Daily Papers

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.

Magnetic resonance imaging (MRI) is the standard modality to understand human brain structure and function in vivo (antemortem). Decades of research in human neuroimaging has led to the widespread development of methods and tools to provide automated volume-based segmentations and surface-based parcellations which help localize brain functions to specialized anatomical regions. Recently ex vivo (postmortem) imaging of the brain has opened-up avenues to study brain structure at sub-millimeter ultra high-resolution revealing details not possible to observe with in vivo MRI. Unfortunately, there has been limited methodological development in ex vivo MRI primarily due to lack of datasets and limited centers with such imaging resources. Therefore, in this work, we present one-of-its-kind dataset of 82 ex vivo T2w whole brain hemispheres MRI at 0.3 mm isotropic resolution spanning Alzheimer's disease and related dementias. We adapted and developed a fast and easy-to-use automated surface-based pipeline to parcellate, for the first time, ultra high-resolution ex vivo brain tissue at the native subject space resolution using the Desikan-Killiany-Tourville (DKT) brain atlas. This allows us to perform vertex-wise analysis in the template space and thereby link morphometry measures with pathology measurements derived from histology. We will open-source our dataset docker container, Jupyter notebooks for ready-to-use out-of-the-box set of tools and command line options to advance ex vivo MRI clinical brain imaging research on the project webpage.

Cell migration in vivo is often guided by chemical signals. Such chemotaxis, such as performed by immune cells migrating to a wound site, is complicated by the complex geometry inside living tissues. In this study, we extend our theoretical model of branched-cell migration on a network by introducing chemokine sources to explore the cellular response. The model predicts a speed-accuracy tradeoff, whereby slow cells are significantly more accurate and able to follow efficiently a weak chemoattractant signal. We then compare the model's predictions with experimental observations of neutrophils migrating to the site of laser-inflicted wound in a zebrafish larva fin, and migrating in-vitro inside a regular lattice of pillars. We find that the model captures the details of the sub-cellular response to the chemokine gradient, as well as the large-scale migration response. This comparison suggests that the neutrophils behave as fast cells, compromising their chemotaxis accuracy, which explains the functionality of these immune cells.

Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, current molecular representation learning methods do not provide a comprehensive view of cell states under these perturbations and struggle to remove noise, hindering model generalization. We introduce the Information Alignment (InfoAlign) approach to learn molecular representations through the information bottleneck method in cells. We integrate molecules and cellular response data as nodes into a context graph, connecting them with weighted edges based on chemical, biological, and computational criteria. For each molecule in a training batch, InfoAlign optimizes the encoder's latent representation with a minimality objective to discard redundant structural information. A sufficiency objective decodes the representation to align with different feature spaces from the molecule's neighborhood in the context graph. We demonstrate that the proposed sufficiency objective for alignment is tighter than existing encoder-based contrastive methods. Empirically, we validate representations from InfoAlign in two downstream tasks: molecular property prediction against up to 19 baseline methods across four datasets, plus zero-shot molecule-morphology matching.

Large language models (LLMs) have revolutionised many fields, with LLM-as-a-service (LLMSaaS) offering accessible, general-purpose solutions without costly task-specific training. In contrast to the widely studied prompt engineering for directly solving tasks (in vivo), this paper explores LLMs' potential for in-vitro applications: using LLM-generated labels to improve supervised training of mainstream models. We examine two strategies - (1) noisy label correction and (2) training data augmentation - in empathy computing, an emerging task to predict psychology-based questionnaire outcomes from inputs like textual narratives. Crowdsourced datasets in this domain often suffer from noisy labels that misrepresent underlying empathy. We show that replacing or supplementing these crowdsourced labels with LLM-generated labels, developed using psychology-based scale-aware prompts, achieves statistically significant accuracy improvements. Notably, the RoBERTa pre-trained language model (PLM) trained with noise-reduced labels yields a state-of-the-art Pearson correlation coefficient of 0.648 on the public NewsEmp benchmarks. This paper further analyses evaluation metric selection and demographic biases to help guide the future development of more equitable empathy computing models. Code and LLM-generated labels are available at https://github.com/hasan-rakibul/LLMPathy.

Segmentation of blood vessels in murine cerebral 3D OCTA images is foundational for in vivo quantitative analysis of the effects of neurovascular disorders, such as stroke or Alzheimer's, on the vascular network. However, to accurately segment blood vessels with state-of-the-art deep learning methods, a vast amount of voxel-level annotations is required. Since cerebral 3D OCTA images are typically plagued by artifacts and generally have a low signal-to-noise ratio, acquiring manual annotations poses an especially cumbersome and time-consuming task. To alleviate the need for manual annotations, we propose utilizing synthetic data to supervise segmentation algorithms. To this end, we extract patches from vessel graphs and transform them into synthetic cerebral 3D OCTA images paired with their matching ground truth labels by simulating the most dominant 3D OCTA artifacts. In extensive experiments, we demonstrate that our approach achieves competitive results, enabling annotation-free blood vessel segmentation in cerebral 3D OCTA images.

Artificially synthesized Janus particles have tremendous prospective as in-vivo drug-delivery agents due to the possibility of self-propulsion by external stimuli. Here we report the first ever computational study of translational and rotational motion of self-propelled Janus tracers in a het- erogeneous polymeric environment. The presence of polymers makes the translational mean square displacement (MSD) of the Janus tracer to grow very slowly as compared to that of a free Janus tracer, but surprisingly the mean square angular displacement (MSAD) is significantly increased as observed in a recent experiment. Moreover, with the increasing propulsion velocity, MSAD grows even faster. However, when the repulsive polymers are replaced with polymers with sticky zones, MSD and MSAD both show sharp decline.

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.

