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A grand challenge in biology is to discover evolutionary traits - features of organisms common to a group of species with a shared ancestor in the tree of life (also referred to as phylogenetic tree). With the growing availability of image repositories in biology, there is a tremendous opportunity to discover evolutionary traits directly from images in the form of a hierarchy of prototypes. However, current prototype-based methods are mostly designed to operate over a flat structure of classes and face several challenges in discovering hierarchical prototypes, including the issue of learning over-specific features at internal nodes. To overcome these challenges, we introduce the framework of Hierarchy aligned Commonality through Prototypical Networks (HComP-Net). We empirically show that HComP-Net learns prototypes that are accurate, semantically consistent, and generalizable to unseen species in comparison to baselines on birds, butterflies, and fishes datasets. The code and datasets are available at https://github.com/Imageomics/HComPNet., Comment: 34 pages, 27 figures

Training emotion recognition models has relied heavily on human annotated data, which present diversity, quality, and cost challenges. In this paper, we explore the potential of Large Language Models (LLMs), specifically GPT4, in automating or assisting emotion annotation. We compare GPT4 with supervised models and or humans in three aspects: agreement with human annotations, alignment with human perception, and impact on model training. We find that common metrics that use aggregated human annotations as ground truth can underestimate the performance, of GPT-4 and our human evaluation experiment reveals a consistent preference for GPT-4 annotations over humans across multiple datasets and evaluators. Further, we investigate the impact of using GPT-4 as an annotation filtering process to improve model training. Together, our findings highlight the great potential of LLMs in emotion annotation tasks and underscore the need for refined evaluation methodologies., Comment: to be published in Interspeech 2024

Harsh working environments and work-related stress have been known to contribute to mental health problems such as anxiety, depression, and suicidal ideation. As such, it is paramount to create solutions that can both detect employee unhappiness and find the root cause of the problem. While prior works have examined causes of mental health using machine learning, they typically focus on general mental health analysis, with few of them focusing on explainable solutions or looking at the workplace-specific setting. r/antiwork is a subreddit for the antiwork movement, which is the desire to stop working altogether. Using this subreddit as a proxy for work environment dissatisfaction, we create a new dataset for antiwork sentiment detection and subsequently train a model that highlights the words with antiwork sentiments. Following this, we performed a qualitative and quantitative analysis to uncover some of the key insights into the mindset of individuals who identify with the antiwork movement and how their working environments influenced them. We find that working environments that do not give employees authority or responsibility, frustrating recruiting experiences, and unfair compensation, are some of the leading causes of the antiwork sentiment, resulting in a lack of self-confidence and motivation among their employees., Comment: 13 pages, 8 figures

Emotion expression and perception are nuanced, complex, and highly subjective processes. When multiple annotators label emotional data, the resulting labels contain high variability. Most speech emotion recognition tasks address this by averaging annotator labels as ground truth. However, this process omits the nuance of emotion and inter-annotator variability, which are important signals to capture. Previous work has attempted to learn distributions to capture emotion variability, but these methods also lose information about the individual annotators. We address these limitations by learning to predict individual annotators and by introducing a novel method to create distributions from continuous model outputs that permit the learning of emotion distributions during model training. We show that this combined approach can result in emotion distributions that are more accurate than those seen in prior work, in both within- and cross-corpus settings., Comment: Accepted to Interspeech 2024 Conference

Aphasia is a language disorder that can lead to speech errors known as paraphasias, which involve the misuse, substitution, or invention of words. Automatic paraphasia detection can help those with Aphasia by facilitating clinical assessment and treatment planning options. However, most automatic paraphasia detection works have focused solely on binary detection, which involves recognizing only the presence or absence of a paraphasia. Multiclass paraphasia detection represents an unexplored area of research that focuses on identifying multiple types of paraphasias and where they occur in a given speech segment. We present novel approaches that use a generative pretrained transformer (GPT) to identify paraphasias from transcripts as well as two end-to-end approaches that focus on modeling both automatic speech recognition (ASR) and paraphasia classification as multiple sequences vs. a single sequence. We demonstrate that a single sequence model outperforms GPT baselines for multiclass paraphasia detection.

The brain's microvascular cerebral capillary network plays a vital role in maintaining neuronal health, yet capillary dynamics are still not well understood due to limitations in existing imaging techniques. Here, we present Single Capillary Reporters (SCaRe) for transcranial Ultrasound Localization Microscopy (ULM), a novel approach enabling non-invasive, whole-brain mapping of single capillaries and estimates of their transit-time as a neurovascular biomarker. We accomplish this first through computational Monte Carlo and ultrasound simulations of microbubbles flowing through a fully-connected capillary network. We unveil distinct capillary flow behaviors which informs methodological changes to ULM acquisitions to better capture capillaries in vivo. Subsequently, applying SCaRe-ULM in vivo, we achieve unprecedented visualization of single capillary tracks across brain regions, analysis of layer-specific capillary heterogeneous transit times (CHT), and characterization of whole microbubble trajectories from arterioles to venules. Lastly, we evaluate capillary biomarkers using injected lipopolysaccharide to induce systemic neuroinflammation and track the increase in SCaRe-ULM CHT, demonstrating the capability to detect subtle capillary functional changes. SCaRe-ULM represents a significant advance in studying microvascular dynamics, offering novel avenues for investigating capillary patterns in neurological disorders and potential diagnostic applications., Comment: 23 pages, 5 figures

