Daily Papers

This work investigates the production of high-resolution images of typical support elements in concrete structures by means of the muon tomography (muography). By exploiting detailed Monte Carlo radiation-matter simulations, we demonstrate the feasibility of the reconstruction of 1 cm--thick iron tubes inside 30 cm--deep concrete blocks, regarded as an important testbed within the structural diagnostics community. In addition, we present a new method for integrating simulated data with advanced deep learning techniques in order to improve the muon imaging of concrete structures. Through deep learning enhancement techniques, this results into a dramatic improvement of the image quality, as well as into a significant reduction of the data acquisition time, which are two critical limitations within the usual practice of muography for civil engineering diagnostics.

We present a comprehensive theoretical and empirical study of the Muon optimizer for training transformers only with a small to medium decoder (30M - 200M parameters), with an emphasis on its mathematical foundations, convergence properties and synergistic interactions with modern architectural optimizations. Building on recent work showing Muon's scalability, we provide rigorous theoretical analysis including: (i)showing the convergence rate under standard assumptions, (ii) spectral regularization properties that prevent gradient explosion, (iii) connection to natural gradient descent on the Stiefel manifold, and (iv) equivalence to steepest gradient descent under the spectral norm. Crucially, we demonstrate that Muon expands the Pareto frontier in the compute-time trade-off by maintaining superior data efficiency at large batch sizes, a key finding of~essentialai2025muon that we validate across our model scales. Empirically, Muon reaches the target loss with 48-52\% of the training calculated by AdamW while maintaining or improving the final perplexity, consistent with larger-scale results. When combined with Multi-Head Latent Attention (MLA) and Mixture-of-Experts (MoE), we observe multiplicative efficiency gains: MLA+MoE+Muon achieves 68\% memory reduction and 3.2times inference speedup, while improving perplexity by 8-12\%. We provide detailed procedures on 15 architectural and optimizer components, stability analyzes across 100+ training runs, and practical implementation guidelines including Newton-Schulz coefficients (3.4445, -4.7750, 2.0315) optimized by~su2024muonblog. Our theoretical analysis and comprehensive experiments establish Muon as a principled, robust alternative to AdamW that particularly excels when combined with modern efficiency techniques and large-batch training regimes.

We demonstrate that Muon, the simplest instantiation of a second-order optimizer, explicitly expands the Pareto frontier over AdamW on the compute-time tradeoff. We find that Muon is more effective than AdamW in retaining data efficiency at large batch sizes, far beyond the so-called critical batch size, while remaining computationally efficient, thus enabling more economical training. We study the combination of Muon and the maximal update parameterization (muP) for efficient hyperparameter transfer and present a simple telescoping algorithm that accounts for all sources of error in muP while introducing only a modest overhead in resources. We validate our findings through extensive experiments with model sizes up to four billion parameters and ablations on the data distribution and architecture.

Recently, the Muon optimizer based on matrix orthogonalization has demonstrated strong results in training small-scale language models, but the scalability to larger models has not been proven. We identify two crucial techniques for scaling up Muon: (1) adding weight decay and (2) carefully adjusting the per-parameter update scale. These techniques allow Muon to work out-of-the-box on large-scale training without the need of hyper-parameter tuning. Scaling law experiments indicate that Muon achieves sim!2times computational efficiency compared to AdamW with compute optimal training. Based on these improvements, we introduce Moonlight, a 3B/16B-parameter Mixture-of-Expert (MoE) model trained with 5.7T tokens using Muon. Our model improves the current Pareto frontier, achieving better performance with much fewer training FLOPs compared to prior models. We open-source our distributed Muon implementation that is memory optimal and communication efficient. We also release the pretrained, instruction-tuned, and intermediate checkpoints to support future research.

In this work, we present a new approach for fast tracking on multiwire proportional chambers with neural networks. The tracking networks are developed and adapted for the first-level trigger at hadron collider experiments. We use Monte Carlo samples generated by Geant4 with a custom muon chamber, which resembles part of the thin gap chambers from the ATLAS experiment, for training and performance evaluations. The chamber has a total of seven gas gaps, where the first and last gas gaps are displaced by ~1.5 m. Each gas gap has 50 channels with a size of 18-20 mm. Two neural network models are developed and presented: a convolutional neural network and a neural network optimized for the detector configuration of this study. In the latter network, a convolution layer is provided for each of three groups formed from 2-3 gas gaps of the chamber, and the outputs are fed into multilayer perceptrons in sequence. Both networks are transformed into hardware description language and implemented in Virtex UltraScale+ FPGA. The angular resolution is 2 mrad, which is comparable to the maximum resolution of the detector estimated by the minimum chi2 method. The latency achieved by the implemented firmware is less than 100 ns, and the throughput rate is 160 MHz.

Mu3e is an experiment currently under construction at the Paul Scherrer Institute in Switzerland, designed to search for the Lepton Flavor Violating (LFV) decay mu^+ rightarrow e^+e^-e^+. In extensions of the Standard Model (SM) that account for neutrino masses, this decay is theoretically allowed but occurs only through extremely rare loop processes, with a predicted branching ratio of approximately O(10^{-54}). Such a small probability implies that any observation of this decay would provide clear evidence for physics beyond the SM. The Mu3e experiment aims to probe the mu^+ rightarrow e^+e^-e^+ decay with a sensitivity of approximately O(10^{-15}) in its Phase-1 and plans to achieve a sensitivity of O(10^{-16}) after future upgrades. To reach its Phase-1 ambitious goals, Mu3e is going to use the most intense continuous muon beam in the world, generating 10^{8} muon stops per second in the target placed at the center of the Mu3e. Mu3e will use three main technologies for particle detection. The tracking will done through ultra-thin (50 - 70 mu m) pixel detectors based on MuPix11 sensors. These are high-voltage monolithic active pixel sensors (HV-MAPS) with a sim 23~mum spatial resolution. The timing will be done through scintillating fibres (sim 250 ps) and tiles (sim 40 ps), coupled to silicon photomultipliers and read out by MuTRiG3 ASICs. A triggerless DAQ system based on FPGAs will collect data from the detectors, which will then undergo reconstruction in a GPU filter farm. The assembly of the detectors has started, with a detector commissioning beam time planned for 2025. This document reports on the status of the construction, installation, and data-taking plans for the near future.

We here propose a machine learning approach for monitoring particle detectors in real-time. The goal is to assess the compatibility of incoming experimental data with a reference dataset, characterising the data behaviour under normal circumstances, via a likelihood-ratio hypothesis test. The model is based on a modern implementation of kernel methods, nonparametric algorithms that can learn any continuous function given enough data. The resulting approach is efficient and agnostic to the type of anomaly that may be present in the data. Our study demonstrates the effectiveness of this strategy on multivariate data from drift tube chamber muon detectors.

The Muon optimizer, based on matrix orthogonalization, has recently shown faster convergence and up to 2x computational efficiency over AdamW in LLM pretraining. Like AdamW, Muon is stateful, requiring storage of both model weights and accumulated gradients. While 8-bit AdamW variants mitigate this overhead using blockwise quantization, they are typically stable only under dynamic quantization - which improves stability on linear quantization for extreme values. In this paper, we introduce the 8-bit Muon optimizer using blockwise quantization, supporting both linear and dynamic schemes. We demonstrate that 8-bit Muon maintains stability under both, while delivering sim74\% reduction in memory footprint compared to full-precision Muon. In extensive experiments, 8-bit Muon closely matches the performance of Muon while outperforming AdamW and 8-bit AdamW in pre-training a 1.6B model on 4B FineWeb tokens. It also shows competitive results when fine-tuning the Llama 3.2 3B model on post-training data. We also provide a theoretical perspective to help explain this robustness under quantization.

We present Monte Carlo (MC) simulation results from a study of a compact plastic-scintillator detector suitable for imaging fast neutrons in the 1 -- 10 MeV energy range: the miniTimeCube (mTC). Originally designed for antineutrino detection, the mTC consists of 24 MultiChannel Plate (MCP) photodetectors surrounding a 13 cm cube of boron-doped plastic scintillator. Our simulation results show that waveform digitization of 1536 optically sensitive channels surrounding the scintillator should allow for spatiotemporal determination of individual neutron-proton scatters in the detector volume to thicksim100 picoseconds and thicksim5 mm. A Bayesian estimation framework is presented for multiple-scatter reconstruction, and is used to estimate the incoming direction and energy of simulated individual neutrons. Finally, we show how populations of reconstructed neutrons can be used to estimate the direction and energy spectrum of nearby simulated neutron sources.

We present a comprehensive study of the Muonic Portal to Vector Dark Matter (MPVDM), a minimal yet phenomenologically rich extension of the Standard Model featuring a new SU(2)_D gauge symmetry and vector-like muons. In this framework the dark sector interacts with the Standard Model only through these heavy leptons, linking dark matter and the muon sector. The MPVDM can simultaneously explain the observed relic abundance and the muon anomalous magnetic moment a_mu under both the "tension" and "compatibility" scenarios motivated by recent (g-2)_mu results. A key finding is a generic off-resonance velocity suppression mechanism that allows light (<1 GeV) vector dark matter to evade CMB limits near 2*m_DM ~ m_H_D. Unlike scenarios based on ultra narrow Breit-Wigner resonances and early kinetic decoupling, the suppression follows from the temperature evolution of the annihilation cross section in a moderately detuned near resonant regime, where being 10-20 percent below resonance gives the required CMB era suppression without fine tuning. A five dimensional parameter scan shows that the tension scenario requires sub GeV dark matter with g_D ~ 1e-3 and TeV scale vector like muons, while the compatibility scenario admits a broad mass range up to multi TeV. Recasting ATLAS and CMS searches for mu+ mu- + E_T^miss sets a lower bound of about 850 GeV on vector like muons. The MPVDM thus offers a unified, predictive, and experimentally accessible framework linking dark matter and muon physics across cosmological and collider frontiers.

Matrix-based preconditioned optimizers, such as Muon, have recently been shown to be more efficient than scalar-based optimizers for training large-scale neural networks, including large language models (LLMs). On the other hand, recent benchmarks on optimizers for LLM pre-training have demonstrated that variance-reduction techniques such as MARS can achieve substantial speedups over standard optimizers that do not employ variance reduction. In this paper, to achieve the best of both worlds, we introduce MARS-M, a new optimizer that integrates the variance reduction technique in MARS with Muon. Under standard regularity conditions, we prove that Muon-M converges to a first-order stationary point at a rate of mathcal{O}(T^{-1/3}), which improves upon mathcal{O}(T^{-1/4}) rate attained by Muon. Our empirical results on language modeling and computer vision tasks demonstrate that MARS-M consistently yields lower losses and improved performance across various downstream benchmarks. The implementation of MARS-M is available at https://github.com/AGI-Arena/MARS/MARS_M.

Any observation of charged lepton flavor violation (CLFV) implies the existence of new physics beyond the SM in charged lepton sector. CLFV interactions may also contribute to the muon magnetic moment and explain the discrepancy between the SM prediction and the recent muon g-2 precision measurement at Fermilab. We consider the most general SM gauge invariant Lagrangian of Delta L=0 bileptons with CLFV couplings and investigate the interplay of low-energy precision experiments and colliders in light of the muon magnetic moment anomaly. We go beyond previous work by demonstrating the sensitivity of the LHC, the MACE experiment, a proposed muonium-antimuonium conversion experiment, and a muon collider. Currently-available LHC data is already able to probe unexplored parameter space via the CLFV process pptogamma^*/Z^*to ell_1^pm ell_1^pm ell_2^mp ell_2^mp.

We show evidence of particle acceleration at GEV energies associated directly with protons from the prompt emission of a long-duration M6-class solar flare on July 17, 2023, rather than from protons acceleration by shocks from its associated Coronal Mass Ejection (CME), which erupted with a speed of 1342 km/s. Solar Energetic Particles (SEP) accelerated by the blast have reached Earth, up to an almost S3 (strong) category of a radiation storm on the NOAA scale. Also, we show a temporal correlation between the fast rising of GOES-16 proton and muon excess at ground level in the count rate of the New-Tupi muon detector at the central SAA region. A Monte Carlo spectral analysis based on muon excess at New-Tupi is consistent with the acceleration of electrons and protons (ions) up to relativistic energies (GeV energy range) in the impulsive phase of the flare. In addition, we present another two marginal particle excesses (with low confidence) at ground-level detectors in correlation with the solar flare prompt emission.

Ultra-high-energy neutrinos and cosmic rays are excellent probes of astroparticle physics phenomena. For astroparticle physics analyses, robust and accurate reconstruction of signal parameters such as arrival direction and energy is essential. Radio detection is an established detector concept explored by many observatories; however, current reconstruction methods ignore bin-to-bin noise correlations, which limits reconstruction resolution and, so far, has prevented calculations of event-by-event uncertainties. In this work, we present a likelihood description of neutrino or cosmic-ray signals in radio detectors with correlated noise, as present in all neutrino and cosmic-ray radio detectors. We demonstrate, with simulation studies of both neutrinos and cosmic-ray radio signals, that signal parameters such as energy and direction, including event-by-event uncertainties with correct coverage, can be obtained. This method reduces reconstruction uncertainties and biases compared to previous approaches. Additionally, the Likelihood can be used for event selection and enables differentiable end-to-end detector optimization. The reconstruction code is available through the open-source software NuRadioReco.

We propose two medium-baseline, kiloton-scale neutrino experiments to study neutrinos from LHC proton-proton collisions: SINE, a surface-based scintillator panel detector observing muon neutrinos from the CMS interaction point, and UNDINE, a water Cherenkov detector submerged in lake Geneva observing all-flavor neutrinos from LHCb. Using a Monte Carlo simulation, we estimate millions of neutrino interactions during the high-luminosity LHC era. We show that these datasets can constrain neutrino cross sections, charm production in pp collisions, and strangeness enhancement as a solution to the cosmic-ray muon puzzle. SINE and UNDINE thus offer a cost-effective medium-baseline complement to the proposed short-baseline forward physics facility.

The choice of optimizer significantly impacts the training efficiency and computational costs of large language models (LLMs). Recently, the Muon optimizer has demonstrated promising results by orthogonalizing parameter updates, improving optimization geometry through better conditioning. Despite Muon's emergence as a candidate successor to Adam, the potential for jointly leveraging their strengths has not been systematically explored. In this work, we bridge this gap by proposing NorMuon (Neuron-wise Normalized Muon), an optimizer that synergistically combines orthogonalization with neuron-level adaptive learning rates. Our analysis reveals that while Muon effectively reduces condition numbers, the resulting updates exhibit highly non-uniform neuron norms, causing certain neurons to dominate the optimization process. NorMuon addresses this imbalance by maintaining second-order momentum statistics for each neuron and applying row-wise normalization after orthogonalization, ensuring balanced parameter utilization while preserving Muon's conditioning benefits. To enable practical deployment at scale, we develop an efficient distributed implementation under the FSDP2 framework that strategically distributes orthogonalization computations across devices. Experiments across multiple model scales demonstrate that NorMuon consistently outperforms both Adam and Muon, achieving 21.74% better training efficiency than Adam and 11.31% improvement over Muon on 1.1 B pretraining setting, while maintaining a comparable memory footprint to Muon. Our findings suggest that orthogonalization and adaptive learning rates are complementary rather than competing approaches, opening new avenues for optimizer design in large-scale deep learning.