This study explores cardiovascular stents fabricated using laser powder bed fusion (LPBF); an emerging method to offer patient-specific customisable parts. Here, the shape memory alloy NiTi, in a near equiatomic composition, was investigated to deconvolve the material response from macroscopic component effects. Specifically, stress-geometry interactions were revealed, in-situ, for a minaturised cardiovascular stent subjected to an externally applied cylindrical stress whilst acquiring synchrotron X-ray imaging and diffraction data. The approach enabled the collection of spatially resolved micromechanical deformation data; the formation of stress-induced martensite and R-phase was evident, occurring in locations near junctions between stent ligaments where stress concentrations exist. In the as-fabricated condition, hardness maps were obtained through nanoindentation, demonstrating that the localised deformation and deformation patterning is further controlled by porosity and microstructural heterogeneity. Electron backscatter diffraction (EBSD) supported these observations, showing a finer grain structure near stent junctions with higher associated lattice curvature. These features, combined with stress concentrations when loaded will initiate localised phase transformations. If the stent was subjected to repeated loading, representing in-vivo conditions, these regions would be susceptible to cyclic damage through transformation memory loss, leading to premature component failure. This study highlights the challenges that must be addressed for the post-processing treatment of LABF-processed stents for healthcare-related applications.

Limitations on bandwidth and power consumption impose strict bounds on data rates of diagnostic imaging systems. Consequently, the design of suitable (i.e. task- and data-aware) compression and reconstruction techniques has attracted considerable attention in recent years. Compressed sensing emerged as a popular framework for sparse signal reconstruction from a small set of compressed measurements. However, typical compressed sensing designs measure a (non)linearly weighted combination of all input signal elements, which poses practical challenges. These designs are also not necessarily task-optimal. In addition, real-time recovery is hampered by the iterative and time-consuming nature of sparse recovery algorithms. Recently, deep learning methods have shown promise for fast recovery from compressed measurements, but the design of adequate and practical sensing strategies remains a challenge. Here, we propose a deep learning solution termed Deep Probabilistic Sub-sampling (DPS), that learns a task-driven sub-sampling pattern, while jointly training a subsequent task model. Once learned, the task-based sub-sampling patterns are fixed and straightforwardly implementable, e.g. by non-uniform analog-to-digital conversion, sparse array design, or slow-time ultrasound pulsing schemes. The effectiveness of our framework is demonstrated in-silico for sparse signal recovery from partial Fourier measurements, and in-vivo for both anatomical image and tissue-motion (Doppler) reconstruction from sub-sampled medical ultrasound imaging data.

The in-vivo identification of the kidney stone types during an ureteroscopy would be a major medical advance in urology, as it could reduce the time of the tedious renal calculi extraction process, while diminishing infection risks. Furthermore, such an automated procedure would make possible to prescribe anti-recurrence treatments immediately. Nowadays, only few experienced urologists are able to recognize the kidney stone types in the images of the videos displayed on a screen during the endoscopy. Thus, several deep learning (DL) models have recently been proposed to automatically recognize the kidney stone types using ureteroscopic images. However, these DL models are of black box nature whicl limits their applicability in clinical settings. This contribution proposes a case-based reasoning DL model which uses prototypical parts (PPs) and generates local and global descriptors. The PPs encode for each class (i.e., kidney stone type) visual feature information (hue, saturation, intensity and textures) similar to that used by biologists. The PPs are optimally generated due a new loss function used during the model training. Moreover, the local and global descriptors of PPs allow to explain the decisions ("what" information, "where in the images") in an understandable way for biologists and urologists. The proposed DL model has been tested on a database including images of the six most widespread kidney stone types. The overall average classification accuracy was 90.37. When comparing this results with that of the eight other DL models of the kidney stone state-of-the-art, it can be seen that the valuable gain in explanability was not reached at the expense of accuracy which was even slightly increased with respect to that (88.2) of the best method of the literature. These promising and interpretable results also encourage urologists to put their trust in AI-based solutions.

Biological tissues exhibit complex behaviors with their dynamics often resembling inert soft matter such as liquids, polymers, colloids, and liquid crystals. These analogies enable physics-based approaches for investigations of emergent behaviors in biological processes. A well-studied case is the spreading of cellular aggregates on solid surfaces, where they display dynamics similar to viscous droplets. In vivo, however, cells and tissues are in a confined environment with varying geometries and mechanical properties to which they need to adapt. In this work, we compressed cellular aggregates between two solid surfaces and studied their dynamics using microscopy, and computer simulations. The confined cellular aggregates transitioned from compressed spheres into dynamic living capillary bridges exhibiting bridge thinning and a convex-to-concave meniscus curvature transition. We found that the stability of the bridge is determined by the interplay between cell growth and cell spreading on the confining surfaces. This interaction leads to bridge rupture at a critical length scale determined by the distance between the plates. The force distributions, formation and stability regimes of the living capillary bridges were characterized with full 3D computer simulations that included cell division, migration and growth dynamics, directly showing how mechanical principles govern the behavior of the living bridges; cellular aggregates display jamming and stiffening analogously to granular matter, and cell division along the long axis enhances thinning. Based on our results, we propose a new class of active soft matter behavior, where cellular aggregates exhibit liquid-like adaptation to confinement, but with self-organized rupturing driven by biological activity.

