Tootfinder

Progress and new challenges in image-based profiling
Erik Serrano, John Peters, Jesko Wagner, Rebecca E. Graham, Zhenghao Chen, Brian Feng, Gisele Miranda, Alexandr A. Kalinin, Loan Vulliard, Jenna Tomkinson, Cameron Mattson, Michael J. Lippincott, Ziqi Kang, Divya Sitani, Dave Bunten, Srijit Seal, Neil O. Carragher, Anne E. Carpenter, Shantanu Singh, Paula A. Marin Zapata, Juan C. Caicedo, Gregory P. Way

Progress and new challenges in image-based profiling
For over two decades, image-based profiling has revolutionized cellular phenotype analysis. Image-based profiling processes rich, high-throughput, microscopy data into unbiased measurements that reveal phenotypic patterns powerful for drug discovery, functional genomics, and cell state classification. Here, we review the evolving computational landscape of image-based profiling, detailing current procedures, discussing limitations, and highlighting future development directions. Deep learning h…

Heat Transport and Dissipation in 2.5D Rotating Internally Heated and Cooled Convection
Tom Joshi-Hartley (University of Exeter), Matthew K. Browning (University of Exeter), Laura K. Currie (Durham University), Neil T. Lewis (University of Exeter), Benjamin P. Brown (University of Colorado at Boulder), Simon R. W. Lance (University of Exeter)
https:/…

Heat Transport and Dissipation in 2.5D Rotating Internally Heated and Cooled Convection
Models of astrophysical convection, such as mixing length theory, typically assume that the heat transport is independent of microphysical diffusivities. Such 'diffusion-free' behaviour is, however, not observed in numerical simulations employing standard fixed-flux or fixed-temperature boundary conditions, except possibly in extreme parameter regimes that are computationally expensive to achieve. Recent numerical and experimental work has suggested that internally heated and cooled convection …

Mitigating Watermark Stealing Attacks in Generative Models via Multi-Key Watermarking
Toluwani Aremu, Noor Hussein, Munachiso Nwadike, Samuele Poppi, Jie Zhang, Karthik Nandakumar, Neil Gong, Nils Lukas
https://arxiv.org/abs/2507.07871

Mitigating Watermark Stealing Attacks in Generative Models via Multi-Key Watermarking
Watermarking offers a promising solution for GenAI providers to establish the provenance of their generated content. A watermark is a hidden signal embedded in the generated content, whose presence can later be verified using a secret watermarking key. A threat to GenAI providers are \emph{watermark stealing} attacks, where users forge a watermark into content that was \emph{not} generated by the provider's models without access to the secret key, e.g., to falsely accuse the provider. Stealing …

Replaced article(s) found for cs.HC. https://arxiv.org/list/cs.HC/new
[2/2]:
- Making Physical Objects with Generative AI and Robotic Assembly: Considering Fabrication Constrai...
Alexander Htet Kyaw, Se Hwan Jeon, Miana Smith, Neil Gershenfeld

Distributionally Robust System Level Synthesis With Output Feedback Affine Control Policy
Yun Li, Jicheng Shi, Colin N. Jones, Neil Yorke-Smith, Tamas Keviczky
https://arxiv.org/abs/2508.05466

Distributionally Robust System Level Synthesis With Output Feedback Affine Control Policy
This paper studies the finite-horizon robust optimal control of linear systems subject to model mismatch and additive stochastic disturbances. Utilizing the system level synthesis (SLS) parameterization, we propose a novel SLS design using output-feedback affine control policy and extend it to a distributionally robust setting to improve system resilience by minimizing the cost function while ensuring constraint satisfaction against the worst-case uncertainty distribution. The scopes of model m…

On groups with square-free gcd of character degree and codegree
Karam Aldahleh, Alan Kappler, Neil Makur, Yong Yang
https://arxiv.org/abs/2507.03100 https:…

Quantising Chiral Bosons On Riemann Surfaces
Chris Hull, Neil Lambert
https://arxiv.org/abs/2508.02865 https://arxiv.org/pdf/2508.02865

Quantising Chiral Bosons On Riemann Surfaces
Sen's action in two dimensions governs a chiral boson coupled to a two-dimensional metric together with a second chiral boson that couples to a flat two-dimensional metric. This second scalar decouples from the physical degrees of freedom. The generalisation of this action to one in which the second chiral scalar couples to an arbitrary second metric is used to formulate the theory on an arbitrary two-dimensional manifold. We use this action with both metrics Riemannian (or complex) to formulat…

