2407.08086
On Feature Learning for Titi Monkey Activity Detection
2024/07/01
Aditya Ravuri,
Neil D. Lawrence,
J. Muir,
(2024)
DOI: 10.48550/arXiv.2407.01452
Advection Augmented Convolutional Neural Networks
2024/06/27
Moshe Eliasof,
N. Zakariaei,
S. Rout,
E. Haber,
(2024)
DOI: 10.48550/arXiv.2406.19253
Requirements are All You Need: The Final Frontier for End-User Software Engineering
2024/05/20
Diana Robinson,
Neil D. Lawrence,
C. Cabrera,
A.D. Gordon,
L. Mennen,
(2024)
DOI: 10.48550/arXiv.2405.13708
Scalable Amortized GPLVMs for Single Cell Transcriptomics Data
2024/05/06
Aditya Ravuri,
Neil D. Lawrence,
S. Zhao,
V. Lalchand,
(2024)
DOI: 10.48550/arXiv.2405.03879
Continuous Learned Primal Dual
2024/05/03
Ander Biguri,
C. Runkel,
C.B. Schonlieb,
(2024)
DOI: 10.48550/arXiv.2405.02478
Uncertainty as a predictor: Leveraging self-supervised learning for zero-shot mos prediction
2024/04/30
Aditya Ravuri,
E. Cooper,
J. Yamagishi,
(2024) 580-584
DOI: 10.1109/ICASSPW62465.2024.10626267
Intelligence in animals, humans and machines: a heliocentric view of intelligence?
2024/04/29
Soumya Banerjee,
Halfdan Holm,
AI & Society (2024)
DOI: 10.1007/s00146-024-01931-1
Enhancing Patient Stratification and Interpretability Through Class-Contrastive and Feature Attribution Techniques
2024/03/25
Soumya Banerjee,
Neil D. Lawrence,
Sharday Olowu,
medrXiv (2024)
DOI: 10.1101/2024.03.25.24304824
Feature transportation improves graph neural networks
2024/03/24
Moshe Eliasof,
E. Haber,
E. Treister,
(2024) 11874-11882
DOI: 10.1609/aaai.v38i11.29073
Physical Yukawa Couplings in Heterotic String Compactifications
2024/01/26
Justin Tan,
Challenger Mishra,
G Butbaia,
D Mayorga Peña,
P Berglund,
T Hübsch,
V Jejjala,
arXiv (2024)
DOI: 10.48550/arXiv.2401.15078
Neural networks for abstraction and reasoning: Towards broad generalization in machines
2024/02/05
Soumya Banerjee,
M Bober-Irizar,
arXiv (2024)
DOI: 10.48550/arXiv.2402.03507
On The Temporal Domain of Differential Equation Inspired Graph Neural Networks
2024/01/20
Moshe Eliasof,
E. Haber,
E. Treister,
C.B.B. Schonlieb,
(2024) 1792-1800
DOI: 10.48550/arXiv.2401.11074
Generating complex explanations for artificial intelligence models: an application to clinical data on severe mental illness
2024/01/10
Soumya Banerjee,
medRxiv (2024)
DOI: https://www.medrxiv.org/content/10.1101/2024.01.09.24300944v1
Predicting ruthenium catalysed hydrogenation of esters using machine learning
2023/11/20
Challenger Mishra,
Neil D. Lawrence,
Aditya Ravuri,
N. von Wolff,
A. Tripathi,
C.N. Brodie,
E. Bremond,
A. Preiss,
A. Kumar,
Digital Discovery (2023)
DOI: /10.1039/D3DD00029J
Involving patients in artificial intelligence research to build trustworthy systems
2023/11/16
Soumya Banerjee,
S. Griffiths,
AI & Society (2023)
DOI: 10.1007/s00146-023-01745-7
Mathematical conjecture generation using machine intelligence
2023/11/16
Challenger Mishra,
S.R. Moulik,
R. Sarkar,
(2023)
Ice Core Dating using Probabilistic Programming
2023/11/13
Aditya Ravuri,
Neil D. Lawrence,
T.R. Andersson,
I. Kazlauskaite,
W. Tebbutt,
R.E. Turner,
J.S. Hosking,
M. Kaiser,
(2023)
DOI: 10.48550/arXiv.2210.16568
Dimensionality Reduction as Probabilistic Inference
2023/11/10
Aditya Ravuri,
Neil D. Lawrence,
F. Vargas,
V. Lalchand,
(2023)
DOI: 10.48550/arXiv.2304.07658
Robust estimation of cortical similarity networks from brain MRI
2023/07/17
Isaac Sebenius,
Sarah Morgan,
Jakob Seidlitz,
Varun Warrier,
Richard AI Bethlehem,
Aaron Alexander-Bloch,
Travis T Mallard,
Rafael Romero Garcia,
Edward T Bullmore,
Nature Neuroscience (2023)
DOI: 10.1038/s41593-023-01376-7
dsSurvival 2.0: privacy enhancing survival curves for survival models in the federated DataSHIELD analysis system
2023/06/06
Soumya Banerjee,
Tom RP Bishop,
BMC Res Notes (2023)
DOI: 10.1186/s13104-023-06372-5