In Ultrasound Localization Microscopy (ULM),achieving high-resolution images relies on the precise localization of contrast agent particles across consecutive beam-formed frames. However, our study uncovers an enormous potential: The process of delay-and-sum beamforming leads to an irreversible reduction of Radio-Frequency (RF) data, while its implications for localization remain largely unexplored. The rich contextual information embedded within RF wavefronts, including their hyperbolic shape and phase, offers great promise for guiding Deep Neural Networks (DNNs) in challenging localization scenarios. To fully exploit this data, we propose to directly localize scatterers in RF signals. Our approach involves a custom super-resolution DNN using learned feature channel shuffling and a novel semi-global convolutional sampling block tailored for reliable and accurate wavefront localization. Additionally, we introduce a geometric point transformation that facilitates seamless mapping between RF and B-mode coordinate space. To understand the impact of beamforming on ULM, we validate the effectiveness of our method by conducting an extensive comparison with State-Of-The-Art (SOTA) techniques. We present the inaugural in vivo results from an RF-trained DNN, highlighting its real-world practicality. Our findings show that RF-ULM bridges the domain gap between synthetic and real datasets, offering a considerable advantage in terms of precision and complexity. To enable the broader research community to benefit from our findings, our code and the associated SOTA methods are made available at https://github.com/hahnec/rf-ulm.

This study presents a deep convolutional autoencoder network for filtering reverberation clutter from transthoracic echocardiographic (TTE) image sequences. Given the spatiotemporal nature of this type of clutter, the filtering network employs 3D convolutional layers to suppress it throughout the cardiac cycle. The design of the network incorporates two key features that contribute to the effectiveness of the filter: 1) an attention mechanism for focusing on cluttered regions and leveraging contextual information, and 2) residual learning for preserving fine image structures. To train the network, a diverse set of artifact patterns was simulated and superimposed onto ultra-realistic synthetic TTE sequences from six ultrasound vendors, generating input for the filtering network. The artifact-free sequences served as ground-truth. Performance of the filtering network was evaluated using unseen synthetic and in vivo artifactual sequences. Results from the in vivo dataset confirmed the network's strong generalization capabilities, despite being trained solely on synthetic data and simulated artifacts. The suitability of the filtered sequences for downstream processing was assessed by computing segmental strain curves. A significant reduction in the discrepancy between strain profiles computed from cluttered and clutter-free segments was observed after filtering the cluttered sequences with the proposed network. The trained network processes a TTE sequence in a fraction of a second, enabling real-time clutter filtering and potentially improving the precision of clinically relevant indices derived from TTE sequences. The source code of the proposed method and example video files of the filtering results are available at: https://github.com/MahdiTabassian/Deep-Clutter-Filtering/tree/main{https://github.com/MahdiTabassian/Deep-Clutter-Filtering/tree/main}.

Many natural dynamic processes -- such as in vivo cellular differentiation or disease progression -- can only be observed through the lens of static sample snapshots. While challenging, reconstructing their temporal evolution to decipher underlying dynamic properties is of major interest to scientific research. Existing approaches enable data transport along a temporal axis but are poorly scalable in high dimension and require restrictive assumptions to be met. To address these issues, we propose \textbf{Multi-Marginal temporal Schr\"odinger Bridge Matching} (MMtSBM) for video generation from unpaired data, extending the theoretical guarantees and empirical efficiency of Diffusion Schr\"odinger Bridge Matching (arXiv:archive/2303.16852) by deriving the Iterative Markovian Fitting algorithm to multiple marginals in a novel factorized fashion. Experiments show that MMtSBM retains theoretical properties on toy examples, achieves state-of-the-art performance on real world datasets such as transcriptomic trajectory inference in 100 dimensions, and for the first time recovers couplings and dynamics in very high dimensional image settings. Our work establishes multi-marginal Schr\"odinger bridges as a practical and principled approach for recovering hidden dynamics from static data.

Echocardiography has been a prominent tool for the diagnosis of cardiac disease. However, these diagnoses can be heavily impeded by poor image quality. Acoustic clutter emerges due to multipath reflections imposed by layers of skin, subcutaneous fat, and intercostal muscle between the transducer and heart. As a result, haze and other noise artifacts pose a real challenge to cardiac ultrasound imaging. In many cases, especially with difficult-to-image patients such as patients with obesity, a diagnosis from B-Mode ultrasound imaging is effectively rendered unusable, forcing sonographers to resort to contrast-enhanced ultrasound examinations or refer patients to other imaging modalities. Tissue harmonic imaging has been a popular approach to combat haze, but in severe cases is still heavily impacted by haze. Alternatively, denoising algorithms are typically unable to remove highly structured and correlated noise, such as haze. It remains a challenge to accurately describe the statistical properties of structured haze, and develop an inference method to subsequently remove it. Diffusion models have emerged as powerful generative models and have shown their effectiveness in a variety of inverse problems. In this work, we present a joint posterior sampling framework that combines two separate diffusion models to model the distribution of both clean ultrasound and haze in an unsupervised manner. Furthermore, we demonstrate techniques for effectively training diffusion models on radio-frequency ultrasound data and highlight the advantages over image data. Experiments on both in-vitro and in-vivo cardiac datasets show that the proposed dehazing method effectively removes haze while preserving signals from weakly reflected tissue.

Magnetic resonance imaging (MRI) is a common and life-saving medical imaging technique. However, acquiring high signal-to-noise ratio MRI scans requires long scan times, resulting in increased costs and patient discomfort, and decreased throughput. Thus, there is great interest in denoising MRI scans, especially for the subtype of diffusion MRI scans that are severely SNR-limited. While most prior MRI denoising methods are supervised in nature, acquiring supervised training datasets for the multitude of anatomies, MRI scanners, and scan parameters proves impractical. Here, we propose Denoising Diffusion Models for Denoising Diffusion MRI (DDM^2), a self-supervised denoising method for MRI denoising using diffusion denoising generative models. Our three-stage framework integrates statistic-based denoising theory into diffusion models and performs denoising through conditional generation. During inference, we represent input noisy measurements as a sample from an intermediate posterior distribution within the diffusion Markov chain. We conduct experiments on 4 real-world in-vivo diffusion MRI datasets and show that our DDM^2 demonstrates superior denoising performances ascertained with clinically-relevant visual qualitative and quantitative metrics.