A comparative study of the high-pressure structural stability of zirconolite materials for nuclear waste immobilisation
Daniel Errandonea, Robin Turnbull, Josu Sanchez-Martin, Robert Oliva, Alfonso Munoz, Silvana Radescu, Andres Mujica, Lewis Blackburn, Neil C. Hyatt, Catalin Popescu, Jordi Ibanez-Insa
https://arxiv.org/abs/2508.03786

A comparative study of the high-pressure structural stability of zirconolite materials for nuclear waste immobilisation
We present a comparative study of the high-pressure behaviours of the nuclear waste immobilisation materials zirconolite-2M, -4M, -3O, and -3T. The materials are studied under high-pressure conditions using synchrotron powder X-ray diffraction. For zirconolite-2M we also performed density-functional theory calculations. A new triclinic crystal structure (space group P-1), instead of the previously assigned monoclinic structure (space group C2/c) is proposed for zirconolite-2M. We named the tric…

Symmetric versus antisymmetric strain tuning of the valence transition in Yb(In$_{1-x}$Ag$_x$)Cu$_4$
Caitlin I. O'Neil, Michelle Ocker, Kristin Kliemt, Cornelius Krellner, Elena Gati
https://arxiv.org/abs/2508.04212

Symmetric versus antisymmetric strain tuning of the valence transition in Yb(In$_{1-x}$Ag$_x$)Cu$_4$
Similar to transitions in a range of correlated quantum materials, the valence transition exhibits a strong coupling to the crystal lattice, rendering it highly sensitive to stress tuning. In the present work, we determine the effect of uniaxial stress, which breaks the lattice symmetry, on the valence transition temperature and its crossover temperature in pure and Ag-substituted YbInCu$_4$. Our key result is that hydrostatic stress is more effective in tuning this transition than uniaxial str…

CoCoLIT: ControlNet-Conditioned Latent Image Translation for MRI to Amyloid PET Synthesis
Alec Sargood, Lemuel Puglisi, James H. Cole, Neil P. Oxtoby, Daniele Rav\`i, Daniel C. Alexander
https://arxiv.org/abs/2508.01292

CoCoLIT: ControlNet-Conditioned Latent Image Translation for MRI to Amyloid PET Synthesis
Synthesizing amyloid PET scans from the more widely available and accessible structural MRI modality offers a promising, cost-effective approach for large-scale Alzheimer's Disease (AD) screening. This is motivated by evidence that, while MRI does not directly detect amyloid pathology, it may nonetheless encode information correlated with amyloid deposition that can be uncovered through advanced modeling. However, the high dimensionality and structural complexity of 3D neuroimaging data pose si…

Water Detection in the Interstellar Object 3I/ATLAS
Zexi Xing, Shawn Oset, John Noonan, Dennis Bodewits
https://arxiv.org/abs/2508.04675 https://arxiv.org/…

Water Detection in the Interstellar Object 3I/ATLAS
We report the first detection of water activity in the third confirmed interstellar object, 3I/ATLAS, based on ultraviolet imaging with the \emph{Neil Gehrels-Swift Observatory}. Observations acquired with the Ultraviolet/Optical Telescope on 2025 July 31st - Aug 1st revealed OH (A$^2Σ$ -- X$^2Π$) emission near 3085~Å. The water production rate results highly depend on the reddening assumption. For a reddening of 38.6\% between 5437.8~Å and 3325.7~Å, the water production rate is $(1.35 \pm…

Modelling Program Spaces in Program Synthesis with Constraints
Tilman Hinnerichs, Bart Swinkels, Jaap de Jong, Reuben Gardos Reid, Tudor Magirescu, Neil Yorke-Smith, Sebastijan Dumancic
https://arxiv.org/abs/2508.00005

Modelling Program Spaces in Program Synthesis with Constraints
A core challenge in program synthesis is taming the large space of possible programs. Since program synthesis is essentially a combinatorial search, the community has sought to leverage powerful combinatorial constraint solvers. Here, constraints are used to express the program semantics, but not as a potentially potent tool to remove unwanted programs. Recent inductive logic programming approaches introduce constraints on the program's syntax to be synthesized. These syntactic constraints allo…

Long-term resilience of online battle over vaccines and beyond
Lucia Illari, Nicholas J. Restrepo, Neil F. Johnson
https://arxiv.org/abs/2508.01398 https://

Long-term resilience of online battle over vaccines and beyond
What has been the impact of the enormous amounts of time, effort and money spent promoting pro-vaccine science from pre-COVID-19 to now? We answer this using a unique mapping of online competition between pro- and anti-vaccination views among ~100M Facebook Page members, tracking 1,356 interconnected communities through platform interventions. Remarkably, the network's fundamental architecture shows no change: the isolation of established expertise and the symbiosis of anti and mainstream neutr…