This paper proposes techniques to enhance the performance of non-causal models for causal inference using data from randomized experiments. In domains like advertising, customer retention, and precision medicine, non-causal models that predict outcomes under no intervention are often used to score individuals and rank them according to the expected effectiveness of an intervention (e.g, an ad, a retention incentive, a nudge). However, these scores may not perfectly correspond to intervention effects due to the inherent non-causal nature of the models. To address this limitation, we propose causal fine-tuning and effect calibration, two techniques that leverage experimental data to refine the output of non-causal models for different causal tasks, including effect estimation, effect ordering, and effect classification. They are underpinned by two key advantages. First, they can effectively integrate the predictive capabilities of general non-causal models with the requirements of a causal task in a specific context, allowing decision makers to support diverse causal applications with a "foundational" scoring model. Second, through simulations and an empirical example, we demonstrate that they can outperform the alternative of building a causal-effect model from scratch, particularly when the available experimental data is limited and the non-causal scores already capture substantial information about the relative sizes of causal effects. Overall, this research underscores the practical advantages of combining experimental data with non-causal models to support causal applications.

The role of brain hemodynamics in neurodegenerative diseases cannot be fully assessed using existing imaging technologies. Recently, 2D Dynamic Ultrasound Localization Microscopy (DULM) has allowed for the quantitative mapping of the pulsatile flow at sub-wavelength resolution. However, to obtain accurate velocity estimates, 3D imaging is more adapted, especially for complex vascularized organs like the brain. 3D+t DULM is achievable using matrix array probes, but suffers from limitations in terms of cost, device complexity associated with the high channel count, and operating frequencies. Alternatively, Row Column Arrays (RCA) can reduce the number of elements while maintaining a large field of view and high frame rate. Herein, we demonstrate the feasibility of performing 3D+t blood flow measurements in the mouse brain using an RCA and a DULM sequence with a high spatiotemporal resolution. Transcranial images of anesthetized mice (n=7) were acquired at a volume rate of 750 Hz using 42 tilted plane waves. After microbubbles localization and tracking, super-resolved dynamic density and velocity maps of the 3D brain vascular network were obtained. Cortical vessels were segmented and pulsatility in the arteries was significantly higher than in veins for all mice, in accordance with the literature. Our results demonstrate the feasibility and reproducibility of achieving high spatiotemporal resolution volumes of the mouse brain vasculature with DULM using a RCA., Comment: 10 pages, 5 figures

Formulating dynamical models for physical phenomena is essential for understanding the interplay between the different mechanisms and predicting the evolution of physical states. However, a dynamical model alone is often insufficient to address these fundamental tasks, as it suffers from model errors and uncertainties. One common remedy is to rely on data assimilation, where the state estimate is updated with observations of the true system. Ensemble filters sequentially assimilate observations by updating a set of samples over time. They operate in two steps: a forecast step that propagates each sample through the dynamical model and an analysis step that updates the samples with incoming observations. For accurate and robust predictions of dynamical systems, discrete solutions must preserve their critical invariants. While modern numerical solvers satisfy these invariants, existing invariant-preserving analysis steps are limited to Gaussian settings and are often not compatible with classical regularization techniques of ensemble filters, e.g., inflation and covariance tapering. The present work focuses on preserving linear invariants, such as mass, stoichiometric balance of chemical species, and electrical charges. Using tools from measure transport theory (Spantini et al., 2022, SIAM Review), we introduce a generic class of nonlinear ensemble filters that automatically preserve desired linear invariants in non-Gaussian filtering problems. By specializing this framework to the Gaussian setting, we recover a constrained formulation of the Kalman filter. Then, we show how to combine existing regularization techniques for the ensemble Kalman filter (Evensen, 1994, J. Geophys. Res.) with the preservation of the linear invariants. Finally, we assess the benefits of preserving linear invariants for the ensemble Kalman filter and nonlinear ensemble filters., Comment: 33 pages, 8 figures

The negatively-charged boron vacancy (V$_\text{B}^-$) center in hexagonal boron nitride (hBN) is currently garnering considerable attention for the design of two-dimensional (2D) quantum sensing units. Such developments require a precise understanding of the spin-dependent optical response of V$_\text{B}^-$ centers, which still remains poorly documented despite its key role for sensing applications. Here we investigate the spin-dependent photodynamics of V$_\text{B}^-$ centers in hBN by a series of time-resolved photoluminescence (PL) measurements. We first introduce a robust all-optical method to infer the spin-dependent lifetime of the excited states and the electron spin polarization of V$_\text{B}^-$ centers under optical pumping. Using these results, we then analyze PL time traces recorded at different optical excitation powers with a seven-level model of the V$_\text{B}^-$ center and we extract all the rates involved in the spin-dependent optical cycles, both under ambient conditions and at liquid helium temperature. These findings are finally used to study the impact of a vector magnetic field on the optical response. More precisely, we analyze PL quenching effects resulting from electron spin mixing induced by the magnetic field component perpendicular to the V$_\text{B}^-$ quantization axis. All experimental results are well reproduced by the seven-level model, illustrating its robustness to describe the spin-dependent photodymanics of V$_\text{B}^-$ centers. This work provides important insights into the properties of V$_\text{B}^-$ centers in hBN, which are valuable for future developments of 2D quantum sensing units., Comment: 11 pages, 9 figures