The diffusion MRI Neurite Exchange Imaging model offers a promising framework for probing gray matter microstructure by estimating parameters such as compartment sizes, diffusivities, and inter-compartmental water exchange time. However, existing protocols require long scan times. This study proposes a reduced acquisition scheme for the Connectome 2.0 scanner that preserves model accuracy while substantially shortening scan duration. We developed a data-driven framework using explainable artificial intelligence with a guided recursive feature elimination strategy to identify an optimal 8-feature subset from a 15-feature protocol. The performance of this optimized protocol was validated in vivo and benchmarked against the full acquisition and alternative reduction strategies. Parameter accuracy, preservation of anatomical contrast, and test-retest reproducibility were assessed. The reduced protocol yielded parameter estimates and cortical maps comparable to the full protocol, with low estimation errors in synthetic data and minimal impact on test-retest variability. Compared to theory-driven and heuristic reduction schemes, the optimized protocol demonstrated superior robustness, reducing the deviation in water exchange time estimates by over two-fold. In conclusion, this hybrid optimization framework enables viable imaging of neurite exchange in 14 minutes without loss of parameter fidelity. This approach supports the broader application of exchange-sensitive diffusion magnetic resonance imaging in neuroscience and clinical research, and offers a generalizable method for designing efficient acquisition protocols in biophysical parameter mapping.

Fluorescence Lifetime Imaging (FLI) is a critical molecular imaging modality that provides unique information about the tissue microenvironment, which is invaluable for biomedical applications. FLI operates by acquiring and analyzing photon time-of-arrival histograms to extract quantitative parameters associated with temporal fluorescence decay. These histograms are influenced by the intrinsic properties of the fluorophore, instrument parameters, time-of-flight distributions associated with pixel-wise variations in the topographic and optical characteristics of the sample. Recent advancements in Deep Learning (DL) have enabled improved fluorescence lifetime parameter estimation. However, existing models are primarily designed for planar surface samples, limiting their applicability in translational scenarios involving complex surface profiles, such as in-vivo whole-animal or imaged guided surgical applications. To address this limitation, we present MFliNet (Macroscopic FLI Network), a novel DL architecture that integrates the Instrument Response Function (IRF) as an additional input alongside experimental photon time-of-arrival histograms. Leveraging the capabilities of a Differential Transformer encoder-decoder architecture, MFliNet effectively focuses on critical input features, such as variations in photon time-of-arrival distributions. We evaluate MFliNet using rigorously designed tissue-mimicking phantoms and preclinical in-vivo cancer xenograft models. Our results demonstrate the model's robustness and suitability for complex macroscopic FLI applications, offering new opportunities for advanced biomedical imaging in diverse and challenging settings.

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein-ligand docking have recently been introduced, to date no prior works have systematically studied the behavior of the latest docking and structure prediction methods within the broadly applicable context of (1) using predicted (apo) protein structures for docking (e.g., for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (e.g., for enzyme design); and (3) having no prior knowledge of binding pockets (e.g., for generalization to unknown pockets). To enable a deeper understanding of docking methods' real-world utility, we introduce PoseBench, the first comprehensive benchmark for broadly applicable protein-ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein-ligand docking and protein-ligand structure prediction using both primary ligand and multi-ligand benchmark datasets, the latter of which we introduce for the first time to the DL community. Empirically, using PoseBench, we find that (1) DL co-folding methods generally outperform comparable conventional and DL docking baselines, yet popular methods such as AlphaFold 3 are still challenged by prediction targets with novel protein sequences; (2) certain DL co-folding methods are highly sensitive to their input multiple sequence alignments, while others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting novel or multi-ligand protein targets. Code, data, tutorials, and benchmark results are available at https://github.com/BioinfoMachineLearning/PoseBench.

Photoacoustic computed tomography (PACT) is a non-invasive imaging modality, similar to ultrasound, with wide-ranging medical applications. Conventional PACT images are degraded by wavefront distortion caused by the heterogeneous speed of sound (SOS) in tissue. Accounting for these effects can improve image quality and provide medically useful information, but measuring the SOS directly is burdensome and the existing joint reconstruction method is computationally expensive. Traditional supervised learning techniques are currently inaccessible in this data-starved domain. In this work, we introduce an efficient, self-supervised joint reconstruction method that recovers SOS and high-quality images for ring array PACT systems. To solve this semi-blind inverse problem, we parametrize the SOS using either a pixel grid or a neural field (NF) and update it directly by backpropagating the gradients through a differentiable imaging forward model. Our method removes SOS aberrations more accurately and 35x faster than the current SOTA. We demonstrate the success of our method quantitatively in simulation and qualitatively on experimentally-collected and in vivo data. Our code and synthetic numerical phantoms are available on our project page: https://lukeli0425.github.io/Coord-SoS-PACT/.

Diffusion Magnetic Resonance Imaging (dMRI) plays a crucial role in the noninvasive investigation of tissue microstructural properties and structural connectivity in the in vivo human brain. However, to effectively capture the intricate characteristics of water diffusion at various directions and scales, it is important to employ comprehensive q-space sampling. Unfortunately, this requirement leads to long scan times, limiting the clinical applicability of dMRI. To address this challenge, we propose SSOR, a Simultaneous q-Space sampling Optimization and Reconstruction framework. We jointly optimize a subset of q-space samples using a continuous representation of spherical harmonic functions and a reconstruction network. Additionally, we integrate the unique properties of diffusion magnetic resonance imaging (dMRI) in both the q-space and image domains by applying l1-norm and total-variation regularization. The experiments conducted on HCP data demonstrate that SSOR has promising strengths both quantitatively and qualitatively and exhibits robustness to noise.