The recently proposed Muon optimizer updates weight matrices via orthogonalized momentum and has demonstrated strong empirical success in large language model training. However, it remains unclear how to determine the learning rates for such orthogonalized updates. AdaGrad, by contrast, is a widely used adaptive method that scales stochastic gradients by accumulated past gradients. We propose a new algorithm, AdaGO, which combines a norm-based AdaGrad-type stepsize with an orthogonalized update direction, bringing together the benefits of both approaches. Unlike other adaptive variants of Muon, AdaGO preserves the orthogonality of the update direction, which can be interpreted as a spectral descent direction, while adapting the stepsizes to the optimization landscape by scaling the direction with accumulated past gradient norms. The implementation of AdaGO requires only minimal modification to Muon, with a single additional scalar variable, the accumulated squared gradient norms, to be computed, making it computationally and memory efficient. Optimal theoretical convergence rates are established for nonconvex functions in both stochastic and deterministic settings under standard smoothness and unbiased bounded-variance noise assumptions. Empirical results on CIFAR-10 classification and function regression demonstrate that AdaGO outperforms Muon and Adam.

Radio detection is now an established technique for the study of ultra-high-energy (UHE) cosmic rays with energies above sim10^{17} eV. The next-generation of radio experiments aims to extend this technique to the observation of UHE earth-skimming neutrinos, which requires the detection of very inclined extensive air showers (EAS). In this article we present a new reconstruction method for the arrival direction and the energy of EAS. It combines a point-source-like description of the radio wavefront with a phenomenological model: the Angular Distribution Function (ADF). The ADF describes the angular distribution of the radio signal amplitude in the 50-200 MHz frequency range, with a particular focus on the Cherenkov angle, a crucial feature of the radio amplitude pattern. The method is applicable to showers with zenith angles larger than 60^circ, and in principle up to neutrino-induced showers with up-going trajectories. It is tested here on a simulated data set of EAS induced by cosmic rays. A resolution better than 4 arc-minutes (0.07^circ) is achieved on arrival direction, as well as an intrinsic resolution of 5% on the electromagnetic energy, and around 15% on the primary energy.

Diffusion models have emerged as the new state-of-the-art generative model with high quality samples, with intriguing properties such as mode coverage and high flexibility. They have also been shown to be effective inverse problem solvers, acting as the prior of the distribution, while the information of the forward model can be granted at the sampling stage. Nonetheless, as the generative process remains in the same high dimensional (i.e. identical to data dimension) space, the models have not been extended to 3D inverse problems due to the extremely high memory and computational cost. In this paper, we combine the ideas from the conventional model-based iterative reconstruction with the modern diffusion models, which leads to a highly effective method for solving 3D medical image reconstruction tasks such as sparse-view tomography, limited angle tomography, compressed sensing MRI from pre-trained 2D diffusion models. In essence, we propose to augment the 2D diffusion prior with a model-based prior in the remaining direction at test time, such that one can achieve coherent reconstructions across all dimensions. Our method can be run in a single commodity GPU, and establishes the new state-of-the-art, showing that the proposed method can perform reconstructions of high fidelity and accuracy even in the most extreme cases (e.g. 2-view 3D tomography). We further reveal that the generalization capacity of the proposed method is surprisingly high, and can be used to reconstruct volumes that are entirely different from the training dataset.

Memory-efficient optimization is critical for training increasingly large language models (LLMs). A popular strategy involves gradient low-rank projection, storing only the projected optimizer states, with GaLore being a representative example. However, a significant drawback of many such methods is their lack of convergence guarantees, as various low-rank projection approaches introduce inherent biases relative to the original optimization algorithms, which contribute to performance gaps compared to full-parameter training. Aiming to tackle this problem, this paper investigates the layerwise sampling technique for debiasing low-rank projection mechanisms. In particular, an instantiation of the paradigm gives rise to a novel and unbiased low-rank optimization method built upon GaLore's mechanism and the Muon algorithm, named GaLore Unbiased with Muon (GUM). We theoretically prove our method matches the convergence guarantees of the base Muon algorithm while preserving the memory efficiency of low-rank techniques. Empirical experiments on LLM fine-tuning and pretraining also demonstrate non-trivial improvements over GaLore and even better performance than full-parameter training. Further investigation shows that the improvement of this technique comes from a more uniform distribution of knowledge inside layers, leading to more efficient utilization of the model parameter space and better memorization.

Results are presented from searches for the standard model Higgs boson in proton-proton collisions at sqrt(s) = 7 and 8 TeV in the Compact Muon Solenoid experiment at the LHC, using data samples corresponding to integrated luminosities of up to 5.1 inverse femtobarns at 7 TeV and 5.3 inverse femtobarns at 8 TeV. The search is performed in five decay modes: gamma gamma, ZZ, WW, tau tau, and b b-bar. An excess of events is observed above the expected background, with a local significance of 5.0 standard deviations, at a mass near 125 GeV, signalling the production of a new particle. The expected significance for a standard model Higgs boson of that mass is 5.8 standard deviations. The excess is most significant in the two decay modes with the best mass resolution, gamma gamma and ZZ; a fit to these signals gives a mass of 125.3 +/- 0.4 (stat.) +/- 0.5 (syst.) GeV. The decay to two photons indicates that the new particle is a boson with spin different from one.

Orthogonal gradient updates have emerged as a promising direction in optimization for machine learning. However, traditional approaches such as SVD/QR decomposition incur prohibitive computational costs of O(n^3) and underperform compared to well-tuned SGD with momentum, since momentum is applied only after strict orthogonalization. Recent advances, such as Muon, improve efficiency by applying momentum before orthogonalization and producing semi-orthogonal matrices via Newton-Schulz iterations, reducing complexity to O(n^2). Nevertheless, quadratic costs remain a bottleneck. In this work, we study the semi-orthogonal properties of momentum-based updates and develop a method to bound momentum updates under a spectral-norm trust region, preserving directional information without requiring explicit semi-orthogonalization. We propose AuON (Alternative Unit-norm momentum updates by Normalized nonlinear scaling), a linear-time optimizer that achieves strong performance without constructing semi-orthogonal matrices, while preserving structural alignment and reconditioning ill-posed updates. Our approach combines hyperbolic-cosine RMS scaling transformations with normalization, demonstrating both effectiveness and computational efficiency compared to Newton-Schulz methods. We further introduce a hybrid variant (Hybrid-AuON) that applies a single Newton-Schulz iteration. Experiments across vision and language benchmarks show that AuON and its hybrid variant achieve performance comparable to strong baselines such as AdamW and Muon. Code is available at: https://github.com/ryyzn9/AuON

This paper proposes a new two-step procedure for sparse-view tomographic image reconstruction. It is called RISING, since it combines an early-stopped Rapid Iterative Solver with a subsequent Iteration Network-based Gaining step. So far, regularized iterative methods have widely been used for X-ray computed tomography image reconstruction from low-sampled data, since they converge to a sparse solution in a suitable domain, as upheld by the Compressed Sensing theory. Unfortunately, their use is practically limited by their high computational cost which imposes to perform only a few iterations in the available time for clinical exams. Data-driven methods, using neural networks to post-process a coarse and noisy image obtained from geometrical algorithms, have been recently studied and appreciated for both their computational speed and accurate reconstructions. However, there is no evidence, neither theoretically nor numerically, that neural networks based algorithms solve the mathematical inverse problem modeling the tomographic reconstruction process. In our two-step approach, the first phase executes very few iterations of a regularized model-based algorithm whereas the second step completes the missing iterations by means of a neural network. The resulting hybrid deep-variational framework preserves the convergence properties of the iterative method and, at the same time, it exploits the computational speed and flexibility of a data-driven approach. Experiments performed on a simulated and a real data set confirm the numerical and visual accuracy of the reconstructed RISING images in short computational times.

Full quantum tomography of high-dimensional quantum systems is experimentally infeasible due to the exponential scaling of the number of required measurements on the number of qubits in the system. However, several ideas were proposed recently for predicting the limited number of features for these states, or estimating the expectation values of operators, without the need for full state reconstruction. These ideas go under the general name of shadow tomography. Here we provide an experimental demonstration of property estimation based on classical shadows proposed in [H.-Y. Huang, R. Kueng, J. Preskill. Nat. Phys. https://doi.org/10.1038/s41567-020-0932-7 (2020)] and study its performance in the quantum optical experiment with high-dimensional spatial states of photons. We show on experimental data how this procedure outperforms conventional state reconstruction in fidelity estimation from a limited number of measurements.

We study the electron-positron to muon--anti-muon cross-section in the asymptotically safe Standard Model. In particular, we include the graviton contributions to the scattering amplitude, which is computed from momentum-dependent time-like one-particle-irreducible correlation functions. Specifically, we employ reconstruction techniques for the graviton spectral functions. We find that the full asymptotically safe quantum cross section decreases in the ultraviolet with the centre-of-mass energy, and is compatible with unitarity bounds. Importantly, our findings provide non-trivial evidence for the unitarity of the asymptotically safe Standard Model.

When reading medical images such as a computed tomography (CT) scan, radiologists generally search across the image to find lesions, characterize and measure them, and then describe them in the radiological report. To automate this process, we propose a multitask universal lesion analysis network (MULAN) for joint detection, tagging, and segmentation of lesions in a variety of body parts, which greatly extends existing work of single-task lesion analysis on specific body parts. MULAN is based on an improved Mask R-CNN framework with three head branches and a 3D feature fusion strategy. It achieves the state-of-the-art accuracy in the detection and tagging tasks on the DeepLesion dataset, which contains 32K lesions in the whole body. We also analyze the relationship between the three tasks and show that tag predictions can improve detection accuracy via a score refinement layer.

We investigate a variational method for ill-posed problems, named graphLa+Psi, which embeds a graph Laplacian operator in the regularization term. The novelty of this method lies in constructing the graph Laplacian based on a preliminary approximation of the solution, which is obtained using any existing reconstruction method Psi from the literature. As a result, the regularization term is both dependent on and adaptive to the observed data and noise. We demonstrate that graphLa+Psi is a regularization method and rigorously establish both its convergence and stability properties. We present selected numerical experiments in 2D computerized tomography, wherein we integrate the graphLa+Psi method with various reconstruction techniques Psi, including Filter Back Projection (graphLa+FBP), standard Tikhonov (graphLa+Tik), Total Variation (graphLa+TV), and a trained deep neural network (graphLa+Net). The graphLa+Psi approach significantly enhances the quality of the approximated solutions for each method Psi. Notably, graphLa+Net is outperforming, offering a robust and stable application of deep neural networks in solving inverse problems.

We propose a WAveform Vector Exploitation (WAVE) deep neural network for full-waveform Time-Of-Flight (TOF) physics detectors, and evaluate its performance against traditional reconstruction techniques via Monte Carlo study of a small plastic-scintillator scatter camera. Ultralytics LLC (www.ultralytics.com) provides WAVE freely under the open source GPL-3.0 license at https://github.com/ultralytics/wave.

Shadow tomography for quantum states provides a sample efficient approach for predicting the properties of quantum systems when the properties are restricted to expectation values of 2-outcome POVMs. However, these shadow tomography procedures yield poor bounds if there are more than 2 outcomes per measurement. In this paper, we consider a general problem of learning properties from unknown quantum states: given an unknown d-dimensional quantum state rho and M unknown quantum measurements M_1,...,M_M with Kgeq 2 outcomes, estimating the probability distribution for applying M_i on rho to within total variation distance epsilon. Compared to the special case when K=2, we need to learn unknown distributions instead of values. We develop an online shadow tomography procedure that solves this problem with high success probability requiring O(Klog^2Mlog d/epsilon^4) copies of rho. We further prove an information-theoretic lower bound that at least Omega(min{d^2,K+log M}/epsilon^2) copies of rho are required to solve this problem with high success probability. Our shadow tomography procedure requires sample complexity with only logarithmic dependence on M and d and is sample-optimal for the dependence on K.

This paper presents a proof-of-concept approach for learned synergistic reconstruction of medical images using multi-branch generative models. Leveraging variational autoencoders (VAEs) and generative adversarial networks (GANs), our models learn from pairs of images simultaneously, enabling effective denoising and reconstruction. Synergistic image reconstruction is achieved by incorporating the trained models in a regularizer that evaluates the distance between the images and the model, in a similar fashion to multichannel dictionary learning (DiL). We demonstrate the efficacy of our approach on both Modified National Institute of Standards and Technology (MNIST) and positron emission tomography (PET)/computed tomography (CT) datasets, showcasing improved image quality and information sharing between modalities. Despite challenges such as patch decomposition and model limitations, our results underscore the potential of generative models for enhancing medical imaging reconstruction.

Deep learning has become the state-of-the-art approach to medical tomographic imaging. A common approach is to feed the result of a simple inversion, for example the backprojection, to a multiscale convolutional neural network (CNN) which computes the final reconstruction. Despite good results on in-distribution test data, this often results in overfitting certain large-scale structures and poor generalization on out-of-distribution (OOD) samples. Moreover, the memory and computational complexity of multiscale CNNs scale unfavorably with image resolution, making them impractical for application at realistic clinical resolutions. In this paper, we introduce Glimpse, a local coordinate-based neural network for computed tomography which reconstructs a pixel value by processing only the measurements associated with the neighborhood of the pixel. Glimpse significantly outperforms successful CNNs on OOD samples, while achieving comparable or better performance on in-distribution test data and maintaining a memory footprint almost independent of image resolution; 5GB memory suffices to train on 1024x1024 images which is orders of magnitude less than CNNs. Glimpse is fully differentiable and can be used plug-and-play in arbitrary deep learning architectures, enabling feats such as correcting miscalibrated projection orientations. Our implementation and Google Colab demo can be accessed at https://github.com/swing-research/Glimpse.

In the diverse field of medical imaging, automatic segmentation has numerous applications and must handle a wide variety of input domains, such as different types of Computed Tomography (CT) scans and Magnetic Resonance (MR) images. This heterogeneity challenges automatic segmentation algorithms to maintain consistent performance across different modalities due to the requirement for spatially aligned and paired images. Typically, segmentation models are trained using a single modality, which limits their ability to generalize to other types of input data without employing transfer learning techniques. Additionally, leveraging complementary information from different modalities to enhance segmentation precision often necessitates substantial modifications to popular encoder-decoder designs, such as introducing multiple branched encoding or decoding paths for each modality. In this work, we propose a simple Multi-Modal Segmentation (MulModSeg) strategy to enhance medical image segmentation across multiple modalities, specifically CT and MR. It incorporates two key designs: a modality-conditioned text embedding framework via a frozen text encoder that adds modality awareness to existing segmentation frameworks without significant structural modifications or computational overhead, and an alternating training procedure that facilitates the integration of essential features from unpaired CT and MR inputs. Through extensive experiments with both Fully Convolutional Network and Transformer-based backbones, MulModSeg consistently outperforms previous methods in segmenting abdominal multi-organ and cardiac substructures for both CT and MR modalities. The code is available in this {https://github.com/ChengyinLee/MulModSeg_2024{link}}.