Replaced article(s) found for cs.LO. https://arxiv.org/list/cs.LO/new
[1/1]:
- On the Number of Quantifiers Needed to Define Boolean Functions
Marco Carmosino, Ronald Fagin, Neil Immerman, Phokion Kolaitis, Jonathan Lenchner, Rik Sengupta

A large, chemically enriched, neutral gas reservoir in a galaxy at z = 6.782
A. Saccardi, S. D. Vergani, L. Izzo, V. D'Elia, K. E. Heintz, A. De Cia, D. B. Malesani, J. T. Palmerio, P. Petitjean, S. Savaglio, N. R. Tanvir, R. Salvaterra, R. Brivio, S. Campana, L. Christensen, S. Covino, J. P. U. Fynbo, D. H. Hartmann, C. Konstantopoulou, A. J. Levan, A. Martin-Carrillo, A. Melandri, L. Piro, G. Pugliese, P. Schady, B. Schneider

A large, chemically enriched, neutral gas reservoir in a galaxy at z = 6.782
The chemical characterization of galaxies in the first billion years after the Big Bang is one of the central goals of current astrophysics. Optical/near-infrared spectroscopy of long gamma-ray bursts (GRBs) have been heralded as an effective diagnostic to probe the interstellar medium of their host galaxies and their metal and dust content, up to the highest redshift. An opportunity to fulfill this expectation was provided by the recent blast triggered by the Neil Gehrels Swift Observatory of …

Replaced article(s) found for math.RA. https://arxiv.org/list/math.RA/new
[1/1]:
- Additive subgroups of a module that are saturated with respect to a subset of the ring
Jesse Elliott, Neil Epstein

The CFT of Sen's Formulation of Chiral Gauge Fields
Chris Hull, Neil Lambert
https://arxiv.org/abs/2508.00199 https://arxiv.org/pdf/2508.00199

The CFT of Sen's Formulation of Chiral Gauge Fields
Sen's action for chiral bosons in 2 dimensions describes two chiral scalars, one of which couples to the physical metric and one of which couples to a flat metric. It has a generalisation in which the flat metric is replaced by an arbitrary second metric and so can be formulated on any curved world-sheet. When the two metrics are equal, the theory reduces to a $βγ$ system, giving a non-unitary $c=2$ conformal field theory. We argue that the relation between this and the theory of two chiral b…

Knot complements decomposing into prisms
Jason Deblois, Arshia Gharagozlou, Neil R Hoffman
https://arxiv.org/abs/2507.01263 https://a…

Knot complements decomposing into prisms
We describe four hyperbolic knot complements in $\mathbb{S}^3$, each of which covers a prism orbifold: the quotient of $\mathbb{H}^3$ by the action of a discrete group generated by reflections in the faces of a polyhedron that has the combinatorial type of a triangular prism. The prism orbifolds are rigid-cusped and contain compact, totally geodesic hyperbolic triangle sub-orbifolds; as a result, the knot complements covering them have hidden symmetries and contain closed, embedded, totally geo…

Measuring the splashback feature: Dependence on halo properties and history
Qiaorong S. Yu (Oxford Math, Oxford Physics), Stephanie O'Neil (UPenn, Princeton, MIT), Xuejian Shen (MIT), Mark Vogelsberger (MIT), Sownak Bose (Durham), Boryana Hadzhyska (Lawrence Berkeley Lab, UC Berkeley, Cambridge Astronomy, Kavli Institute Cambridge), Lars Hernquist (CfA Harvard), Rahul Kannan (York), Monica Wu (NYU Math), Ziang Wu (NYU Math, NYU Engineering)

Measuring the splashback feature: Dependence on halo properties and history
In this study, we define the novel splashback depth $\mathcal{D}$ and width $\mathcal{W}$ to examine how the splashback features of dark matter haloes are affected by the physical properties of haloes themselves. We use the largest simulation run in the hydrodynamic MillenniumTNG project. By stacking haloes in bins of halo mass, redshift, mass-dependent properties such as peak height and concentration, and halo formation history, we measure the shape of the logarithmic slope of the density prof…

Ten simple rules for PIs to integrate Research Software Engineering into their research group
Stuart M. Allen, Neil Chue Hong, Stephan Druskat, Toby Hodges, Daniel S. Katz, Jan Linxweiler, Frank L\"offler, Lars Grunske, Heidi Seibold, Jan Philipp Thiele, Samantha Wittke
https://arxiv.org/abs/2506.20217