Cancer is the second leading cause of death, with chemotherapy as one of the primary forms of treatment. As a result, researchers are turning to drug combination therapy to decrease drug resistance and increase efficacy. Current methods of drug combination screening, such as in vivo and in vitro, are inefficient due to stark time and monetary costs. In silico methods have become increasingly important for screening drugs, but current methods are inaccurate and generalize poorly to unseen anticancer drugs. In this paper, I employ a geometric deep-learning model utilizing a graph attention network that is equivariant to 3D rotations, translations, and reflections with structural motifs. Additionally, the gene expression of cancer cell lines is utilized to classify synergistic drug combinations specific to each cell line. I compared the proposed geometric deep learning framework to current state-of-the-art (SOTA) methods, and the proposed model architecture achieved greater performance on all 12 benchmark tasks performed on the DrugComb dataset. Specifically, the proposed framework outperformed other SOTA methods by an accuracy difference greater than 28%. Based on these results, I believe that the equivariant graph attention network's capability of learning geometric data accounts for the large performance improvements. The model's ability to generalize to foreign drugs is thought to be due to the structural motifs providing a better representation of the molecule. Overall, I believe that the proposed equivariant geometric deep learning framework serves as an effective tool for virtually screening anticancer drug combinations for further validation in a wet lab environment. The code for this work is made available online at: https://github.com/WeToTheMoon/EGAT_DrugSynergy.

Ultrasound Localization Microscopy (ULM) enables imaging of vascular structures in the micrometer range by accumulating contrast agent particle locations over time. Precise and efficient target localization accuracy remains an active research topic in the ULM field to further push the boundaries of this promising medical imaging technology. Existing work incorporates Delay-And-Sum (DAS) beamforming into particle localization pipelines, which ultimately determines the ULM image resolution capability. In this paper we propose to feed unprocessed Radio-Frequency (RF) data into a super-resolution network while bypassing DAS beamforming and its limitations. To facilitate this, we demonstrate label projection and inverse point transformation between B-mode and RF coordinate space as required by our approach. We assess our method against state-of-the-art techniques based on a public dataset featuring in silico and in vivo data. Results from our RF-trained network suggest that excluding DAS beamforming offers a great potential to optimize on the ULM resolution performance.

Training of neural networks for automated diagnosis of pigmented skin lesions is hampered by the small size and lack of diversity of available datasets of dermatoscopic images. We tackle this problem by releasing the HAM10000 ("Human Against Machine with 10000 training images") dataset. We collected dermatoscopic images from different populations acquired and stored by different modalities. Given this diversity we had to apply different acquisition and cleaning methods and developed semi-automatic workflows utilizing specifically trained neural networks. The final dataset consists of 10015 dermatoscopic images which are released as a training set for academic machine learning purposes and are publicly available through the ISIC archive. This benchmark dataset can be used for machine learning and for comparisons with human experts. Cases include a representative collection of all important diagnostic categories in the realm of pigmented lesions. More than 50% of lesions have been confirmed by pathology, while the ground truth for the rest of the cases was either follow-up, expert consensus, or confirmation by in-vivo confocal microscopy.

Research on autonomous surgery has largely focused on simple task automation in controlled environments. However, real-world surgical applications demand dexterous manipulation over extended durations and generalization to the inherent variability of human tissue. These challenges remain difficult to address using existing logic-based or conventional end-to-end learning approaches. To address this gap, we propose a hierarchical framework for performing dexterous, long-horizon surgical steps. Our approach utilizes a high-level policy for task planning and a low-level policy for generating robot trajectories. The high-level planner plans in language space, generating task-level or corrective instructions that guide the robot through the long-horizon steps and correct for the low-level policy's errors. We validate our framework through ex vivo experiments on cholecystectomy, a commonly-practiced minimally invasive procedure, and conduct ablation studies to evaluate key components of the system. Our method achieves a 100\% success rate across eight unseen ex vivo gallbladders, operating fully autonomously without human intervention. This work demonstrates step-level autonomy in a surgical procedure, marking a milestone toward clinical deployment of autonomous surgical systems.

Vision-language models have recently evolved into versatile systems capable of high performance across a range of tasks, such as document understanding, visual question answering, and grounding, often in zero-shot settings. Comics Understanding, a complex and multifaceted field, stands to greatly benefit from these advances. Comics, as a medium, combine rich visual and textual narratives, challenging AI models with tasks that span image classification, object detection, instance segmentation, and deeper narrative comprehension through sequential panels. However, the unique structure of comics -- characterized by creative variations in style, reading order, and non-linear storytelling -- presents a set of challenges distinct from those in other visual-language domains. In this survey, we present a comprehensive review of Comics Understanding from both dataset and task perspectives. Our contributions are fivefold: (1) We analyze the structure of the comics medium, detailing its distinctive compositional elements; (2) We survey the widely used datasets and tasks in comics research, emphasizing their role in advancing the field; (3) We introduce the Layer of Comics Understanding (LoCU) framework, a novel taxonomy that redefines vision-language tasks within comics and lays the foundation for future work; (4) We provide a detailed review and categorization of existing methods following the LoCU framework; (5) Finally, we highlight current research challenges and propose directions for future exploration, particularly in the context of vision-language models applied to comics. This survey is the first to propose a task-oriented framework for comics intelligence and aims to guide future research by addressing critical gaps in data availability and task definition. A project associated with this survey is available at https://github.com/emanuelevivoli/awesome-comics-understanding.

Tables are widely used in several types of documents since they can bring important information in a structured way. In scientific papers, tables can sum up novel discoveries and summarize experimental results, making the research comparable and easily understandable by scholars. Several methods perform table analysis working on document images, losing useful information during the conversion from the PDF files since OCR tools can be prone to recognition errors, in particular for text inside tables. The main contribution of this work is to tackle the problem of table extraction, exploiting Graph Neural Networks. Node features are enriched with suitably designed representation embeddings. These representations help to better distinguish not only tables from the other parts of the paper, but also table cells from table headers. We experimentally evaluated the proposed approach on a new dataset obtained by merging the information provided in the PubLayNet and PubTables-1M datasets.