Computed tomography and magnetic resonance imaging are two widely used clinical imaging modalities for non-invasive diagnosis. However, both of these modalities come with certain problems. CT uses harmful ionising radiation, and MRI suffers from slow acquisition speed. Both problems can be tackled by undersampling, such as sparse sampling. However, such undersampled data leads to lower resolution and introduces artefacts. Several techniques, including deep learning based methods, have been proposed to reconstruct such data. However, the undersampled reconstruction problem for these two modalities was always considered as two different problems and tackled separately by different research works. This paper proposes a unified solution for both sparse CT and undersampled radial MRI reconstruction, achieved by applying Fourier transform-based pre-processing on the radial MRI and then finally reconstructing both modalities using sinogram upsampling combined with filtered back-projection. The Primal-Dual network is a deep learning based method for reconstructing sparsely-sampled CT data. This paper introduces Primal-Dual UNet, which improves the Primal-Dual network in terms of accuracy and reconstruction speed. The proposed method resulted in an average SSIM of 0.932\textpm0.021 while performing sparse CT reconstruction for fan-beam geometry with a sparsity level of 16, achieving a statistically significant improvement over the previous model, which resulted in 0.919\textpm0.016. Furthermore, the proposed model resulted in 0.903\textpm0.019 and 0.957\textpm0.023 average SSIM while reconstructing undersampled brain and abdominal MRI data with an acceleration factor of 16, respectively - statistically significant improvements over the original model, which resulted in 0.867\textpm0.025 and 0.949\textpm0.025.

The training of diffusion models is often absent in the evaluation of new optimization techniques. In this work, we benchmark recent optimization algorithms for training a diffusion model for denoising flow trajectories. We observe that Muon and SOAP are highly efficient alternatives to AdamW (18% lower final loss). We also revisit several recent phenomena related to the training of models for text or image applications in the context of diffusion model training. This includes the impact of the learning-rate schedule on the training dynamics, and the performance gap between Adam and SGD.

This paper focuses on the development of a space-variant regularization model for solving an under-determined linear inverse problem. The case study is a medical image reconstruction from few-view tomographic noisy data. The primary objective of the proposed optimization model is to achieve a good balance between denoising and the preservation of fine details and edges, overcoming the performance of the popular and largely used Total Variation (TV) regularization through the application of appropriate pixel-dependent weights. The proposed strategy leverages the role of gradient approximations for the computation of the space-variant TV weights. For this reason, a convolutional neural network is designed, to approximate both the ground truth image and its gradient using an elastic loss function in its training. Additionally, the paper provides a theoretical analysis of the proposed model, showing the uniqueness of its solution, and illustrates a Chambolle-Pock algorithm tailored to address the specific problem at hand. This comprehensive framework integrates innovative regularization techniques with advanced neural network capabilities, demonstrating promising results in achieving high-quality reconstructions from low-sampled tomographic data.

Non-ideal measurement computed tomography (NICT), which sacrifices optimal imaging standards for new advantages in CT imaging, is expanding the clinical application scope of CT images. However, with the reduction of imaging standards, the image quality has also been reduced, extremely limiting the clinical acceptability. Although numerous studies have demonstrated the feasibility of deep learning for the NICT enhancement in specific scenarios, their high data cost and limited generalizability have become large obstacles. The recent research on the foundation model has brought new opportunities for building a universal NICT enhancement model - bridging the image quality degradation with minimal data cost. However, owing to the challenges in the collection of large pre-training datasets and the compatibility of data variation, no success has been reported. In this paper, we propose a multi-scale integrated Transformer AMPlifier (TAMP), the first imaging foundation model for universal NICT enhancement. It has been pre-trained on a large-scale physical-driven simulation dataset with 3.6 million NICT-ICT image pairs, and is able to directly generalize to the NICT enhancement tasks with various non-ideal settings and body regions. Via the adaptation with few data, it can further achieve professional performance in real-world specific scenarios. Our extensive experiments have demonstrated that the proposed TAMP has significant potential for promoting the exploration and application of NICT and serving a wider range of medical scenarios.

We introduce Kimi K2, a Mixture-of-Experts (MoE) large language model with 32 billion activated parameters and 1 trillion total parameters. We propose the MuonClip optimizer, which improves upon Muon with a novel QK-clip technique to address training instability while enjoying the advanced token efficiency of Muon. Based on MuonClip, K2 was pre-trained on 15.5 trillion tokens with zero loss spike. During post-training, K2 undergoes a multi-stage post-training process, highlighted by a large-scale agentic data synthesis pipeline and a joint reinforcement learning (RL) stage, where the model improves its capabilities through interactions with real and synthetic environments. Kimi K2 achieves state-of-the-art performance among open-source non-thinking models, with strengths in agentic capabilities. Notably, K2 obtains 66.1 on Tau2-Bench, 76.5 on ACEBench (En), 65.8 on SWE-Bench Verified, and 47.3 on SWE-Bench Multilingual -- surpassing most open and closed-sourced baselines in non-thinking settings. It also exhibits strong capabilities in coding, mathematics, and reasoning tasks, with a score of 53.7 on LiveCodeBench v6, 49.5 on AIME 2025, 75.1 on GPQA-Diamond, and 27.1 on OJBench, all without extended thinking. These results position Kimi K2 as one of the most capable open-source large language models to date, particularly in software engineering and agentic tasks. We release our base and post-trained model checkpoints to facilitate future research and applications of agentic intelligence.

Ultrasound computed tomography (USCT) is a radiation-free, high-resolution modality but remains limited for musculoskeletal imaging due to conventional ray-based reconstructions that neglect strong scattering. We propose a generative neural physics framework that couples generative networks with physics-informed neural simulation for fast, high-fidelity 3D USCT. By learning a compact surrogate of ultrasonic wave propagation from only dozens of cross-modality images, our method merges the accuracy of wave modeling with the efficiency and stability of deep learning. This enables accurate quantitative imaging of in vivo musculoskeletal tissues, producing spatial maps of acoustic properties beyond reflection-mode images. On synthetic and in vivo data (breast, arm, leg), we reconstruct 3D maps of tissue parameters in under ten minutes, with sensitivity to biomechanical properties in muscle and bone and resolution comparable to MRI. By overcoming computational bottlenecks in strongly scattering regimes, this approach advances USCT toward routine clinical assessment of musculoskeletal disease.

This study presents the development of a spatially adaptive weighting strategy for Total Variation regularization, aimed at addressing under-determined linear inverse problems. The method leverages the rapid computation of an accurate approximation of the true image (or its gradient magnitude) through a neural network. Our approach operates without requiring prior knowledge of the noise intensity in the data and avoids the iterative recomputation of weights. Additionally, the paper includes a theoretical analysis of the proposed method, establishing its validity as a regularization approach. This framework integrates advanced neural network capabilities within a regularization context, thereby making the results of the networks interpretable. The results are promising as they enable high-quality reconstructions from limited-view tomographic measurements.

We explore the use of topological data analysis (TDA) combined with machine learning for discriminating standard model backgrounds from the invisible decay of the Z^prime boson associated with monophoton emission at a 3 TeV muon collider. Reconstructed events are mapped into a six-dimensional kinematic space and aggregated into bags of events, from which persistent homology is used to extract Betti number distributions. Within the Multiple Instance Learning paradigm, classifiers trained on these topological descriptors demonstrate significantly improved classification accuracy compared to the conventional ML approaches based on event-wise kinematic inputs. We also draw exclusion contours at 95\% CL in the (m_{Z^prime}, m_chi) parameter space, highlighting the potential of topological features to extend the discovery reach of future collider experiments.

In this work we demonstrate that significant gains in performance and data efficiency can be achieved in High Energy Physics (HEP) by moving beyond the standard paradigm of sequential optimization or reconstruction and analysis components. We conceptually connect HEP reconstruction and analysis to modern machine learning workflows such as pretraining, finetuning, domain adaptation and high-dimensional embedding spaces and quantify the gains in the example usecase of searches of heavy resonances decaying via an intermediate di-Higgs system to four b-jets.

An ultra high energy electromagnetic cascade, a purely leptonic process and initiated by either photons or e^pm, can be a source of high energy neutrinos. We present a public python3 code, MUNHECA, to compute the neutrino spectrum by taking into account various QED processes, with the cascade developing either along the propagation in the cosmic microwave background in the high-redshift universe or in a predefined photon background surrounding the astrophysical source. The user can adjust various settings of MUNHECA, including the spectrum of injected high energy photons, the background photon field and the QED processes governing the cascade evolution. We improve the modeling of several processes, provide examples of the execution of MUNHECA and compare it with some earlier and more simplified estimates of the neutrino spectrum from electromagnetic cascades.

Optimization with matrix gradient orthogonalization has recently demonstrated impressive results in the training of deep neural networks (Jordan et al., 2024; Liu et al., 2025). In this paper, we provide a theoretical analysis of this approach. In particular, we show that the orthogonalized gradient method can be seen as a first-order trust-region optimization method, where the trust-region is defined in terms of the matrix spectral norm. Motivated by this observation, we develop the stochastic non-Euclidean trust-region gradient method with momentum, which recovers the Muon optimizer (Jordan et al., 2024) as a special case, along with normalized SGD and signSGD with momentum (Cutkosky and Mehta, 2020; Sun et al., 2023). In addition, we prove state-of-the-art convergence results for the proposed algorithm in a range of scenarios, which involve arbitrary non-Euclidean norms, constrained and composite problems, and non-convex, star-convex, first- and second-order smooth functions. Finally, our theoretical findings provide an explanation for several practical observations, including the practical superiority of Muon compared to the Orthogonal-SGDM algorithm of Tuddenham et al. (2022) and the importance of weight decay in the training of large-scale language models.

Radiography imaging protocols focus on particular body regions, therefore producing images of great similarity and yielding recurrent anatomical structures across patients. To exploit this structured information, we propose the use of Space-aware Memory Queues for In-painting and Detecting anomalies from radiography images (abbreviated as SQUID). We show that SQUID can taxonomize the ingrained anatomical structures into recurrent patterns; and in the inference, it can identify anomalies (unseen/modified patterns) in the image. SQUID surpasses 13 state-of-the-art methods in unsupervised anomaly detection by at least 5 points on two chest X-ray benchmark datasets measured by the Area Under the Curve (AUC). Additionally, we have created a new dataset (DigitAnatomy), which synthesizes the spatial correlation and consistent shape in chest anatomy. We hope DigitAnatomy can prompt the development, evaluation, and interpretability of anomaly detection methods.

This study developed a novel method for detecting hypernuclear events recorded in nuclear emulsion sheets using machine learning techniques. The artificial neural network-based object detection model was trained on surrogate images created through Monte Carlo simulations and image-style transformations using generative adversarial networks. The performance of the proposed model was evaluated using alpha-decay events obtained from the J-PARC E07 emulsion data. The model achieved approximately twice the detection efficiency of conventional image processing and reduced the time spent on manual visual inspection by approximately 1/17. The established method was successfully applied to the detection of hypernuclear events. This approach is a state-of-the-art tool for discovering rare events recorded in nuclear emulsion sheets without any real data for training.

Conventional Computed Tomography (CT) methods require large numbers of noise-free projections for accurate density reconstructions, limiting their applicability to the more complex class of Cone Beam Geometry CT (CBCT) reconstruction. Recently, deep learning methods have been proposed to overcome these limitations, with methods based on neural fields (NF) showing strong performance, by approximating the reconstructed density through a continuous-in-space coordinate based neural network. Our focus is on improving such methods, however, unlike previous work, which requires training an NF from scratch for each new set of projections, we instead propose to leverage anatomical consistencies over different scans by training a single conditional NF on a dataset of projections. We propose a novel conditioning method where local modulations are modeled per patient as a field over the input domain through a Neural Modulation Field (NMF). The resulting Conditional Cone Beam Neural Tomography (CondCBNT) shows improved performance for both high and low numbers of available projections on noise-free and noisy data.

Cell tracking is a subject of active research gathering great interest in medicine and biology. Positron emission tomography (PET) is well suited for tracking radio-labeled cells in vivo due to its exceptional sensitivity and whole-body capability. For validation, ground-truth data are desirable that realistically mimic the flow of cells in a clinical situation. This study develops a workflow (CeFloPS) for simulating moving radio-labeled cells in a human phantom. From the XCAT phantom, the blood vessels are reduced to nodal networks along which cells can move and distribute to organs and tissues. The movement is directed by the blood flow, which is calculated in each node using the Hagen-Pooiseuille equation and Kirchhoff's laws assuming laminar flow. Organs are voxelized and movement of cells from artery entry to vein exit is generated via a biased 3D random walk. The probabilities of cells moving or remaining in tissues are derived from rate constants of tracer kinetic-based compartment modeling. PET listmode data is generated using the Monte-Carlo simulation framework GATE based on the definition of a large-body PET scanner with cell paths as moving radioactive sources and the XCAT phantom providing attenuation data. From the flow simulation of 100,000 cells, 100 sample cells were further processed by GATE and listmode data was reconstructed into images for comparison. As demonstrated by comparisons of simulated and reconstructed cell distributions, CeFloPS is capable of simulating cell behavior in whole-body PET. It achieves this simulation in a way that is anatomically and physiologically reasonable, thereby providing valuable data for the development and validation of cell tracking algorithms.

Cerebrovascular disease often requires multiple imaging modalities for accurate diagnosis, treatment, and monitoring. Computed Tomography Angiography (CTA) and Time-of-Flight Magnetic Resonance Angiography (TOF-MRA) are two common non-invasive angiography techniques, each with distinct strengths in accessibility, safety, and diagnostic accuracy. While CTA is more widely used in acute stroke due to its faster acquisition times and higher diagnostic accuracy, TOF-MRA is preferred for its safety, as it avoids radiation exposure and contrast agent-related health risks. Despite the predominant role of CTA in clinical workflows, there is a scarcity of open-source CTA data, limiting the research and development of AI models for tasks such as large vessel occlusion detection and aneurysm segmentation. This study explores diffusion-based image-to-image translation models to generate synthetic CTA images from TOF-MRA input. We demonstrate the modality conversion from TOF-MRA to CTA and show that diffusion models outperform a traditional U-Net-based approach. Our work compares different state-of-the-art diffusion architectures and samplers, offering recommendations for optimal model performance in this cross-modality translation task.

Reconstructing medical images from partial measurements is an important inverse problem in Computed Tomography (CT) and Magnetic Resonance Imaging (MRI). Existing solutions based on machine learning typically train a model to directly map measurements to medical images, leveraging a training dataset of paired images and measurements. These measurements are typically synthesized from images using a fixed physical model of the measurement process, which hinders the generalization capability of models to unknown measurement processes. To address this issue, we propose a fully unsupervised technique for inverse problem solving, leveraging the recently introduced score-based generative models. Specifically, we first train a score-based generative model on medical images to capture their prior distribution. Given measurements and a physical model of the measurement process at test time, we introduce a sampling method to reconstruct an image consistent with both the prior and the observed measurements. Our method does not assume a fixed measurement process during training, and can thus be flexibly adapted to different measurement processes at test time. Empirically, we observe comparable or better performance to supervised learning techniques in several medical imaging tasks in CT and MRI, while demonstrating significantly better generalization to unknown measurement processes.