Ten simple rules for PIs to integrate Research Software Engineering into their research group
Research Software Engineering (RSEng) is a key success factor in producing high-quality research software, which in turn enables and improves research outcomes. However, as a principal investigator or leader of a research group you may not know what RSEng is, where to get started with it, or how to use it to maximize its benefit for your research. RSEng also often comes with technical complexity, and therefore reduced accessibility to some researchers. The ten simple rules presented in this pap…

Reduced and mixed precision turbulent flow simulations using explicit finite difference schemes
B\'alint Sikl\'osi, Pushpender K. Sharma, David J. Lusher, Istv\'an Z. Reguly, Neil D. Sandham
https://arxiv.org/abs/2505.20911

Reduced and mixed precision turbulent flow simulations using explicit finite difference schemes
The use of reduced and mixed precision computing has gained increasing attention in high-performance computing (HPC) as a means to improve computational efficiency, particularly on modern hardware architectures like GPUs. In this work, we explore the application of mixed precision arithmetic in compressible turbulent flow simulations using explicit finite difference schemes. We extend the OPS and OpenSBLI frameworks to support customizable precision levels, enabling fine-grained control over pr…

Transient MeV radiation from a relativistic tidal disruption candidate
Gor Oganesyan, Elias Kammoun, Annarita Ierardi, Alessio Ludovico De Santis, Biswajit Banerjee, Emanuele Sobacchi, Felix Aharonian, Samanta Macera, Pawan Tiwari, Alessio Mei, Shraddha Mohnani, Stefano Ascenzi, Samuele Ronchini, Marica Branchesi
https://arxiv.org/abs/2507…

Transient MeV radiation from a relativistic tidal disruption candidate
On July 2, 2025, the Gamma-ray Burst Monitor (GBM) onboard the Fermi Gamma-ray space telescope detected three short-duration MeV transients with overlapping sky locations. These events, named as GRB 250702D, B, and E (collectively referred to as DBE), triggered the detector with delays of approximately 1-2 hours between each burst. Follow-up observations of this unusually long MeV transient (lasting >3 hours) by the Neil Gehrels Swift Observatory and the Nuclear Spectroscopic Telescope Array ov…

The spectrum of global representations for families of bounded rank and VI-modules
Miguel Barrero, Tobias Barthel, Luca Pol, Neil Strickland, Jordan Williamson
https://arxiv.org/abs/2506.21525

The spectrum of global representations for families of bounded rank and VI-modules
A global representation is a compatible collection of representations of the outer automorphism groups of the finite groups belonging to a family $\mathscr{U}$. These arise in classical representation theory, in the study of representation stability, as well as in global homotopy theory. In this paper we begin a systematic study of the derived category $\mathsf{D}(\mathscr{U};k)$ of global representations over fields $k$ of characteristic zero, from the point-of-view of tensor-triangular geomet…

Overcoming Data Scarcity in Scanning Tunnelling Microscopy Image Segmentation
Nikola L. Kolev, Max Trouton, Filippo Federici Canova, Geoff Thornton, David Z. Gao, Neil J. Curson, Taylor J. Z. Stock
https://arxiv.org/abs/2506.01678

Overcoming Data Scarcity in Scanning Tunnelling Microscopy Image Segmentation
Scanning tunnelling microscopy (STM) is a powerful technique for imaging surfaces with atomic resolution, providing insight into physical and chemical processes at the level of single atoms and molecules. A regular task of STM image analysis is the identification and labelling of features of interest against a uniform background. Performing this manually is a labour-intensive task, requiring significant human effort. To reduce this burden, we propose an automated approach to the segmentation of…

The LHCb Sprucing and Analysis Productions
Ahmed Abdelmotteleb, Alessandro Bertolin, Chris Burr, Ben Couturier, Ellinor Eckstein, Davide Fazzini, Nathan Grieser, Christophe Haen, Ryunosuke O'Neil, Eduardo Rodrigues, Nicole Skidmore, Mark Smith, Aidan R. Wiederhold, Shunan Zhang
https://arxiv.org/abs/2506.20309

The LHCb Sprucing and Analysis Productions
The LHCb detector underwent a comprehensive upgrade in preparation for the third data-taking run of the Large Hadron Collider (LHC), known as LHCb Upgrade I. The increased data rate of Run 3 not only posed data collection (Online) challenges but also significant Offline data processing and analysis ones. The offline processing and analysis model was consequently upgraded to handle the factor 30 increase in data volume and the associated demands of ever-growing analyst-level datasets, led by the…