This paper introduces CoSMo, a novel multimodal Transformer for Page Stream Segmentation (PSS) in comic books, a critical task for automated content understanding, as it is a necessary first stage for many downstream tasks like character analysis, story indexing, or metadata enrichment. We formalize PSS for this unique medium and curate a new 20,800-page annotated dataset. CoSMo, developed in vision-only and multimodal variants, consistently outperforms traditional baselines and significantly larger general-purpose vision-language models across F1-Macro, Panoptic Quality, and stream-level metrics. Our findings highlight the dominance of visual features for comic PSS macro-structure, yet demonstrate multimodal benefits in resolving challenging ambiguities. CoSMo establishes a new state-of-the-art, paving the way for scalable comic book analysis.

In this paper, we present a framework for Multilingual Scene Text Visual Question Answering that deals with new languages in a zero-shot fashion. Specifically, we consider the task of Scene Text Visual Question Answering (STVQA) in which the question can be asked in different languages and it is not necessarily aligned to the scene text language. Thus, we first introduce a natural step towards a more generalized version of STVQA: MUST-VQA. Accounting for this, we discuss two evaluation scenarios in the constrained setting, namely IID and zero-shot and we demonstrate that the models can perform on a par on a zero-shot setting. We further provide extensive experimentation and show the effectiveness of adapting multilingual language models into STVQA tasks.

The comic domain is rapidly advancing with the development of single- and multi-page analysis and synthesis models. Recent benchmarks and datasets have been introduced to support and assess models' capabilities in tasks such as detection (panels, characters, text), linking (character re-identification and speaker identification), and analysis of comic elements (e.g., dialog transcription). However, to provide a comprehensive understanding of the storyline, a model must not only extract elements but also understand their relationships and generate highly informative captions. In this work, we propose a pipeline that leverages Vision-Language Models (VLMs) to obtain dense, grounded captions. To construct our pipeline, we introduce an attribute-retaining metric that assesses whether all important attributes are identified in the caption. Additionally, we created a densely annotated test set to fairly evaluate open-source VLMs and select the best captioning model according to our metric. Our pipeline generates dense captions with bounding boxes that are quantitatively and qualitatively superior to those produced by specifically trained models, without requiring any additional training. Using this pipeline, we annotated over 2 million panels across 13,000 books, which will be available on the project page https://github.com/emanuelevivoli/ComiCap.

The detection and removal of landmines is a complex and risky task that requires advanced remote sensing techniques to reduce the risk for the professionals involved in this task. In this paper, we propose a novel synthetic dataset for buried landmine detection to provide researchers with a valuable resource to observe, measure, locate, and address issues in landmine detection. The dataset consists of 41,800 microwave holographic images (2D) and their holographic inverted scans (3D) of different types of buried objects, including landmines, clutter, and pottery objects, and is collected by means of a microwave holography sensor. We evaluate the performance of several state-of-the-art deep learning models trained on our synthetic dataset for various classification tasks. While the results do not yield yet high performances, showing the difficulty of the proposed task, we believe that our dataset has significant potential to drive progress in the field of landmine detection thanks to the accuracy and resolution obtainable using holographic radars. To the best of our knowledge, our dataset is the first of its kind and will help drive further research on computer vision methods to automatize mine detection, with the overall goal of reducing the risks and the costs of the demining process.

This work explores a closure task in comics, a medium where visual and textual elements are intricately intertwined. Specifically, Text-cloze refers to the task of selecting the correct text to use in a comic panel, given its neighboring panels. Traditional methods based on recurrent neural networks have struggled with this task due to limited OCR accuracy and inherent model limitations. We introduce a novel Multimodal Large Language Model (Multimodal-LLM) architecture, specifically designed for Text-cloze, achieving a 10% improvement over existing state-of-the-art models in both its easy and hard variants. Central to our approach is a Domain-Adapted ResNet-50 based visual encoder, fine-tuned to the comics domain in a self-supervised manner using SimCLR. This encoder delivers comparable results to more complex models with just one-fifth of the parameters. Additionally, we release new OCR annotations for this dataset, enhancing model input quality and resulting in another 1% improvement. Finally, we extend the task to a generative format, establishing new baselines and expanding the research possibilities in the field of comics analysis.

Comics, as a medium, uniquely combine text and images in styles often distinct from real-world visuals. For the past three decades, computational research on comics has evolved from basic object detection to more sophisticated tasks. However, the field faces persistent challenges such as small datasets, inconsistent annotations, inaccessible model weights, and results that cannot be directly compared due to varying train/test splits and metrics. To address these issues, we aim to standardize annotations across datasets, introduce a variety of comic styles into the datasets, and establish benchmark results with clear, replicable settings. Our proposed Comics Datasets Framework standardizes dataset annotations into a common format and addresses the overrepresentation of manga by introducing Comics100, a curated collection of 100 books from the Digital Comics Museum, annotated for detection in our uniform format. We have benchmarked a variety of detection architectures using the Comics Datasets Framework. All related code, model weights, and detailed evaluation processes are available at https://github.com/emanuelevivoli/cdf, ensuring transparency and facilitating replication. This initiative is a significant advancement towards improving object detection in comics, laying the groundwork for more complex computational tasks dependent on precise object recognition.