Brain MRI scans are often found in four modalities, consisting of T1-weighted with and without contrast enhancement (T1ce and T1w), T2-weighted imaging (T2w), and Flair. Leveraging complementary information from these different modalities enables models to learn richer, more discriminative features for understanding brain anatomy, which could be used in downstream tasks such as anomaly detection. However, in clinical practice, not all MRI modalities are always available due to various reasons. This makes missing modality generation a critical challenge in medical image analysis. In this paper, we propose SLaM-DiMM, a novel missing modality generation framework that harnesses the power of diffusion models to synthesize any of the four target MRI modalities from other available modalities. Our approach not only generates high-fidelity images but also ensures structural coherence across the depth of the volume through a dedicated coherence enhancement mechanism. Qualitative and quantitative evaluations on the BraTS-Lighthouse-2025 Challenge dataset demonstrate the effectiveness of the proposed approach in synthesizing anatomically plausible and structurally consistent results. Code is available at https://github.com/BheeshmSharma/SLaM-DiMM-MICCAI-BraTS-Challenge-2025.

Positron emission tomography (PET) is a cornerstone of modern oncologic and neurologic imaging, distinguished by its unique ability to illuminate dynamic metabolic processes that transcend the anatomical focus of traditional imaging technologies. Radiology reports are essential for clinical decision making, yet their manual creation is labor-intensive and time-consuming. Recent advancements of vision-language models (VLMs) have shown strong potential in medical applications, presenting a promising avenue for automating report generation. However, existing applications of VLMs in the medical domain have predominantly focused on structural imaging modalities, while the unique characteristics of molecular PET imaging have largely been overlooked. To bridge the gap, we introduce PET2Rep, a large-scale comprehensive benchmark for evaluation of general and medical VLMs for radiology report generation for PET images. PET2Rep stands out as the first dedicated dataset for PET report generation with metabolic information, uniquely capturing whole-body image-report pairs that cover dozens of organs to fill the critical gap in existing benchmarks and mirror real-world clinical comprehensiveness. In addition to widely recognized natural language generation metrics, we introduce a series of clinical efficiency metrics to evaluate the quality of radiotracer uptake pattern description in key organs in generated reports. We conduct a head-to-head comparison of 30 cutting-edge general-purpose and medical-specialized VLMs. The results show that the current state-of-the-art VLMs perform poorly on PET report generation task, falling considerably short of fulfilling practical needs. Moreover, we identify several key insufficiency that need to be addressed to advance the development in medical applications.

AI is revolutionizing MRI along the acquisition and processing chain. Advanced AI frameworks have been developed to apply AI in various successive tasks, such as image reconstruction, quantitative parameter map estimation, and image segmentation. Existing frameworks are often designed to perform tasks independently or are focused on specific models or datasets, limiting generalization. We introduce ATOMMIC, an open-source toolbox that streamlines AI applications for accelerated MRI reconstruction and analysis. ATOMMIC implements several tasks using DL networks and enables MultiTask Learning (MTL) to perform related tasks integrated, targeting generalization in the MRI domain. We first review the current state of AI frameworks for MRI through a comprehensive literature search and by parsing 12,479 GitHub repositories. We benchmark 25 DL models on eight publicly available datasets to present distinct applications of ATOMMIC on accelerated MRI reconstruction, image segmentation, quantitative parameter map estimation, and joint accelerated MRI reconstruction and image segmentation utilizing MTL. Our findings demonstrate that ATOMMIC is the only MTL framework with harmonized complex-valued and real-valued data support. Evaluations on single tasks show that physics-based models, which enforce data consistency by leveraging the physical properties of MRI, outperform other models in reconstructing highly accelerated acquisitions. Physics-based models that produce high reconstruction quality can accurately estimate quantitative parameter maps. When high-performing reconstruction models are combined with robust segmentation networks utilizing MTL, performance is improved in both tasks. ATOMMIC facilitates MRI reconstruction and analysis by standardizing workflows, enhancing data interoperability, integrating unique features like MTL, and effectively benchmarking DL models.

Medical image arbitrary-scale super-resolution (MIASSR) has recently gained widespread attention, aiming to super sample medical volumes at arbitrary scales via a single model. However, existing MIASSR methods face two major limitations: (i) reliance on high-resolution (HR) volumes and (ii) limited generalization ability, which restricts their application in various scenarios. To overcome these limitations, we propose Cube-based Neural Radiance Field (CuNeRF), a zero-shot MIASSR framework that can yield medical images at arbitrary scales and viewpoints in a continuous domain. Unlike existing MIASSR methods that fit the mapping between low-resolution (LR) and HR volumes, CuNeRF focuses on building a coordinate-intensity continuous representation from LR volumes without the need for HR references. This is achieved by the proposed differentiable modules: including cube-based sampling, isotropic volume rendering, and cube-based hierarchical rendering. Through extensive experiments on magnetic resource imaging (MRI) and computed tomography (CT) modalities, we demonstrate that CuNeRF outperforms state-of-the-art MIASSR methods. CuNeRF yields better visual verisimilitude and reduces aliasing artifacts at various upsampling factors. Moreover, our CuNeRF does not need any LR-HR training pairs, which is more flexible and easier to be used than others. Our code will be publicly available soon.

Head and neck (H&N) cancers are among the most prevalent types of cancer worldwide, and [18F]F-FDG PET/CT is widely used for H&N cancer management. Recently, the diffusion model has demonstrated remarkable performance in various image-generation tasks. In this work, we proposed a 3D diffusion model to accurately perform H&N tumor segmentation from 3D PET and CT volumes. The 3D diffusion model was developed considering the 3D nature of PET and CT images acquired. During the reverse process, the model utilized a 3D UNet structure and took the concatenation of PET, CT, and Gaussian noise volumes as the network input to generate the tumor mask. Experiments based on the HECKTOR challenge dataset were conducted to evaluate the effectiveness of the proposed diffusion model. Several state-of-the-art techniques based on U-Net and Transformer structures were adopted as the reference methods. Benefits of employing both PET and CT as the network input as well as further extending the diffusion model from 2D to 3D were investigated based on various quantitative metrics and the uncertainty maps generated. Results showed that the proposed 3D diffusion model could generate more accurate segmentation results compared with other methods. Compared to the diffusion model in 2D format, the proposed 3D model yielded superior results. Our experiments also highlighted the advantage of utilizing dual-modality PET and CT data over only single-modality data for H&N tumor segmentation.

Optimizers are crucial for the efficient training of Large Language Models (LLMs). While AdamW is the de facto standard, recent structure-aware optimizers like Muon have emerged, which regularize gradient updates by operating on entire weight matrices. The Muon optimizer balances the gradient updates along all the directions. However, Muon's reliance on the matrix sign function can lead to training instability, exhibits incompatibility when fine-tuning models pre-trained with AdamW. To address these limitations, we propose REG, a novel optimizer that replaces Muon's aggressive matrix sign operator with the Row-and-Column-Scaling (RACS) operator. Theoretically grounded in balancing a matrix, the RACS operator regularizes the update steps in a less drastic manner, making it simpler to implement and more compatible with established training dynamics. Through extensive empirical experiments on LLM training, we demonstrate that our REG optimizer not only achieves superior performance and stability over AdamW, but also maintains consistency with the AdamW training paradigm. This consistency is particularly evident during the fine-tuning stage, where REG optimizer avoids the performance degradation observed with Muon.

This article presents a review about the main CERN n\_TOF contributions to the field of neutron-capture experiments of interest for s-process nucleosynthesis studies over the last 25 years, with special focus on the measurement of radioactive isotopes. A few recent capture experiments on stable isotopes of astrophysical interest are also discussed. Results on s-process branching nuclei are appropriate to illustrate how advances in detection systems and upgrades in the facility have enabled increasingly challenging experiments and, as a consequence, have led to a better understanding and modeling of the s-process mechanism of nucleosynthesis. New endeavors combining radioactive-ion beams from ISOLDE for the production of radioisotopically pure samples for activation experiments at the new NEAR facility at n\_TOF are briefly discussed. On the basis of these new exciting results, also current limitations of state-of-the-art TOF and activation techniques will be depicted, thereby showing the pressing need for further upgrades and enhancements on both facilities and detection systems. A brief account of the potential technique based on inverse kinematics for direct neutron-capture measurements is also presented.

A range of recent optimizers have emerged that approximate the same "matrix-whitening" transformation in various ways. In this work, we systematically deconstruct such optimizers, aiming to disentangle the key components that explain performance. Across tuned hyperparameters across the board, all flavors of matrix-whitening methods reliably outperform elementwise counterparts, such as Adam. Matrix-whitening is often related to spectral descent -- however, experiments reveal that performance gains are *not explained solely by accurate spectral normalization* -- particularly, SOAP displays the largest per-step gain, even though Muon more accurately descends along the steepest spectral descent direction. Instead, we argue that matrix-whitening serves two purposes, and the variance adaptation component of matrix-whitening is the overlooked ingredient explaining this performance gap. Experiments show that variance-adapted versions of optimizers consistently outperform their sign-descent counterparts, including an adaptive version of Muon. We further ablate variance adaptation strategies, finding that while lookahead style approximations are not as effective, low-rank variance estimators can effectively reduce memory costs without a performance loss.

The Muon optimizer is consistently faster than Adam in training Large Language Models (LLMs), yet the mechanism underlying its success remains unclear. This paper demystifies this mechanism through the lens of associative memory. By ablating the transformer components optimized by Muon, we reveal that the associative memory parameters of LLMs, namely the Value and Output (VO) attention weights and Feed-Forward Networks (FFNs), are the primary contributors to Muon's superiority. Motivated by this associative memory view, we then explain Muon's superiority on real-world corpora, which are intrinsically heavy-tailed: a few classes (tail classes) appear far less frequently than others. The superiority is explained through two key properties: (i) its update rule consistently yields a more isotropic singular spectrum than Adam; and as a result, (ii) on heavy-tailed data, it optimizes tail classes more effectively than Adam. Beyond empirical evidence, we theoretically confirm these findings by analyzing a one-layer associative memory model under class-imbalanced data. We prove that Muon consistently achieves balanced learning across classes regardless of feature embeddings, whereas Adam can induce large disparities in learning errors depending on embedding properties. In summary, our empirical observations and theoretical analyses reveal Muon's core advantage: its update rule aligns with the outer-product structure of linear associative memories, enabling more balanced and effective learning of tail classes in heavy-tailed distributions than Adam.

Cryo-electron tomography (Cryo-ET) is a powerful tool in structural biology for 3D visualization of cells and biological systems at resolutions sufficient to identify individual proteins in situ. The measurements are collected by tilting the frozen specimen and exposing it to an electron beam of known dosage. As the biological samples are prone to electron damage, the samples can be exposed to only a limited dosage of electrons, leading to noisy and incomplete measurements. Thus, the reconstructions are noisy and incomplete, leading to the missing wedge problem. Currently, self-supervised learning is used to compensate for this issue. This typically involves, for each volume to recover, training a large 3D UNet on the initial noisy reconstruction, leading to large training time and memory requirements. In this work, we exploit the local nature of the forward model to train a lightweight network using only localized data from the measurements. This design provides flexibility in balancing computational and time requirements while reconstructing the volumes with high accuracy. We observe experimentally that this network can work well on unseen datasets, despite using a network trained on a few measurements.

Neutron tagging in Gadolinium-doped water may play a significant role in reducing backgrounds from atmospheric neutrinos in next generation proton-decay searches using megaton-scale Water Cherenkov detectors. Similar techniques might also be useful in the detection of supernova neutrinos. Accurate determination of neutron tagging efficiencies will require a detailed understanding of the number of neutrons produced by neutrino interactions in water as a function of momentum transferred. We propose the Atmospheric Neutrino Neutron Interaction Experiment (ANNIE), designed to measure the neutron yield of atmospheric neutrino interactions in gadolinium-doped water. An innovative aspect of the ANNIE design is the use of precision timing to localize interaction vertices in the small fiducial volume of the detector. We propose to achieve this by using early production of LAPPDs (Large Area Picosecond Photodetectors). This experiment will be a first application of these devices demonstrating their feasibility for Water Cherenkov neutrino detectors.

Neutron tagging in Gadolinium-doped water may play a significant role in reducing backgrounds from atmospheric neutrinos in next generation proton-decay searches using megaton-scale Water Cherenkov detectors. Similar techniques might also be useful in the detection of supernova neutrinos. Accurate determination of neutron tagging efficiencies will require a detailed understanding of the number of neutrons produced by neutrino interactions in water as a function of momentum transferred. We propose the Atmospheric Neutrino Neutron Interaction Experiment (ANNIE), designed to measure the neutron yield of atmospheric neutrino interactions in gadolinium-doped water. An innovative aspect of the ANNIE design is the use of precision timing to localize interaction vertices in the small fiducial volume of the detector. We propose to achieve this by using early production of LAPPDs (Large Area Picosecond Photodetectors). This experiment will be a first application of these devices demonstrating their feasibility for Water Cherenkov neutrino detectors.

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 significant challenges for existing MRI-to-PET translation methods. Modeling the cross-modality relationship in a lower-dimensional latent space can simplify the learning task and enable more effective translation. As such, we present CoCoLIT (ControlNet-Conditioned Latent Image Translation), a diffusion-based latent generative framework that incorporates three main innovations: (1) a novel Weighted Image Space Loss (WISL) that improves latent representation learning and synthesis quality; (2) a theoretical and empirical analysis of Latent Average Stabilization (LAS), an existing technique used in similar generative models to enhance inference consistency; and (3) the introduction of ControlNet-based conditioning for MRI-to-PET translation. We evaluate CoCoLIT's performance on publicly available datasets and find that our model significantly outperforms state-of-the-art methods on both image-based and amyloid-related metrics. Notably, in amyloid-positivity classification, CoCoLIT outperforms the second-best method with improvements of +10.5% on the internal dataset and +23.7% on the external dataset. The code and models of our approach are available at https://github.com/brAIn-science/CoCoLIT.

Radiation therapy plays a crucial role in cancer treatment, necessitating precise delivery of radiation to tumors while sparing healthy tissues over multiple days. Computed tomography (CT) is integral for treatment planning, offering electron density data crucial for accurate dose calculations. However, accurately representing patient anatomy is challenging, especially in adaptive radiotherapy, where CT is not acquired daily. Magnetic resonance imaging (MRI) provides superior soft-tissue contrast. Still, it lacks electron density information while cone beam CT (CBCT) lacks direct electron density calibration and is mainly used for patient positioning. Adopting MRI-only or CBCT-based adaptive radiotherapy eliminates the need for CT planning but presents challenges. Synthetic CT (sCT) generation techniques aim to address these challenges by using image synthesis to bridge the gap between MRI, CBCT, and CT. The SynthRAD2023 challenge was organized to compare synthetic CT generation methods using multi-center ground truth data from 1080 patients, divided into two tasks: 1) MRI-to-CT and 2) CBCT-to-CT. The evaluation included image similarity and dose-based metrics from proton and photon plans. The challenge attracted significant participation, with 617 registrations and 22/17 valid submissions for tasks 1/2. Top-performing teams achieved high structural similarity indices (>0.87/0.90) and gamma pass rates for photon (>98.1%/99.0%) and proton (>99.0%/97.3%) plans. However, no significant correlation was found between image similarity metrics and dose accuracy, emphasizing the need for dose evaluation when assessing the clinical applicability of sCT. SynthRAD2023 facilitated the investigation and benchmarking of sCT generation techniques, providing insights for developing MRI-only and CBCT-based adaptive radiotherapy.