Machine Learning for Optical Motion Capture-Driven Musculoskeletal Modelling from Inertial Motion Capture Data
2023/04/24
Challenger Mishra,
Abhishek Dasgupta,
Rahul Sharma,
Vikranth H Nagaraja,
Bioengineering (2023) 510
DOI: 10.3390/bioengineering10050510
Semantic Speech Networks Linked to Formal Thought Disorder in Early Psychosis
2023/03/22
Sarah Morgan,
Caroline Nettekoven,
Kelly Diederen,
Oscar Giles,
Helen Duncan,
Iain Stenson,
Julianna Olah,
Toni Gibbs-Dean,
Nigel Collier,
Petra E Vértes,
Tom J Spencer,
Philip McGuire,
Schizophrenia Bulletin (2023) S142–S152
DOI: 10.1093/schbul/sbac056
AI for Science: An Emerging Agenda
2023/03/07
Neil D. Lawrence,
Jess Montgomery,
Philipp Berens,
Kyle Cranmer,
Ulrike von Luxburg,
arXiv (2023)
DOI: 10.48550/arXiv.2303.04217
Bayesian learning via neural Schrödinger–Föllmer flows
2022/11/23
Neil D. Lawrence,
Francisco Vargas,
Andrius Ovsianas,
David Fernandes,
Mark Girolami,
Nikolas Nüsken,
Statistics and Computing (2022)
DOI: 10.1007/s11222-022-10172-5
Software Application Profile: ShinyDataSHIELD—an R Shiny application to perform federated non-disclosive data analysis in multicohort studies
2022/10/27
Soumya Banerjee,
Xavier Escribà-Montagut,
Yannick Marcon,
Demetris Avraam,
Tom R P Bishop,
Paul Burton,
Juan R González,
International Journal of Epidemiology (2022)
DOI: https://doi.org/10.1093/ije/dyac201
Machine Learning for Musculoskeletal Modeling of Upper Extremity
2022/10/01
Challenger Mishra,
Rahul Sharma,
Abhishek Dasgupta,
Runbei Cheng,
Vikranth H. Nagaraja,
,
IEEE (2022) 18684-18697
DOI: 10.1109/JSEN.2022.3197461.
Neural network approximations for Calabi-Yau metrics
2022/08/08
Challenger Mishra,
Vishnu Jejjala,
Damián Kaloni Mayorga Peña,
Journal of High Energy Physics (2022)
DOI: https://doi.org/10.1007/JHEP08(2022)105
Natural Language Processing markers in First Episode Psychosis and People at Clinical High-risk
2021/12/13
Sarah E. Morgan,
Kelly Diederen,
Petra E. Vértes,
Samantha H. Y. Ip,
Bo Wang,
Bethany Thompson,
Arsime Demjaha,
Andrea Micheli,
Dominic Oliver,
Maria Liakata,
Paolo Fusar-Poli,
Tom J. Spencer,
Philip McGuire,
Translational Psychiatry (2021)
DOI: 10.1038/s41398-021-01722-y
Multimodal Graph Coarsening for Interpretable, MRI-Based Brain Graph Neural Network
2021/10/25
Isaac Sebenius,
Alexander Campbell,
Sarah E. Morgan,
Edward T. Bullmore,
Pietro Liò,
(2021)
DOI: 10.1109/MLSP52302.2021.9690626
Phase Behaviours of Superionic Water at Planetary Conditions
2021/09/23
Bingqing Cheng,
Mandy Bethkenhagen,
Chris J. Pickard,
Sebastien Hamel,
Nature Physics (2021) 1228--1232
DOI: 10.1038/s41567-021-01334-9
Deep learning for Bioimage Analysis in Developmental Biology
2021/09/07
Adrien Hallou,
Hannah G. Yevick,
Bianca Dumitrascu,
Virginie Uhlmann,
Development (2021) dev199616
DOI: 10.1242/dev.199616
Solving Schrödinger Bridges via Maximum Likelihood
2021/08/31
Neil D. Lawrence,
Austen Lamacraft,
Entropy (2021) 1134
DOI: 10.3390/e23091134
Ranking the Information Content of Distance Measures
2021/04/30
Aldo Glielmo,
Claudio Zeni,
Bingqing Cheng,
Gabor Csanyi,
Alessandro Laio,
(2021)
DOI: 10.48550/ARXIV.2104.15079
Optimal marker gene selection for cell type discrimination in single cell analyses
2021/02/19
Bianca Dumitrascu,
Soledad Villar,
Dustin G. Mixon,
Barbara Englehardt,
Nature Communications (2021)
DOI: 10.1038/s41467-021-21453-4
Quantum-Mechanical Exploration of the Phase Diagram of Water
2021/01/26
Aleks Reinhardt,
Bingqing Cheng,
Nature Communications (2021)
DOI: 10.1038/s41467-020-20821-w
Gaussian Process Latent Variable Flows for Massively Missing Data
2021/01/15
Aditya Ravuri,
Neil D. Lawrence,
Vidhi Lalchand,
(2021)
Liquid Water Contains the Building Blocks of Diverse Ice Phases
2020/11/13
Bartomeu Monserrat,
Jan Gerit Brandenburg,
Edgar A. Engel,
Bingqing Cheng,
Nature Communications (2020) 2041-1723
DOI: 10.1038/s41467-020-19606-y