Large multimodal models (LMMs) have made impressive strides in image captioning, VQA, and video comprehension, yet they still struggle with the intricate temporal and spatial cues found in comics. To address this gap, we introduce ComicsPAP, a large-scale benchmark designed for comic strip understanding. Comprising over 100k samples and organized into 5 subtasks under a Pick-a-Panel framework, ComicsPAP demands models to identify the missing panel in a sequence. Our evaluations, conducted under both multi-image and single-image protocols, reveal that current state-of-the-art LMMs perform near chance on these tasks, underscoring significant limitations in capturing sequential and contextual dependencies. To close the gap, we adapted LMMs for comic strip understanding, obtaining better results on ComicsPAP than 10x bigger models, demonstrating that ComicsPAP offers a robust resource to drive future research in multimodal comic comprehension.

The comic domain is rapidly advancing with the development of single-page analysis and synthesis models. However, evaluation metrics and datasets lag behind, often limited to small-scale or single-style test sets. We introduce a novel benchmark, CoMix, designed to evaluate the multi-task capabilities of models in comic analysis. Unlike existing benchmarks that focus on isolated tasks such as object detection or text recognition, CoMix addresses a broader range of tasks including object detection, speaker identification, character re-identification, reading order, and multi-modal reasoning tasks like character naming and dialogue generation. Our benchmark comprises three existing datasets with expanded annotations to support multi-task evaluation. To mitigate the over-representation of manga-style data, we have incorporated a new dataset of carefully selected American comic-style books, thereby enriching the diversity of comic styles. CoMix is designed to assess pre-trained models in zero-shot and limited fine-tuning settings, probing their transfer capabilities across different comic styles and tasks. The validation split of the benchmark is publicly available for research purposes, and an evaluation server for the held-out test split is also provided. Comparative results between human performance and state-of-the-art models reveal a significant performance gap, highlighting substantial opportunities for advancements in comic understanding. The dataset, baseline models, and code are accessible at the repository link. This initiative sets a new standard for comprehensive comic analysis, providing the community with a common benchmark for evaluation on a large and varied set.

Relevant information in documents is often summarized in tables, helping the reader to identify useful facts. Most benchmark datasets support either document layout analysis or table understanding, but lack in providing data to apply both tasks in a unified way. We define the task of Contextualized Table Extraction (CTE), which aims to extract and define the structure of tables considering the textual context of the document. The dataset comprises 75k fully annotated pages of scientific papers, including more than 35k tables. Data are gathered from PubMed Central, merging the information provided by annotations in the PubTables-1M and PubLayNet datasets. The dataset can support CTE and adds new classes to the original ones. The generated annotations can be used to develop end-to-end pipelines for various tasks, including document layout analysis, table detection, structure recognition, and functional analysis. We formally define CTE and evaluation metrics, showing which subtasks can be tackled, describing advantages, limitations, and future works of this collection of data. Annotations and code will be accessible a https://github.com/AILab-UniFI/cte-dataset.

Hyperspectral pansharpening consists of fusing a high-resolution panchromatic band and a low-resolution hyperspectral image to obtain a new image with high resolution in both the spatial and spectral domains. These remote sensing products are valuable for a wide range of applications, driving ever growing research efforts. Nonetheless, results still do not meet application demands. In part, this comes from the technical complexity of the task: compared to multispectral pansharpening, many more bands are involved, in a spectral range only partially covered by the panchromatic component and with overwhelming noise. However, another major limiting factor is the absence of a comprehensive framework for the rapid development and accurate evaluation of new methods. This paper attempts to address this issue. We started by designing a dataset large and diverse enough to allow reliable training (for data-driven methods) and testing of new methods. Then, we selected a set of state-of-the-art methods, following different approaches, characterized by promising performance, and reimplemented them in a single PyTorch framework. Finally, we carried out a critical comparative analysis of all methods, using the most accredited quality indicators. The analysis highlights the main limitations of current solutions in terms of spectral/spatial quality and computational efficiency, and suggests promising research directions. To ensure full reproducibility of the results and support future research, the framework (including codes, evaluation procedures and links to the dataset) is shared on https://github.com/matciotola/hyperspectral_pansharpening_toolbox, as a single Python-based reference benchmark toolbox.

In this paper we study the out-of-equilibrium phase diagram of the quantum version of Derrida's Random Energy Model, which is the simplest model of mean-field spin glasses. We interpret its corresponding quantum dynamics in Fock space as a one-particle problem in very high dimension to which we apply different theoretical methods tailored for high-dimensional lattices: the Forward-Scattering Approximation, a mapping to the Rosenzweig-Porter model, and the cavity method. Our results indicate the existence of two transition lines and three distinct dynamical phases: a completely many-body localized phase at low energy, a fully ergodic phase at high energy, and a multifractal "bad metal" phase at intermediate energy. In the latter, eigenfunctions occupy a diverging volume, yet an exponentially vanishing fraction of the total Hilbert space. We discuss the limitations of our approximations and the relationship with previous studies.

Hyperspectral pansharpening is receiving a growing interest since the last few years as testified by a large number of research papers and challenges. It consists in a pixel-level fusion between a lower-resolution hyperspectral datacube and a higher-resolution single-band image, the panchromatic image, with the goal of providing a hyperspectral datacube at panchromatic resolution. Thanks to their powerful representational capabilities, deep learning models have succeeded to provide unprecedented results on many general purpose image processing tasks. However, when moving to domain specific problems, as in this case, the advantages with respect to traditional model-based approaches are much lesser clear-cut due to several contextual reasons. Scarcity of training data, lack of ground-truth, data shape variability, are some such factors that limit the generalization capacity of the state-of-the-art deep learning networks for hyperspectral pansharpening. To cope with these limitations, in this work we propose a new deep learning method which inherits a simple single-band unsupervised pansharpening model nested in a sequential band-wise adaptive scheme, where each band is pansharpened refining the model tuned on the preceding one. By doing so, a simple model is propagated along the wavelength dimension, adaptively and flexibly, with no need to have a fixed number of spectral bands, and, with no need to dispose of large, expensive and labeled training datasets. The proposed method achieves very good results on our datasets, outperforming both traditional and deep learning reference methods. The implementation of the proposed method can be found on https://github.com/giu-guarino/R-PNN