In this work, we show that, if axion-like particles (ALPs) from core-collapse supernovae (SNe) couple to protons, they would produce very characteristic signatures in neutrino water Cherenkov detectors through their scattering off free protons via a , p rightarrow p , gamma interactions. Specifically, sub-MeV ALPs would generate photons with energies sim 30 MeV, which could be observed by Super-Kamiokande and Hyper-Kamiokande as a delayed signal after a future detection of SN neutrinos. We apply this to a hypothetical neighbouring SN (at a maximum distance of 100 kpc) and demonstrate that the region in the parameter space with ALP masses between 10^{-4} MeV and 1 MeV and ALP-proton couplings in the range 3 times 10^{-6}-4 times 10^{-5} could be probed. We argue that this new signature, combined with the one expected at sim 7 MeV from oxygen de-excitation, would allow us to disentangle ALP-neutron and ALP-proton couplings.

We introduce the Discrete Min-Max Violation (DMMV) as a general optimization problem which seeks an assignment of discrete values to variables that minimizes the largest constraint violation. This context-free mathematical formulation is applicable to a wide range of use cases that have worst-case performance requirements. After defining the DMMV problem mathematically, we explore its properties to establish a foundational understanding. To tackle DMMV instance sizes of practical relevance, we develop a GPU-accelerated heuristic that takes advantage of the mathematical properties of DMMV for speeding up the solution process. We demonstrate the versatile applicability of our heuristic by solving three optimization problems as use cases: (1) post-training quantization of language models, (2) discrete tomography, and (3) Finite Impulse Response (FIR) filter design. In quantization without outlier separation, our heuristic achieves 14% improvement on average over existing methods. In discrete tomography, it reduces reconstruction error by 16% under uniform noise and accelerates computations by a factor of 6 on GPU. For FIR filter design, it nearly achieves 50% ripple reduction compared to using the commercial integer optimization solver, Gurobi. Our comparative results point to the benefits of studying DMMV as a context-free optimization problem and the advantages that our proposed heuristic offers on three distinct problems. Our GPU-accelerated heuristic will be made open-source to further stimulate research on DMMV and its other applications. The code is available at https://anonymous.4open.science/r/AMVM-5F3E/

In this paper we introduce the concept of what we call "NUDAR" (NeUtrino Direction and Ranging), making the point that measurements of the observed energy and direction vectors can be employed to passively deduce the exact three-dimensional location and thermal power of geophysical and anthropogenic neutrino sources from even a single detector. We present the most precise background estimates to date, all handled in full three dimensions, as functions of depth and geographical location. For the present calculations, we consider a hypothetical 138 kiloton detector which can be transported to an ocean site and deployed to an operational depth. We present a Bayesian estimation framework to incorporate any a priori knowledge of the reactor that we are trying to detect, as well as the estimated uncertainty in the background and the oscillation parameters. Most importantly, we fully employ the knowledge of the reactor spectrum and the distance-dependent effects of neutrino oscillations on such spectra. The latter, in particular, makes possible determination of range from one location, given adequate signal statistics. Further, we explore the rich potential of improving detection with even modest improvements in individual neutrino direction determination. We conclude that a 300 MWth reactor can indeed be geolocated, and its operating power estimated with one or two detectors in the hundred kiloton class at ranges out to a few hundred kilometers. We note that such detectors would have natural and non-interfering utility for scientific studies of geo-neutrinos, neutrino oscillations, and astrophysical neutrinos. This motivates the development of cost effective methods of constructing and deploying such next generation detectors.

Accurate medical image segmentation is crucial for precise anatomical delineation. Deep learning models like U-Net have shown great success but depend heavily on large datasets and struggle with domain shifts, complex structures, and limited training samples. Recent studies have explored diffusion models for segmentation by iteratively refining masks. However, these methods still retain the conventional image-to-mask mapping, making them highly sensitive to input data, which hampers stability and generalization. In contrast, we introduce DiffAtlas, a novel generative framework that models both images and masks through diffusion during training, effectively ``GenAI-fying'' atlas-based segmentation. During testing, the model is guided to generate a specific target image-mask pair, from which the corresponding mask is obtained. DiffAtlas retains the robustness of the atlas paradigm while overcoming its scalability and domain-specific limitations. Extensive experiments on CT and MRI across same-domain, cross-modality, varying-domain, and different data-scale settings using the MMWHS and TotalSegmentator datasets demonstrate that our approach outperforms existing methods, particularly in limited-data and zero-shot modality segmentation. Code is available at https://github.com/M3DV/DiffAtlas.

Gate set tomography (GST) is a protocol for detailed, predictive characterization of logic operations (gates) on quantum computing processors. Early versions of GST emerged around 2012-13, and since then it has been refined, demonstrated, and used in a large number of experiments. This paper presents the foundations of GST in comprehensive detail. The most important feature of GST, compared to older state and process tomography protocols, is that it is calibration-free. GST does not rely on pre-calibrated state preparations and measurements. Instead, it characterizes all the operations in a gate set simultaneously and self-consistently, relative to each other. Long sequence GST can estimate gates with very high precision and efficiency, achieving Heisenberg scaling in regimes of practical interest. In this paper, we cover GST's intellectual history, the techniques and experiments used to achieve its intended purpose, data analysis, gauge freedom and fixing, error bars, and the interpretation of gauge-fixed estimates of gate sets. Our focus is fundamental mathematical aspects of GST, rather than implementation details, but we touch on some of the foundational algorithmic tricks used in the pyGSTi implementation.

Medical imaging is essential in modern radiotherapy, supporting diagnosis, treatment planning, and monitoring. Synthetic imaging, particularly synthetic computed tomography (sCT), is gaining traction in radiotherapy. The SynthRAD2025 dataset and Grand Challenge promote advancements in sCT generation by providing a benchmarking platform for algorithms using cone-beam CT (CBCT) and magnetic resonance imaging (MRI). The dataset includes 2362 cases: 890 MRI-CT and 1472 CBCT-CT pairs from head-and-neck, thoracic, and abdominal cancer patients treated at five European university medical centers (UMC Groningen, UMC Utrecht, Radboud UMC, LMU University Hospital Munich, and University Hospital of Cologne). Data were acquired with diverse scanners and protocols. Pre-processing, including rigid and deformable image registration, ensures high-quality, modality-aligned images. Extensive quality assurance validates image consistency and usability. All imaging data is provided in MetaImage (.mha) format, ensuring compatibility with medical image processing tools. Metadata, including acquisition parameters and registration details, is available in structured CSV files. To maintain dataset integrity, SynthRAD2025 is divided into training (65%), validation (10%), and test (25%) sets. The dataset is accessible at https://doi.org/10.5281/zenodo.14918089 under the SynthRAD2025 collection. This dataset supports benchmarking and the development of synthetic imaging techniques for radiotherapy applications. Use cases include sCT generation for MRI-only and MR-guided photon/proton therapy, CBCT-based dose calculations, and adaptive radiotherapy workflows. By integrating diverse acquisition settings, SynthRAD2025 fosters robust, generalizable image synthesis algorithms, advancing personalized cancer care and adaptive radiotherapy.

Every second greater than 10^{25} antineutrinos radiate to space from Earth, shining like a faint antineutrino star. Underground antineutrino detectors have revealed the rapidly decaying fission products inside nuclear reactors, verified the long-lived radioactivity inside our planet, and informed sensitive experiments for probing fundamental physics. Mapping the anisotropic antineutrino flux and energy spectrum advance geoscience by defining the amount and distribution of radioactive power within Earth while critically evaluating competing compositional models of the planet. We present the Antineutrino Global Map 2015 (AGM2015), an experimentally informed model of Earth's surface antineutrino flux over the 0 to 11 MeV energy spectrum, along with an assessment of systematic errors. The open source AGM2015 provides fundamental predictions for experiments, assists in strategic detector placement to determine neutrino mass hierarchy, and aids in identifying undeclared nuclear reactors. We use cosmochemically and seismologically informed models of the radiogenic lithosphere/mantle combined with the estimated antineutrino flux, as measured by KamLAND and Borexino, to determine the Earth's total antineutrino luminosity at 3.4^{+2.3}_{-2.2} times 10^{25} nu_e. We find a dominant flux of geo-neutrinos, predict sub-equal crust and mantle contributions, with sim1% of the total flux from man-made nuclear reactors.

Binary classical information is routinely encoded in the two metastable states of a dynamical system. Since these states may exhibit macroscopic lifetimes, the encoded information inherits a strong protection against bit-flips. A recent qubit - the cat-qubit - is encoded in the manifold of metastable states of a quantum dynamical system, thereby acquiring bit-flip protection. An outstanding challenge is to gain quantum control over such a system without breaking its protection. If this challenge is met, significant shortcuts in hardware overhead are forecast for quantum computing. In this experiment, we implement a cat-qubit with bit-flip times exceeding ten seconds. This is a four order of magnitude improvement over previous cat-qubit implementations, and six orders of magnitude enhancement over the single photon lifetime that compose this dynamical qubit. This was achieved by introducing a quantum tomography protocol that does not break bit-flip protection. We prepare and image quantum superposition states, and measure phase-flip times above 490 nanoseconds. Most importantly, we control the phase of these superpositions while maintaining the bit-flip time above ten seconds. This work demonstrates quantum operations that preserve macroscopic bit-flip times, a necessary step to scale these dynamical qubits into fully protected hardware-efficient architectures.

Geometry-aware optimization algorithms, such as Muon, have achieved remarkable success in training deep neural networks (DNNs). These methods leverage the underlying geometry of DNNs by selecting appropriate norms for different layers and updating parameters via norm-constrained linear minimization oracles (LMOs). However, even within a group of layers associated with the same norm, the local curvature can be heterogeneous across layers and vary dynamically over the course of training. For example, recent work shows that sharpness varies substantially across transformer layers and throughout training, yet standard geometry-aware optimizers impose fixed learning rates to layers within the same group, which may be inefficient for DNN training. In this paper, we introduce a noise-adaptive layerwise learning rate scheme on top of geometry-aware optimization algorithms and substantially accelerate DNN training compared to methods that use fixed learning rates within each group. Our method estimates gradient variance in the dual norm induced by the chosen LMO on the fly, and uses it to assign time-varying noise-adaptive layerwise learning rates within each group. We provide a theoretical analysis showing that our algorithm achieves a sharp convergence rate. Empirical results on transformer architectures such as LLaMA and GPT demonstrate that our approach achieves faster convergence than state-of-the-art optimizers.

Many low-dose CT imaging methods rely on supervised learning, which requires a large number of paired noisy and clean images. However, obtaining paired images in clinical practice is challenging. To address this issue, zero-shot self-supervised methods train denoising networks using only the information within a single image, such as ZS-N2N. However, these methods often employ downsampling operations that degrade image resolution. Additionally, the training dataset is inherently constrained to the image itself. In this paper, we propose a zero-shot low-dose CT imaging method based on sinogram flicking, which operates within a single image but generates many copies via random conjugate ray matching. Specifically, two conjugate X-ray pencil beams measure the same path; their expected values should be identical, while their noise levels vary during measurements. By randomly swapping portions of the conjugate X-rays in the sinogram domain, we generate a large set of sinograms with consistent content but varying noise patterns. When displayed dynamically, these sinograms exhibit a flickering effect due to their identical structural content but differing noise patterns-hence the term sinogram flicking. We train the network on pairs of sinograms with the same content but different noise distributions using a lightweight model adapted from ZS-NSN. This process is repeated to obtain the final results. A simulation study demonstrates that our method outperforms state-of-the-art approaches such as ZS-N2N.

We introduce a Three-Dimensional Convolutional Variational Autoencoder (3D-CVAE) for automated anomaly detection in Electron Energy Loss Spectroscopy Spectrum Imaging (EELS-SI) data. Our approach leverages the full three-dimensional structure of EELS-SI data to detect subtle spectral anomalies while preserving both spatial and spectral correlations across the datacube. By employing negative log-likelihood loss and training on bulk spectra, the model learns to reconstruct bulk features characteristic of the defect-free material. In exploring methods for anomaly detection, we evaluated both our 3D-CVAE approach and Principal Component Analysis (PCA), testing their performance using Fe L-edge peak shifts designed to simulate material defects. Our results show that 3D-CVAE achieves superior anomaly detection and maintains consistent performance across various shift magnitudes. The method demonstrates clear bimodal separation between normal and anomalous spectra, enabling reliable classification. Further analysis verifies that lower dimensional representations are robust to anomalies in the data. While performance advantages over PCA diminish with decreasing anomaly concentration, our method maintains high reconstruction quality even in challenging, noise-dominated spectral regions. This approach provides a robust framework for unsupervised automated detection of spectral anomalies in EELS-SI data, particularly valuable for analyzing complex material systems.

We show, for the first time, radio measurements of the depth of shower maximum (X_max) of air showers induced by cosmic rays that are compared to measurements of the established fluorescence method at the same location. Using measurements at the Pierre Auger Observatory we show full compatibility between our radio and the previously published fluorescence data set, and between a subset of air showers observed simultaneously with both radio and fluorescence techniques, a measurement setup unique to the Pierre Auger Observatory. Furthermore, we show radio X_max resolution as a function of energy and demonstrate the ability to make competitive high-resolution X_max measurements with even a sparse radio array. With this, we show that the radio technique is capable of cosmic-ray mass composition studies, both at Auger and at other experiments.

This work introduces a highly efficient implementation of the transformer architecture on a Field-Programmable Gate Array (FPGA) by using the hls4ml tool. Given the demonstrated effectiveness of transformer models in addressing a wide range of problems, their application in experimental triggers within particle physics becomes a subject of significant interest. In this work, we have implemented critical components of a transformer model, such as multi-head attention and softmax layers. To evaluate the effectiveness of our implementation, we have focused on a particle physics jet flavor tagging problem, employing a public dataset. We recorded latency under 2 mus on the Xilinx UltraScale+ FPGA, which is compatible with hardware trigger requirements at the CERN Large Hadron Collider experiments.

Foundation Models are neural networks that are capable of simultaneously solving many problems. Large Language Foundation Models like ChatGPT have revolutionized many aspects of daily life, but their impact for science is not yet clear. In this paper, we use a new Foundation Model for hadronic jets to solve three key challenges in collider physics. In particular, we show how experiments can (1) save significant computing power when developing reconstruction algorithms, (2) perform a complete uncertainty quantification for high-dimensional measurements, and (3) search for new physics with model agnostic methods using low-level inputs. In each case, there are significant computational or methodological challenges with current methods that limit the science potential of deep learning algorithms. By solving each problem, we take jet Foundation Models beyond proof-of-principle studies and into the toolkit of practitioners.