Effect of Static vs. Conversational AI-Generated Messages on Colorectal Cancer Screening Intent: a Randomized Controlled Trial
Neil K. R. Sehgal, Manuel Tonneau, Andy Tan, Shivan J. Mehta, Alison Buttenheim, Lyle Ungar, Anish K. Agarwal, Sharath Chandra Guntuku
https://arxiv.org/abs/2507.08211

Effect of Static vs. Conversational AI-Generated Messages on Colorectal Cancer Screening Intent: a Randomized Controlled Trial
Large language model (LLM) chatbots show increasing promise in persuasive communication. Yet their real-world utility remains uncertain, particularly in clinical settings where sustained conversations are difficult to scale. In a pre-registered randomized controlled trial, we enrolled 915 U.S. adults (ages 45-75) who had never completed colorectal cancer (CRC) screening. Participants were randomized to: (1) no message control, (2) expert-written patient materials, (3) single AI-generated messag…

phylo2vec: a library for vector-based phylogenetic tree manipulation
Neil Scheidwasser, Ayush Nag, Matthew J Penn, Anthony MV Jakob, Frederik M{\o}lkj{\ae}r Andersen, Mark P Khurana, Landung Setiawan, Madeline Gordon, David A Duch\^ene, Samir Bhatt
https://arxiv.org/abs/2506.19490

phylo2vec: a library for vector-based phylogenetic tree manipulation
Phylogenetics is a fundamental component of many analysis frameworks in biology as well as linguistics to study the evolutionary relationships of different entities. Recently, the advent of large-scale genomics and the SARS-CoV-2 pandemic has underscored the necessity for phylogenetic software to handle large datasets of genomes or phylogenetic trees. While significant efforts have focused on scaling optimisation algorithms, visualization, and lineage identification, an emerging body of researc…

Filter Equivariant Functions: A symmetric account of length-general extrapolation on lists
Owen Lewis, Neil Ghani, Andrew Dudzik, Christos Perivolaropoulos, Razvan Pascanu, Petar Veli\v{c}kovi\'c
https://arxiv.org/abs/2507.08796

Filter Equivariant Functions: A symmetric account of length-general extrapolation on lists
What should a function that extrapolates beyond known input/output examples look like? This is a tricky question to answer in general, as any function matching the outputs on those examples can in principle be a correct extrapolant. We argue that a "good" extrapolant should follow certain kinds of rules, and here we study a particularly appealing criterion for rule-following in list functions: that the function should behave predictably even when certain elements are removed. In functional prog…

Prompt Variability Effects On LLM Code Generation
Andrei Paleyes, Radzim Sendyka, Diana Robinson, Christian Cabrera, Neil D. Lawrence
https://arxiv.org/abs/2506.10204

Prompt Variability Effects On LLM Code Generation
Code generation is one of the most active areas of application of Large Language Models (LLMs). While LLMs lower barriers to writing code and accelerate development process, the overall quality of generated programs depends on the quality of given prompts. Specifically, functionality and quality of generated code can be sensitive to user's background and familiarity with software development. It is therefore important to quantify LLM's sensitivity to variations in the input. To this end we prop…

Discovery and Localization of the Swift-Observed FRB 20241228A in a Star-forming Host Galaxy
Alice P. Curtin, Shion Andrew, Sunil Simha, Alice Cai, Kenzie Nimmo, Shami Chatterjee, Amanda M. Cook, Fengqiu Adam Dong, Yuxin Dong, Tarraneh Eftekhari, Wen-fai Fong, Emmanuel Fonseca, Jason W. T. Hessels, Ronniy C. Joseph, Victoria Kaspi, Calvin Leung, Robert Main, Kiyoshi W. Masui, Ryan Mckinven, Daniele Michilli, Mason Ng, Ayush Pandhi, Aaron B. Pearlman, Ziggy Pleunis, Mawson W. Sammons, K…

Discovery and Localization of the Swift-Observed FRB 20241228A in a Star-forming Host Galaxy
On 2024 December 28, CHIME/FRB detected the thus-far non-repeating FRB 20241228A with a real-time signal-to-noise ratio of $>50$. Approximately 112~s later, the X-ray Telescope onboard the Neil Gehrels Swift Observatory was on source, the fastest follow-up to-date of a non-repeating FRB (Tohuvavohu et al. in prep.). Using CHIME/FRB and two of the three CHIME/FRB Outriggers, we obtained a Very Long Baseline Interferometry localization for FRB 20241228A with a 1$σ$ confidence ellipse of 11$^{\pr…