Hyperspectral pansharpening has received much attention in recent years due to technological and methodological advances that open the door to new application scenarios. However, research on this topic is only now gaining momentum. The most popular methods are still borrowed from the more mature field of multispectral pansharpening and often overlook the unique challenges posed by hyperspectral data fusion, such as i) the very large number of bands, ii) the overwhelming noise in selected spectral ranges, iii) the significant spectral mismatch between panchromatic and hyperspectral components, iv) a typically high resolution ratio. Imprecise data modeling especially affects spectral fidelity. Even state-of-the-art methods perform well in certain spectral ranges and much worse in others, failing to ensure consistent quality across all bands, with the risk of generating unreliable results. Here, we propose a hyperspectral pansharpening method that explicitly addresses this problem and ensures uniform spectral quality. To this end, a single lightweight neural network is used, with weights that adapt on the fly to each band. During fine-tuning, the spatial loss is turned on and off to ensure a fast convergence of the spectral loss to the desired level, according to a hysteresis-like dynamic. Furthermore, the spatial loss itself is appropriately redefined to account for nonlinear dependencies between panchromatic and spectral bands. Overall, the proposed method is fully unsupervised, with no prior training on external data, flexible, and low-complexity. Experiments on a recently published benchmarking toolbox show that it ensures excellent sharpening quality, competitive with the state-of-the-art, consistently across all bands. The software code and the full set of results are shared online on https://github.com/giu-guarino/rho-PNN.

We study the statistics of the local resolvent and non-ergodic properties of eigenvectors for a generalised Rosenzweig-Porter Ntimes N random matrix model, undergoing two transitions separated by a delocalised non-ergodic phase. Interpreting the model as the combination of on-site random energies {a_i} and a structurally disordered hopping, we found that each eigenstate is delocalised over N^{2-gamma} sites close in energy |a_j-a_i|leq N^{1-gamma} in agreement with Kravtsov et al, arXiv:1508.01714. Our other main result, obtained combining a recurrence relation for the resolvent matrix with insights from Dyson's Brownian motion, is to show that the properties of the non-ergodic delocalised phase can be probed studying the statistics of the local resolvent in a non-standard scaling limit.

Although foundational vision-language models (VLMs) have proven to be very successful for various semantic discrimination tasks, they still struggle to perform faithfully for fine-grained categorization. Moreover, foundational models trained on one domain do not generalize well on a different domain without fine-tuning. We attribute these to the limitations of the VLM's semantic representations and attempt to improve their fine-grained visual awareness using generative modeling. Specifically, we propose two novel methods: Generative Class Prompt Learning (GCPL) and Contrastive Multi-class Prompt Learning (CoMPLe). Utilizing text-to-image diffusion models, GCPL significantly improves the visio-linguistic synergy in class embeddings by conditioning on few-shot exemplars with learnable class prompts. CoMPLe builds on this foundation by introducing a contrastive learning component that encourages inter-class separation during the generative optimization process. Our empirical results demonstrate that such a generative class prompt learning approach substantially outperform existing methods, offering a better alternative to few shot image recognition challenges. The source code will be made available at: https://github.com/soumitri2001/GCPL.

In 2015 we began a sub-challenge at the EndoVis workshop at MICCAI in Munich using endoscope images of ex-vivo tissue with automatically generated annotations from robot forward kinematics and instrument CAD models. However, the limited background variation and simple motion rendered the dataset uninformative in learning about which techniques would be suitable for segmentation in real surgery. In 2017, at the same workshop in Quebec we introduced the robotic instrument segmentation dataset with 10 teams participating in the challenge to perform binary, articulating parts and type segmentation of da Vinci instruments. This challenge included realistic instrument motion and more complex porcine tissue as background and was widely addressed with modifications on U-Nets and other popular CNN architectures. In 2018 we added to the complexity by introducing a set of anatomical objects and medical devices to the segmented classes. To avoid over-complicating the challenge, we continued with porcine data which is dramatically simpler than human tissue due to the lack of fatty tissue occluding many organs.

Generating accurate 3D reconstructions from endoscopic video is a promising avenue for longitudinal radiation-free analysis of sinus anatomy and surgical outcomes. Several methods for monocular reconstruction have been proposed, yielding visually pleasant 3D anatomical structures by retrieving relative camera poses with structure-from-motion-type algorithms and fusion of monocular depth estimates. However, due to the complex properties of the underlying algorithms and endoscopic scenes, the reconstruction pipeline may perform poorly or fail unexpectedly. Further, acquiring medical data conveys additional challenges, presenting difficulties in quantitatively benchmarking these models, understanding failure cases, and identifying critical components that contribute to their precision. In this work, we perform a quantitative analysis of a self-supervised approach for sinus reconstruction using endoscopic sequences paired with optical tracking and high-resolution computed tomography acquired from nine ex-vivo specimens. Our results show that the generated reconstructions are in high agreement with the anatomy, yielding an average point-to-mesh error of 0.91 mm between reconstructions and CT segmentations. However, in a point-to-point matching scenario, relevant for endoscope tracking and navigation, we found average target registration errors of 6.58 mm. We identified that pose and depth estimation inaccuracies contribute equally to this error and that locally consistent sequences with shorter trajectories generate more accurate reconstructions. These results suggest that achieving global consistency between relative camera poses and estimated depths with the anatomy is essential. In doing so, we can ensure proper synergy between all components of the pipeline for improved reconstructions that will facilitate clinical application of this innovative technology.