Objective: While recent advances in text-conditioned generative models have enabled the synthesis of realistic medical images, progress has been largely confined to 2D modalities such as chest X-rays. Extending text-to-image generation to volumetric Computed Tomography (CT) remains a significant challenge, due to its high dimensionality, anatomical complexity, and the absence of robust frameworks that align vision-language data in 3D medical imaging. Methods: We introduce a novel architecture for Text-to-CT generation that combines a latent diffusion model with a 3D contrastive vision-language pretraining scheme. Our approach leverages a dual-encoder CLIP-style model trained on paired CT volumes and radiology reports to establish a shared embedding space, which serves as the conditioning input for generation. CT volumes are compressed into a low-dimensional latent space via a pretrained volumetric VAE, enabling efficient 3D denoising diffusion without requiring external super-resolution stages. Results: We evaluate our method on the CT-RATE dataset and conduct a comprehensive assessment of image fidelity, clinical relevance, and semantic alignment. Our model achieves competitive performance across all tasks, significantly outperforming prior baselines for text-to-CT generation. Moreover, we demonstrate that CT scans synthesized by our framework can effectively augment real data, improving downstream diagnostic performance. Conclusion: Our results show that modality-specific vision-language alignment is a key component for high-quality 3D medical image generation. By integrating contrastive pretraining and volumetric diffusion, our method offers a scalable and controllable solution for synthesizing clinically meaningful CT volumes from text, paving the way for new applications in data augmentation, medical education, and automated clinical simulation.

We present the development of the miniTimeCube (mTC), a novel compact neutrino detector. The mTC is a multipurpose detector, aiming to detect not only neutrinos but also fast/thermal neutrons. Potential applications include the counterproliferation of nuclear materials and the investigation of antineutrino short-baseline effects. The mTC is a plastic 0.2% ^{10}B - doped scintillator (13 cm)^3 cube surrounded by 24 Micro-Channel Plate (MCP) photon detectors, each with an 8times8 anode totaling 1536 individual channels/pixels viewing the scintillator. It uses custom-made electronics modules which mount on top of the MCPs, making our detector compact and able to both distinguish different types of events and reject noise in real time. The detector is currently deployed and being tested at the National Institute of Standards and Technology (NIST) Center for Neutron Research (NCNR) nuclear reactor (20 MW_th) in Gaithersburg, MD. A shield for further tests is being constructed, and calibration and upgrades are ongoing. The mTC's improved spatiotemporal resolution will allow for determination of incident particle directions beyond previous capabilities.

Deep learning has been wildly successful in practice and most state-of-the-art machine learning methods are based on neural networks. Lacking, however, is a rigorous mathematical theory that adequately explains the amazing performance of deep neural networks. In this article, we present a relatively new mathematical framework that provides the beginning of a deeper understanding of deep learning. This framework precisely characterizes the functional properties of neural networks that are trained to fit to data. The key mathematical tools which support this framework include transform-domain sparse regularization, the Radon transform of computed tomography, and approximation theory, which are all techniques deeply rooted in signal processing. This framework explains the effect of weight decay regularization in neural network training, the use of skip connections and low-rank weight matrices in network architectures, the role of sparsity in neural networks, and explains why neural networks can perform well in high-dimensional problems.

About 90% of the computing resources available to the LHCb experiment has been spent to produce simulated data samples for Run 2 of the Large Hadron Collider at CERN. The upgraded LHCb detector will be able to collect larger data samples, requiring many more simulated events to analyze the data to be collected in Run 3. Simulation is a key necessity of analysis to interpret signal, reject background and measure efficiencies. The needed simulation will far exceed the pledged resources, requiring an evolution in technologies and techniques to produce these simulated data samples. In this contribution, we discuss Lamarr, a Gaudi-based framework to speed-up the simulation production parameterizing both the detector response and the reconstruction algorithms of the LHCb experiment. Deep Generative Models powered by several algorithms and strategies are employed to effectively parameterize the high-level response of the single components of the LHCb detector, encoding within neural networks the experimental errors and uncertainties introduced in the detection and reconstruction phases. Where possible, models are trained directly on real data, statistically subtracting any background components by applying appropriate reweighing procedures. Embedding Lamarr in the general LHCb Gauss Simulation framework allows to combine its execution with any of the available generators in a seamless way. The resulting software package enables a simulation process independent of the detailed simulation used to date.

Accurate segmentation of tumors in PET/CT images is important in computer-aided diagnosis and treatment of cancer. The key issue of such a segmentation problem lies in the effective integration of complementary information from PET and CT images. However, the quality of PET and CT images varies widely in clinical settings, which leads to uncertainty in the modality information extracted by networks. To take the uncertainty into account in multi-modal information fusion, this paper proposes a novel Multi-modal Evidential Fusion Network (MEFN) comprising a Cross-Modal Feature Learning (CFL) module and a Multi-modal Trusted Fusion (MTF) module. The CFL module reduces the domain gap upon modality conversion and highlights common tumor features, thereby alleviating the needs of the segmentation module to handle modality specificity. The MTF module utilizes mutual attention mechanisms and an uncertainty calibrator to fuse modality features based on modality uncertainty and then fuse the segmentation results under the guidance of Dempster-Shafer Theory. Besides, a new uncertainty perceptual loss is introduced to force the model focusing on uncertain features and hence improve its ability to extract trusted modality information. Extensive comparative experiments are conducted on two publicly available PET/CT datasets to evaluate the performance of our proposed method whose results demonstrate that our MEFN significantly outperforms state-of-the-art methods with improvements of 2.15% and 3.23% in DSC scores on the AutoPET dataset and the Hecktor dataset, respectively. More importantly, our model can provide radiologists with credible uncertainty of the segmentation results for their decision in accepting or rejecting the automatic segmentation results, which is particularly important for clinical applications. Our code will be available at https://github.com/QPaws/MEFN.

This paper introduces an innovative methodology for producing high-quality 3D lung CT images guided by textual information. While diffusion-based generative models are increasingly used in medical imaging, current state-of-the-art approaches are limited to low-resolution outputs and underutilize radiology reports' abundant information. The radiology reports can enhance the generation process by providing additional guidance and offering fine-grained control over the synthesis of images. Nevertheless, expanding text-guided generation to high-resolution 3D images poses significant memory and anatomical detail-preserving challenges. Addressing the memory issue, we introduce a hierarchical scheme that uses a modified UNet architecture. We start by synthesizing low-resolution images conditioned on the text, serving as a foundation for subsequent generators for complete volumetric data. To ensure the anatomical plausibility of the generated samples, we provide further guidance by generating vascular, airway, and lobular segmentation masks in conjunction with the CT images. The model demonstrates the capability to use textual input and segmentation tasks to generate synthesized images. The results of comparative assessments indicate that our approach exhibits superior performance compared to the most advanced models based on GAN and diffusion techniques, especially in accurately retaining crucial anatomical features such as fissure lines, airways, and vascular structures. This innovation introduces novel possibilities. This study focuses on two main objectives: (1) the development of a method for creating images based on textual prompts and anatomical components, and (2) the capability to generate new images conditioning on anatomical elements. The advancements in image generation can be applied to enhance numerous downstream tasks.

Incorporating prior information into inverse problems, e.g. via maximum-a-posteriori estimation, is an important technique for facilitating robust inverse problem solutions. In this paper, we devise two novel approaches for linear inverse problems that permit problem-specific statistical prior selections within the compound Gaussian (CG) class of distributions. The CG class subsumes many commonly used priors in signal and image reconstruction methods including those of sparsity-based approaches. The first method developed is an iterative algorithm, called generalized compound Gaussian least squares (G-CG-LS), that minimizes a regularized least squares objective function where the regularization enforces a CG prior. G-CG-LS is then unrolled, or unfolded, to furnish our second method, which is a novel deep regularized (DR) neural network, called DR-CG-Net, that learns the prior information. A detailed computational theory on convergence properties of G-CG-LS and thorough numerical experiments for DR-CG-Net are provided. Due to the comprehensive nature of the CG prior, these experiments show that DR-CG-Net outperforms competitive prior art methods in tomographic imaging and compressive sensing, especially in challenging low-training scenarios.

To evaluate the variability of multi-phase flow properties of porous media at the pore scale, it is necessary to acquire a number of representative samples of the void-solid structure. While modern x-ray computer tomography has made it possible to extract three-dimensional images of the pore space, assessment of the variability in the inherent material properties is often experimentally not feasible. We present a novel method to reconstruct the solid-void structure of porous media by applying a generative neural network that allows an implicit description of the probability distribution represented by three-dimensional image datasets. We show, by using an adversarial learning approach for neural networks, that this method of unsupervised learning is able to generate representative samples of porous media that honor their statistics. We successfully compare measures of pore morphology, such as the Euler characteristic, two-point statistics and directional single-phase permeability of synthetic realizations with the calculated properties of a bead pack, Berea sandstone, and Ketton limestone. Results show that GANs can be used to reconstruct high-resolution three-dimensional images of porous media at different scales that are representative of the morphology of the images used to train the neural network. The fully convolutional nature of the trained neural network allows the generation of large samples while maintaining computational efficiency. Compared to classical stochastic methods of image reconstruction, the implicit representation of the learned data distribution can be stored and reused to generate multiple realizations of the pore structure very rapidly.

The rapid increase of computed tomography (CT) scans and their time-consuming manual analysis have created an urgent need for robust automated analysis techniques in clinical settings. These aim to assist radiologists and help them managing their growing workload. Existing methods typically generate entire reports directly from 3D CT images, without explicitly focusing on observed abnormalities. This unguided approach often results in repetitive content or incomplete reports, failing to prioritize anomaly-specific descriptions. We propose a new anomaly-guided report generation model, which first predicts abnormalities and then generates targeted descriptions for each. Evaluation on a public dataset demonstrates significant improvements in report quality and clinical relevance. We extend our work by conducting an ablation study to demonstrate its effectiveness.

We describe a new detector, called NuLat, to study electron anti-neutrinos a few meters from a nuclear reactor, and search for anomalous neutrino oscillations. Such oscillations could be caused by sterile neutrinos, and might explain the "Reactor Antineutrino Anomaly". NuLat, is made possible by a natural synergy between the miniTimeCube and mini-LENS programs described in this paper. It features a "Raghavan Optical Lattice" (ROL) consisting of 3375 boron or ^6Li loaded plastic scintillator cubical cells 6.3\,cm (2.500") on a side. Cell boundaries have a 0.127\,mm (0.005") air gap, resulting in total internal reflection guiding most of the light down the 3 cardinal directions. The ROL detector technology for NuLat gives excellent spatial and energy resolution and allows for in-depth event topology studies. These features allow us to discern inverse beta decay (IBD) signals and the putative oscillation pattern, even in the presence of other backgrounds. We discuss here test venues, efficiency, sensitivity and project status.

Sparse-view computed tomography (CT) -- using a small number of projections for tomographic reconstruction -- enables much lower radiation dose to patients and accelerated data acquisition. The reconstructed images, however, suffer from strong artifacts, greatly limiting their diagnostic value. Current trends for sparse-view CT turn to the raw data for better information recovery. The resultant dual-domain methods, nonetheless, suffer from secondary artifacts, especially in ultra-sparse view scenarios, and their generalization to other scanners/protocols is greatly limited. A crucial question arises: have the image post-processing methods reached the limit? Our answer is not yet. In this paper, we stick to image post-processing methods due to great flexibility and propose global representation (GloRe) distillation framework for sparse-view CT, termed GloReDi. First, we propose to learn GloRe with Fourier convolution, so each element in GloRe has an image-wide receptive field. Second, unlike methods that only use the full-view images for supervision, we propose to distill GloRe from intermediate-view reconstructed images that are readily available but not explored in previous literature. The success of GloRe distillation is attributed to two key components: representation directional distillation to align the GloRe directions, and band-pass-specific contrastive distillation to gain clinically important details. Extensive experiments demonstrate the superiority of the proposed GloReDi over the state-of-the-art methods, including dual-domain ones. The source code is available at https://github.com/longzilicart/GloReDi.

Diffusion models (DMs) have proven to be effective in modeling high-dimensional distributions, leading to their widespread adoption for representing complex priors in Bayesian inverse problems (BIPs). However, current DM-based posterior sampling methods proposed for solving common BIPs rely on heuristic approximations to the generative process. To exploit the generative capability of DMs and avoid the usage of such approximations, we propose an ensemble-based algorithm that performs posterior sampling without the use of heuristic approximations. Our algorithm is motivated by existing works that combine DM-based methods with the sequential Monte Carlo (SMC) method. By examining how the prior evolves through the diffusion process encoded by the pre-trained score function, we derive a modified partial differential equation (PDE) governing the evolution of the corresponding posterior distribution. This PDE includes a modified diffusion term and a reweighting term, which can be simulated via stochastic weighted particle methods. Theoretically, we prove that the error between the true posterior distribution can be bounded in terms of the training error of the pre-trained score function and the number of particles in the ensemble. Empirically, we validate our algorithm on several inverse problems in imaging to show that our method gives more accurate reconstructions compared to existing DM-based methods.

Clinical monitoring of metastatic disease to the brain can be a laborious and time-consuming process, especially in cases involving multiple metastases when the assessment is performed manually. The Response Assessment in Neuro-Oncology Brain Metastases (RANO-BM) guideline, which utilizes the unidimensional longest diameter, is commonly used in clinical and research settings to evaluate response to therapy in patients with brain metastases. However, accurate volumetric assessment of the lesion and surrounding peri-lesional edema holds significant importance in clinical decision-making and can greatly enhance outcome prediction. The unique challenge in performing segmentations of brain metastases lies in their common occurrence as small lesions. Detection and segmentation of lesions that are smaller than 10 mm in size has not demonstrated high accuracy in prior publications. The brain metastases challenge sets itself apart from previously conducted MICCAI challenges on glioma segmentation due to the significant variability in lesion size. Unlike gliomas, which tend to be larger on presentation scans, brain metastases exhibit a wide range of sizes and tend to include small lesions. We hope that the BraTS-METS dataset and challenge will advance the field of automated brain metastasis detection and segmentation.

The mass composition of ultra-high-energy cosmic rays is an open problem in astroparticle physics. It is usually inferred from the depth of the shower maximum (Xmax) of cosmic-ray showers, which is only ambiguously determined by modern hadronic interaction models. We examine a data-driven scenario, in which we consider the expectation value of Xmax as a free parameter. We test the novel hypothesis whether the cosmic-ray data from the Pierre Auger Observatory can be interpreted in a consistent picture, under the assumption that the mass composition of cosmic rays at the highest energies is dominated by high metallicity, resulting in pure iron nuclei at energies above ~40 EeV. We investigate the implications on astrophysical observations and hadronic interactions, and we discuss the global consistency of the data assuming this heavy-metal scenario. We conclude that the data from the Pierre Auger Observatory can be interpreted consistently if the expectation values for Xmax from modern hadronic interaction models are shifted to larger values.

We introduce a novel neural network, SkyReconNet, which combines the expanded receptive fields of dilated convolutional layers along with standard convolutions, to capture both the global and local features for reconstructing the missing information in an image. We implement our network to inpaint the masked regions in a full-sky Cosmic Microwave Background (CMB) map. Inpainting CMB maps is a particularly formidable challenge when dealing with extensive and irregular masks, such as galactic masks which can obscure substantial fractions of the sky. The hybrid design of SkyReconNet leverages the strengths of standard and dilated convolutions to accurately predict CMB fluctuations in the masked regions, by effectively utilizing the information from surrounding unmasked areas. During training, the network optimizes its weights by minimizing a composite loss function that combines the Structural Similarity Index Measure (SSIM) and mean squared error (MSE). SSIM preserves the essential structural features of the CMB, ensuring an accurate and coherent reconstruction of the missing CMB fluctuations, while MSE minimizes the pixel-wise deviations, enhancing the overall accuracy of the predictions. The predicted CMB maps and their corresponding angular power spectra align closely with the targets, achieving the performance limited only by the fundamental uncertainty of cosmic variance. The network's generic architecture enables application to other physics-based challenges involving data with missing or defective pixels, systematic artefacts etc. Our results demonstrate its effectiveness in addressing the challenges posed by large irregular masks, offering a significant inpainting tool not only for CMB analyses but also for image-based experiments across disciplines where such data imperfections are prevalent.

We reconstruct the extra-galactic gamma-ray source-count distribution, or dN/dS, of resolved and unresolved sources by adopting machine learning techniques. Specifically, we train a convolutional neural network on synthetic 2-dimensional sky-maps, which are built by varying parameters of underlying source-counts models and incorporate the Fermi-LAT instrumental response functions. The trained neural network is then applied to the Fermi-LAT data, from which we estimate the source count distribution down to flux levels a factor of 50 below the Fermi-LAT threshold. We perform our analysis using 14 years of data collected in the (1,10) GeV energy range. The results we obtain show a source count distribution which, in the resolved regime, is in excellent agreement with the one derived from catalogued sources, and then extends as dN/dS sim S^{-2} in the unresolved regime, down to fluxes of 5 cdot 10^{-12} cm^{-2} s^{-1}. The neural network architecture and the devised methodology have the flexibility to enable future analyses to study the energy dependence of the source-count distribution.

We participated in the SynthRAD2025 challenge (Tasks 1 and 2) with a unified pipeline for synthetic CT (sCT) generation from MRI and CBCT, implemented using the KonfAI framework. Our model is a 2.5D U-Net++ with a ResNet-34 encoder, trained jointly across anatomical regions and fine-tuned per region. The loss function combined pixel-wise L1 loss with IMPACT-Synth, a perceptual loss derived from SAM and TotalSegmentator to enhance structural fidelity. Training was performed using AdamW (initial learning rate = 0.001, halved every 25k steps) on patch-based, normalized, body-masked inputs (320x320 for MRI, 256x256 for CBCT), with random flipping as the only augmentation. No post-processing was applied. Final predictions leveraged test-time augmentation and five-fold ensembling. The best model was selected based on validation MAE. Two registration strategies were evaluated: (i) Elastix with mutual information, consistent with the challenge pipeline, and (ii) IMPACT, a feature-based similarity metric leveraging pretrained segmentation networks. On the local test sets, IMPACT-based registration achieved more accurate and anatomically consistent alignments than mutual-information-based registration, resulting in improved sCT synthesis with lower MAE and more realistic anatomical structures. On the public validation set, however, models trained with Elastix-aligned data achieved higher scores, reflecting a registration bias favoring alignment strategies consistent with the evaluation pipeline. This highlights how registration errors can propagate into supervised learning, influencing both training and evaluation, and potentially inflating performance metrics at the expense of anatomical fidelity. By promoting anatomically consistent alignment, IMPACT helps mitigate this bias and supports the development of more robust and generalizable sCT synthesis models.

Recently, diffusion models have been used to solve various inverse problems in an unsupervised manner with appropriate modifications to the sampling process. However, the current solvers, which recursively apply a reverse diffusion step followed by a projection-based measurement consistency step, often produce suboptimal results. By studying the generative sampling path, here we show that current solvers throw the sample path off the data manifold, and hence the error accumulates. To address this, we propose an additional correction term inspired by the manifold constraint, which can be used synergistically with the previous solvers to make the iterations close to the manifold. The proposed manifold constraint is straightforward to implement within a few lines of code, yet boosts the performance by a surprisingly large margin. With extensive experiments, we show that our method is superior to the previous methods both theoretically and empirically, producing promising results in many applications such as image inpainting, colorization, and sparse-view computed tomography. Code available https://github.com/HJ-harry/MCG_diffusion

In the radiation therapy of nasopharyngeal carcinoma (NPC), clinicians typically delineate the gross tumor volume (GTV) using non-contrast planning computed tomography to ensure accurate radiation dose delivery. However, the low contrast between tumors and adjacent normal tissues necessitates that radiation oncologists manually delineate the tumors, often relying on diagnostic MRI for guidance. % In this study, we propose a novel approach to directly segment NPC gross tumors on non-contrast planning CT images, circumventing potential registration errors when aligning MRI or MRI-derived tumor masks to planning CT. To address the low contrast issues between tumors and adjacent normal structures in planning CT, we introduce a 3D Semantic Asymmetry Tumor segmentation (SATs) method. Specifically, we posit that a healthy nasopharyngeal region is characteristically bilaterally symmetric, whereas the emergence of nasopharyngeal carcinoma disrupts this symmetry. Then, we propose a Siamese contrastive learning segmentation framework that minimizes the voxel-wise distance between original and flipped areas without tumor and encourages a larger distance between original and flipped areas with tumor. Thus, our approach enhances the sensitivity of features to semantic asymmetries. % Extensive experiments demonstrate that the proposed SATs achieves the leading NPC GTV segmentation performance in both internal and external testing, e.g., with at least 2\% absolute Dice score improvement and 12\% average distance error reduction when compared to other state-of-the-art methods in the external testing.

Chest X-rays (CXRs) are commonly utilized as a low-dose modality for lung screening. Nonetheless, the efficacy of CXRs is somewhat impeded, given that approximately 75% of the lung area overlaps with bone, which in turn hampers the detection and diagnosis of diseases. As a remedial measure, bone suppression techniques have been introduced. The current dual-energy subtraction imaging technique in the clinic requires costly equipment and subjects being exposed to high radiation. To circumvent these issues, deep learning-based image generation algorithms have been proposed. However, existing methods fall short in terms of producing high-quality images and capturing texture details, particularly with pulmonary vessels. To address these issues, this paper proposes a new bone suppression framework, termed BS-Diff, that comprises a conditional diffusion model equipped with a U-Net architecture and a simple enhancement module to incorporate an autoencoder. Our proposed network cannot only generate soft tissue images with a high bone suppression rate but also possesses the capability to capture fine image details. Additionally, we compiled the largest dataset since 2010, including data from 120 patients with high-definition, high-resolution paired CXRs and soft tissue images collected by our affiliated hospital. Extensive experiments, comparative analyses, ablation studies, and clinical evaluations indicate that the proposed BS-Diff outperforms several bone-suppression models across multiple metrics. Our code can be accessed at https://github.com/Benny0323/BS-Diff.

Purpose: Medical imaging has become increasingly important in diagnosing and treating oncological patients, particularly in radiotherapy. Recent advances in synthetic computed tomography (sCT) generation have increased interest in public challenges to provide data and evaluation metrics for comparing different approaches openly. This paper describes a dataset of brain and pelvis computed tomography (CT) images with rigidly registered CBCT and MRI images to facilitate the development and evaluation of sCT generation for radiotherapy planning. Acquisition and validation methods: The dataset consists of CT, CBCT, and MRI of 540 brains and 540 pelvic radiotherapy patients from three Dutch university medical centers. Subjects' ages ranged from 3 to 93 years, with a mean age of 60. Various scanner models and acquisition settings were used across patients from the three data-providing centers. Details are available in CSV files provided with the datasets. Data format and usage notes: The data is available on Zenodo (https://doi.org/10.5281/zenodo.7260705) under the SynthRAD2023 collection. The images for each subject are available in nifti format. Potential applications: This dataset will enable the evaluation and development of image synthesis algorithms for radiotherapy purposes on a realistic multi-center dataset with varying acquisition protocols. Synthetic CT generation has numerous applications in radiation therapy, including diagnosis, treatment planning, treatment monitoring, and surgical planning.

We present a neural network emulator to constrain the thermal parameters of the intergalactic medium (IGM) at 5.4z6.0 using the Lyman-displaystylealpha (Lydisplaystylealpha) forest flux auto-correlation function. Our auto-differentiable JAX-based framework accelerates the surrogate model generation process using approximately 100 sparsely sampled Nyx hydrodynamical simulations with varying combinations of thermal parameters, i.e., the temperature at mean density T_{{0}}, the slope of the temperaturedisplaystyle-density relation displaystylegamma, and the mean transmission flux langle{F}{rangle}. We show that this emulator has a typical accuracy of 1.0% across the specified redshift range. Bayesian inference of the IGM thermal parameters, incorporating emulator uncertainty propagation, is further expedited using NumPyro Hamiltonian Monte Carlo. We compare both the inference results and computational cost of our framework with the traditional nearest-neighbor interpolation approach applied to the same set of mock Lyalpha flux. By examining the credibility contours of the marginalized posteriors for T_{{0}},gamma,and{langle}{F}{rangle} obtained using the emulator, the statistical reliability of measurements is established through inference on 100 realistic mock data sets of the auto-correlation function.

Diffusion models have achieved remarkable success in imaging inverse problems owing to their powerful generative capabilities. However, existing approaches typically rely on models trained for specific degradation types, limiting their generalizability to various degradation scenarios. To address this limitation, we propose a zero-shot framework capable of handling various imaging inverse problems without model retraining. We introduce a likelihood-guided noise refinement mechanism that derives a closed-form approximation of the likelihood score, simplifying score estimation and avoiding expensive gradient computations. This estimated score is subsequently utilized to refine the model-predicted noise, thereby better aligning the restoration process with the generative framework of diffusion models. In addition, we integrate the Denoising Diffusion Implicit Models (DDIM) sampling strategy to further improve inference efficiency. The proposed mechanism can be applied to both optimization-based and sampling-based schemes, providing an effective and flexible zero-shot solution for imaging inverse problems. Extensive experiments demonstrate that our method achieves superior performance across multiple inverse problems, particularly in compressive sensing, delivering high-quality reconstructions even at an extremely low sampling rate (5%).

Diffusion models have become a popular approach for image generation and reconstruction due to their numerous advantages. However, most diffusion-based inverse problem-solving methods only deal with 2D images, and even recently published 3D methods do not fully exploit the 3D distribution prior. To address this, we propose a novel approach using two perpendicular pre-trained 2D diffusion models to solve the 3D inverse problem. By modeling the 3D data distribution as a product of 2D distributions sliced in different directions, our method effectively addresses the curse of dimensionality. Our experimental results demonstrate that our method is highly effective for 3D medical image reconstruction tasks, including MRI Z-axis super-resolution, compressed sensing MRI, and sparse-view CT. Our method can generate high-quality voxel volumes suitable for medical applications.

We explore a generative machine learning-based approach for estimating multi-dimensional probability density functions (PDFs) in a target sample using a statistically independent but related control sample - a common challenge in particle physics data analysis. The generative model must accurately reproduce individual observable distributions while preserving the correlations between them, based on the input multidimensional distribution from the control sample. Here we present a conditional normalizing flow model (CNF) based on a chain of bijectors which learns to transform unpaired simulation events to data events. We assess the performance of the CNF model in the context of LHC Higgs to diphoton analysis, where we use the CNF model to convert a Monte Carlo diphoton sample to one that models data. We show that the CNF model can accurately model complex data distributions and correlations. We also leverage the recently popularized Modified Differential Multiplier Method (MDMM) to improve the convergence of our model and assign physical meaning to usually arbitrary loss-function parameters.

Breast density estimation is one of the key tasks in recognizing individuals predisposed to breast cancer. It is often challenging because of low contrast and fluctuations in mammograms' fatty tissue background. Most of the time, the breast density is estimated manually where a radiologist assigns one of the four density categories decided by the Breast Imaging and Reporting Data Systems (BI-RADS). There have been efforts in the direction of automating a breast density classification pipeline. Breast density estimation is one of the key tasks performed during a screening exam. Dense breasts are more susceptible to breast cancer. The density estimation is challenging because of low contrast and fluctuations in mammograms' fatty tissue background. Traditional mammograms are being replaced by tomosynthesis and its other low radiation dose variants (for example Hologic' Intelligent 2D and C-View). Because of the low-dose requirement, increasingly more screening centers are favoring the Intelligent 2D view and C-View. Deep-learning studies for breast density estimation use only a single modality for training a neural network. However, doing so restricts the number of images in the dataset. In this paper, we show that a neural network trained on all the modalities at once performs better than a neural network trained on any single modality. We discuss these results using the area under the receiver operator characteristics curves.

Generating synthetic Computed Tomography (CT) images from Cone Beam Computed Tomography (CBCT) is desirable for improving the image quality of CBCT. Existing synthetic CT (sCT) generation methods using Convolutional Neural Networks (CNN) and Transformers often face difficulties in effectively capturing both global and local features and contrasts for high-quality sCT generation. In this work, we propose a Global-Local Feature and Contrast learning (GLFC) framework for sCT generation. First, a Mamba-Enhanced UNet (MEUNet) is introduced by integrating Mamba blocks into the skip connections of a high-resolution UNet for effective global and local feature learning. Second, we propose a Multiple Contrast Loss (MCL) that calculates synthetic loss at different intensity windows to improve quality for both soft tissues and bone regions. Experiments on the SynthRAD2023 dataset demonstrate that GLFC improved the SSIM of sCT from 77.91% to 91.50% compared with the original CBCT, and significantly outperformed several existing methods for sCT generation. The code is available at https://github.com/HiLab-git/GLFC

Segment Anything Model (SAM) has gained significant attention because of its ability to segment a variety of objects in images given a prompt. The recently developed SAM 2 has extended this ability to video inputs. This opens an opportunity to apply SAM to 3D images, one of the fundamental tasks in the medical imaging field. In this paper, we provide an extensive evaluation of SAM 2's ability to segment both 2D and 3D medical images. We collect 18 medical imaging datasets, including common 3D modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET) as well as 2D modalities such as X-ray and ultrasound. We consider two evaluation pipelines of SAM 2: (1) multi-frame 3D segmentation, where prompts are provided to one or multiple slice(s) selected from the volume, and (2) single-frame 2D segmentation, where prompts are provided to each slice. The former is only applicable to 3D modalities, while the latter applies to both 2D and 3D modalities. We learn that SAM 2 exhibits similar performance as SAM under single-frame 2D segmentation, and has variable performance under multi-frame 3D segmentation depending on the choices of slices to annotate, the direction of the propagation, the predictions utilized during the propagation, etc.

Large-Area Picosecond Photo-Detectors (LAPPDs) show great potential for expanding the performance envelope of Micro-Channel Plates (MCPs) to areas of up to 20 x 20 cm and larger. Such scaling introduces new challenges, including how to meet the electronics readout burden of ever larger area MCPs. One solution is to replace the traditional grid anode used for readout with a microwave stripline anode, thus allowing the channel count to scale with MCP width rather than area. However, stripline anodes introduce new issues not commonly dealt with in grid-anodes, especially as their length increases. One of these issues is the near simultaneous arrival of multiple photons on the detector, creating possible confusion about how to reconstruct their arrival times and positions. We propose a maximum a posteriori solution to the problem and verify its performance in simulated scintillator and water-Cherenkov detectors.

Score-based generative modeling, informally referred to as diffusion models, continue to grow in popularity across several important domains and tasks. While they provide high-quality and diverse samples from empirical distributions, important questions remain on the reliability and trustworthiness of these sampling procedures for their responsible use in critical scenarios. Conformal prediction is a modern tool to construct finite-sample, distribution-free uncertainty guarantees for any black-box predictor. In this work, we focus on image-to-image regression tasks and we present a generalization of the Risk-Controlling Prediction Sets (RCPS) procedure, that we term K-RCPS, which allows to (i) provide entrywise calibrated intervals for future samples of any diffusion model, and (ii) control a certain notion of risk with respect to a ground truth image with minimal mean interval length. Differently from existing conformal risk control procedures, ours relies on a novel convex optimization approach that allows for multidimensional risk control while provably minimizing the mean interval length. We illustrate our approach on two real-world image denoising problems: on natural images of faces as well as on computed tomography (CT) scans of the abdomen, demonstrating state of the art performance.

We introduce MURA, a large dataset of musculoskeletal radiographs containing 40,561 images from 14,863 studies, where each study is manually labeled by radiologists as either normal or abnormal. To evaluate models robustly and to get an estimate of radiologist performance, we collect additional labels from six board-certified Stanford radiologists on the test set, consisting of 207 musculoskeletal studies. On this test set, the majority vote of a group of three radiologists serves as gold standard. We train a 169-layer DenseNet baseline model to detect and localize abnormalities. Our model achieves an AUROC of 0.929, with an operating point of 0.815 sensitivity and 0.887 specificity. We compare our model and radiologists on the Cohen's kappa statistic, which expresses the agreement of our model and of each radiologist with the gold standard. Model performance is comparable to the best radiologist performance in detecting abnormalities on finger and wrist studies. However, model performance is lower than best radiologist performance in detecting abnormalities on elbow, forearm, hand, humerus, and shoulder studies. We believe that the task is a good challenge for future research. To encourage advances, we have made our dataset freely available at https://stanfordmlgroup.github.io/competitions/mura .

Measurements of Higgs boson production cross-sections are carried out in the diphoton decay channel using 139 fb^{-1} of pp collision data at s = 13 TeV collected by the ATLAS experiment at the LHC. The analysis is based on the definition of 101 distinct signal regions using machine-learning techniques. The inclusive Higgs boson signal strength in the diphoton channel is measured to be 1.04^{+0.10}_{-0.09}. Cross-sections for gluon-gluon fusion, vector-boson fusion, associated production with a W or Z boson, and top associated production processes are reported. An upper limit of 10 times the Standard Model prediction is set for the associated production process of a Higgs boson with a single top quark, which has a unique sensitivity to the sign of the top quark Yukawa coupling. Higgs boson production is further characterized through measurements of Simplified Template Cross-Sections (STXS). In total, cross-sections of 28 STXS regions are measured. The measured STXS cross-sections are compatible with their Standard Model predictions, with a p-value of 93%. The measurements are also used to set constraints on Higgs boson coupling strengths, as well as on new interactions beyond the Standard Model in an effective field theory approach. No significant deviations from the Standard Model predictions are observed in these measurements, which provide significant sensitivity improvements compared to the previous ATLAS results.

Pre-trained on a large and diverse dataset, the segment anything model (SAM) is the first promptable foundation model in computer vision aiming at object segmentation tasks. In this work, we evaluate SAM for the task of nuclear instance segmentation performance with zero-shot learning and finetuning. We compare SAM with other representative methods in nuclear instance segmentation, especially in the context of model generalisability. To achieve automatic nuclear instance segmentation, we propose using a nuclei detection model to provide bounding boxes or central points of nu-clei as visual prompts for SAM in generating nuclear instance masks from histology images.

Expert interpretation of anatomical images of the human brain is the central part of neuro-radiology. Several machine learning-based techniques have been proposed to assist in the analysis process. However, the ML models typically need to be trained to perform a specific task, e.g., brain tumour segmentation or classification. Not only do the corresponding training data require laborious manual annotations, but a wide variety of abnormalities can be present in a human brain MRI - even more than one simultaneously, which renders representation of all possible anomalies very challenging. Hence, a possible solution is an unsupervised anomaly detection (UAD) system that can learn a data distribution from an unlabelled dataset of healthy subjects and then be applied to detect out of distribution samples. Such a technique can then be used to detect anomalies - lesions or abnormalities, for example, brain tumours, without explicitly training the model for that specific pathology. Several Variational Autoencoder (VAE) based techniques have been proposed in the past for this task. Even though they perform very well on controlled artificially simulated anomalies, many of them perform poorly while detecting anomalies in clinical data. This research proposes a compact version of the "context-encoding" VAE (ceVAE) model, combined with pre and post-processing steps, creating a UAD pipeline (StRegA), which is more robust on clinical data, and shows its applicability in detecting anomalies such as tumours in brain MRIs. The proposed pipeline achieved a Dice score of 0.642pm0.101 while detecting tumours in T2w images of the BraTS dataset and 0.859pm0.112 while detecting artificially induced anomalies, while the best performing baseline achieved 0.522pm0.135 and 0.783pm0.111, respectively.

Large language models (LLMs) have demonstrated impressive generalization and emergent capabilities, yet their pre-training remains computationally expensive and sensitive to optimization dynamics. While Adam-based optimizers offer fast convergence by adapting learning rates coordinate-wise, recent studies reveal that their updates often suffer from poor spectral conditioning and low-rank structures, hindering efficiency. Muon addresses this issue via global spectral normalization but lacks the per-coordinate adaptivity of Adam. In this work, we propose Column-Normalized Adam (Conda), a novel optimizer that bridges the strengths of both approaches. Conda projects updates into an orthogonal subspace and applies column-wise second moment normalization based on the projected gradients, thereby achieving both improved spectral conditioning and maintaining coordinate-wise adaptivity. This design alleviates the spectral pathologies of Adam while preserving its fast convergence behavior. Extensive experiments on the LLaMA and GPT-2 series show that Conda consistently outperforms AdamW, Muon, and other baselines in pre-training. Remarkably, on the LLaMA series, Conda achieves 2-2.5 the convergence speed of AdamW, measured in both training steps and training time. Further ablations demonstrate its robustness under diverse training setups. These results collectively highlight Conda as an effective and broadly applicable optimizer for large-scale LLM training. The code is released on https://github.com/jie040109/Conda

Multimodal MRI provides critical complementary information for accurate brain tumor segmentation. However, conventional methods struggle when certain modalities are missing due to issues such as image quality, protocol inconsistencies, patient allergies, or financial constraints. To address this, we propose a robust single-modality parallel processing framework that achieves high segmentation accuracy even with incomplete modalities. Leveraging Holder divergence and mutual information, our model maintains modality-specific features while dynamically adjusting network parameters based on the available inputs. By using these divergence- and information-based loss functions, the framework effectively quantifies discrepancies between predictions and ground-truth labels, resulting in consistently accurate segmentation. Extensive evaluations on the BraTS 2018 and BraTS 2020 datasets demonstrate superior performance over existing methods in handling missing modalities.

Autoencoders have been proposed as a powerful tool for model-independent anomaly detection in high-energy physics. The operating principle is that events which do not belong to the space of training data will be reconstructed poorly, thus flagging them as anomalies. We point out that in a variety of examples of interest, the connection between large reconstruction error and anomalies is not so clear. In particular, for data sets with nontrivial topology, there will always be points that erroneously seem anomalous due to global issues. Conversely, neural networks typically have an inductive bias or prior to locally interpolate such that undersampled or rare events may be reconstructed with small error, despite actually being the desired anomalies. Taken together, these facts are in tension with the simple picture of the autoencoder as an anomaly detector. Using a series of illustrative low-dimensional examples, we show explicitly how the intrinsic and extrinsic topology of the dataset affects the behavior of an autoencoder and how this topology is manifested in the latent space representation during training. We ground this analysis in the discussion of a mock "bump hunt" in which the autoencoder fails to identify an anomalous "signal" for reasons tied to the intrinsic topology of n-particle phase space.

Unsupervised anomaly detection (UAD) aims to find anomalous images by optimising a detector using a training set that contains only normal images. UAD approaches can be based on reconstruction methods, self-supervised approaches, and Imagenet pre-trained models. Reconstruction methods, which detect anomalies from image reconstruction errors, are advantageous because they do not rely on the design of problem-specific pretext tasks needed by self-supervised approaches, and on the unreliable translation of models pre-trained from non-medical datasets. However, reconstruction methods may fail because they can have low reconstruction errors even for anomalous images. In this paper, we introduce a new reconstruction-based UAD approach that addresses this low-reconstruction error issue for anomalous images. Our UAD approach, the memory-augmented multi-level cross-attentional masked autoencoder (MemMC-MAE), is a transformer-based approach, consisting of a novel memory-augmented self-attention operator for the encoder and a new multi-level cross-attention operator for the decoder. MemMCMAE masks large parts of the input image during its reconstruction, reducing the risk that it will produce low reconstruction errors because anomalies are likely to be masked and cannot be reconstructed. However, when the anomaly is not masked, then the normal patterns stored in the encoder's memory combined with the decoder's multi-level cross attention will constrain the accurate reconstruction of the anomaly. We show that our method achieves SOTA anomaly detection and localisation on colonoscopy, pneumonia, and covid-19 chest x-ray datasets.

Computed tomography (CT) serves as an effective tool for lung cancer screening, diagnosis, treatment, and prognosis, providing a rich source of features to quantify temporal and spatial tumor changes. Nonetheless, the diversity of CT scanners and customized acquisition protocols can introduce significant inconsistencies in texture features, even when assessing the same patient. This variability poses a fundamental challenge for subsequent research that relies on consistent image features. Existing CT image standardization models predominantly utilize GAN-based supervised or semi-supervised learning, but their performance remains limited. We present DiffusionCT, an innovative score-based DDPM model that operates in the latent space to transform disparate non-standard distributions into a standardized form. The architecture comprises a U-Net-based encoder-decoder, augmented by a DDPM model integrated at the bottleneck position. First, the encoder-decoder is trained independently, without embedding DDPM, to capture the latent representation of the input data. Second, the latent DDPM model is trained while keeping the encoder-decoder parameters fixed. Finally, the decoder uses the transformed latent representation to generate a standardized CT image, providing a more consistent basis for downstream analysis. Empirical tests on patient CT images indicate notable improvements in image standardization using DiffusionCT. Additionally, the model significantly reduces image noise in SPAD images, further validating the effectiveness of DiffusionCT for advanced imaging tasks.

Most existing learning-based methods for solving imaging inverse problems can be roughly divided into two classes: iterative algorithms, such as plug-and-play and diffusion methods, that leverage pretrained denoisers, and unrolled architectures that are trained end-to-end for specific imaging problems. Iterative methods in the first class are computationally costly and often provide suboptimal reconstruction performance, whereas unrolled architectures are generally specific to a single inverse problem and require expensive training. In this work, we propose a novel non-iterative, lightweight architecture that incorporates knowledge about the forward operator (acquisition physics and noise parameters) without relying on unrolling. Our model is trained to solve a wide range of inverse problems beyond denoising, including deblurring, magnetic resonance imaging, computed tomography, inpainting, and super-resolution. The proposed model can be easily adapted to unseen inverse problems or datasets with a few fine-tuning steps (up to a few images) in a self-supervised way, without ground-truth references. Throughout a series of experiments, we demonstrate state-of-the-art performance from medical imaging to low-photon imaging and microscopy.

Vision-language models can connect the text description of an object to its specific location in an image through visual grounding. This has potential applications in enhanced radiology reporting. However, these models require large annotated image-text datasets, which are lacking for PET/CT. We developed an automated pipeline to generate weak labels linking PET/CT report descriptions to their image locations and used it to train a 3D vision-language visual grounding model. Our pipeline finds positive findings in PET/CT reports by identifying mentions of SUVmax and axial slice numbers. From 25,578 PET/CT exams, we extracted 11,356 sentence-label pairs. Using this data, we trained ConTEXTual Net 3D, which integrates text embeddings from a large language model with a 3D nnU-Net via token-level cross-attention. The model's performance was compared against LLMSeg, a 2.5D version of ConTEXTual Net, and two nuclear medicine physicians. The weak-labeling pipeline accurately identified lesion locations in 98% of cases (246/251), with 7.5% requiring boundary adjustments. ConTEXTual Net 3D achieved an F1 score of 0.80, outperforming LLMSeg (F1=0.22) and the 2.5D model (F1=0.53), though it underperformed both physicians (F1=0.94 and 0.91). The model achieved better performance on FDG (F1=0.78) and DCFPyL (F1=0.75) exams, while performance dropped on DOTATE (F1=0.58) and Fluciclovine (F1=0.66). The model performed consistently across lesion sizes but showed reduced accuracy on lesions with low uptake. Our novel weak labeling pipeline accurately produced an annotated dataset of PET/CT image-text pairs, facilitating the development of 3D visual grounding models. ConTEXTual Net 3D significantly outperformed other models but fell short of the performance of nuclear medicine physicians. Our study suggests that even larger datasets may be needed to close this performance gap.

Compressed Sensing MRI reconstructs images of the body's internal anatomy from undersampled measurements, thereby reducing scan time. Recently, deep learning has shown great potential for reconstructing high-fidelity images from highly undersampled measurements. However, one needs to train multiple models for different undersampling patterns and desired output image resolutions, since most networks operate on a fixed discretization. Such approaches are highly impractical in clinical settings, where undersampling patterns and image resolutions are frequently changed to accommodate different real-time imaging and diagnostic requirements. We propose a unified MRI reconstruction model robust to various measurement undersampling patterns and image resolutions. Our approach uses neural operators, a discretization-agnostic architecture applied in both image and measurement spaces, to capture local and global features. Empirically, our model improves SSIM by 11% and PSNR by 4 dB over a state-of-the-art CNN (End-to-End VarNet), with 600times faster inference than diffusion methods. The resolution-agnostic design also enables zero-shot super-resolution and extended field-of-view reconstruction, offering a versatile and efficient solution for clinical MR imaging. Our unified model offers a versatile solution for MRI, adapting seamlessly to various measurement undersampling and imaging resolutions, making it highly effective for flexible and reliable clinical imaging. Our code is available at https://armeet.ca/nomri.

Computed Tomography (CT) is one of the most popular modalities for medical imaging. By far, CT images have contributed to the largest publicly available datasets for volumetric medical segmentation tasks, covering full-body anatomical structures. Large amounts of full-body CT images provide the opportunity to pre-train powerful models, e.g., STU-Net pre-trained in a supervised fashion, to segment numerous anatomical structures. However, it remains unclear in which conditions these pre-trained models can be transferred to various downstream medical segmentation tasks, particularly segmenting the other modalities and diverse targets. To address this problem, a large-scale benchmark for comprehensive evaluation is crucial for finding these conditions. Thus, we collected 87 public datasets varying in modality, target, and sample size to evaluate the transfer ability of full-body CT pre-trained models. We then employed a representative model, STU-Net with multiple model scales, to conduct transfer learning across modalities and targets. Our experimental results show that (1) there may be a bottleneck effect concerning the dataset size in fine-tuning, with more improvement on both small- and large-scale datasets than medium-size ones. (2) Models pre-trained on full-body CT demonstrate effective modality transfer, adapting well to other modalities such as MRI. (3) Pre-training on the full-body CT not only supports strong performance in structure detection but also shows efficacy in lesion detection, showcasing adaptability across target tasks. We hope that this large-scale open evaluation of transfer learning can direct future research in volumetric medical image segmentation.