Hemodynamic changes occur in stroke and neurodegenerative diseases. Developing imaging techniques allowing the in vivo visualization and quantification of cerebral blood flow would help better understand the underlying mechanism of those cerebrovascular diseases. 3D ultrasound localization microscopy (ULM) is a novel technology that can map the microvasculature of the brain at large depth and has been mainly used until now in rodents. Here, we demonstrated the feasibility of 3D ULM of the nonhuman primate (NHP) brain with a single 256-channels programmable ultrasound scanner. We achieved a highly resolved vascular map of the macaque brain at large depth in presence of craniotomy and durectomy using an 8-MHz multiplexed matrix probe. We were able to distinguish vessels as small as 26.9 {\mu}m. We also demonstrated that transcranial imaging of the macaque brain at similar depth was feasible using a 3-MHz probe and achieved a resolution of 60.4 {\mu}m. This work paves the way to clinical application of 3D ULM.

Color Doppler echocardiography enables visualization of blood flow within the heart. However, the limited frame rate impedes the quantitative assessment of blood velocity throughout the cardiac cycle, thereby compromising a comprehensive analysis of ventricular filling. Concurrently, deep learning is demonstrating promising outcomes in post-processing of echocardiographic data for various applications. This work explores the use of deep learning models for intracardiac Doppler velocity estimation from a reduced number of filtered I/Q signals. We used a supervised learning approach by simulating patient-based cardiac color Doppler acquisitions and proposed data augmentation strategies to enlarge the training dataset. We implemented architectures based on convolutional neural networks. In particular, we focused on comparing the U-Net model and the recent ConvNeXt models, alongside assessing real-valued versus complex-valued representations. We found that both models outperformed the state-of-the-art autocorrelator method, effectively mitigating aliasing and noise. We did not observe significant differences between the use of real and complex data. Finally, we validated the models on in vitro and in vivo experiments. All models produced quantitatively comparable results to the baseline and were more robust to noise. ConvNeXt emerged as the sole model to achieve high-quality results on in vivo aliased samples. These results demonstrate the interest of supervised deep learning methods for Doppler velocity estimation from a reduced number of acquisitions.

Ultrasound Localization Microscopy (ULM) is a non-invasive technique that allows for the imaging of micro-vessels in vivo, at depth and with a resolution on the order of ten microns. ULM is based on the sub-resolution localization of individual microbubbles injected in the bloodstream. Mapping the whole angioarchitecture requires the accumulation of microbubbles trajectories from thousands of frames, typically acquired over a few minutes. ULM acquisition times can be reduced by increasing the microbubble concentration, but requires more advanced algorithms to detect them individually. Several deep learning approaches have been proposed for this task, but they remain limited to 2D imaging, in part due to the associated large memory requirements. Herein, we propose to use sparse tensor neural networks to reduce memory usage in 2D and to improve the scaling of the memory requirement for the extension of deep learning architecture to 3D. We study several approaches to efficiently convert ultrasound data into a sparse format and study the impact of the associated loss of information. When applied in 2D, the sparse formulation reduces the memory requirements by a factor 2 at the cost of a small reduction of performance when compared against dense networks. In 3D, the proposed approach reduces memory requirements by two order of magnitude while largely outperforming conventional ULM in high concentration settings. We show that Sparse Tensor Neural Networks in 3D ULM allow for the same benefits as dense deep learning based method in 2D ULM i.e. the use of higher concentration in silico and reduced acquisition time.

In this article, we explore the notion of infinity by studying Cantor's contribution to this field. A brief history of set theory is given. As an example of infinity, we consider Hilbert's famous hotel. A graphical construction is used to demonstrate the countability of rationals. Cantor's diagonal procedure is explored, demonstrating that the infinity of real numbers is greater than that of integers. There is therefore a hierarchy of infinities, enabling us to elaborate on the continuum hypothesis, which remains an unsolved problem in mathematics., Comment: 14 pages, in French language, 4 figures,5 Pictures

In ultraviolet communications, the transceiver jitter effects have been ignored in previous studies, which can result in non-negligible performance degradation especially in vibration states or in mobile scenes. To address this issue, we model the relationship between the received power and transceiver jitter by making use of a moment-based density function approximation method. Based on this relationship, we incorporate the transceiver jitter effects in combination with Poisson distribution. The error rate results are obtained assuming on-off key modulation with optimal threshold based detection. We validate the error rate expressions by comparing the analytical results with Monte-Carlo simulation results. The results show that the transceiver jitter effects cause performance degradation especially in smaller transceiver elevation angles or in shorter distances, which are often adopted in short-range ultraviolet communications. The results also show that larger elevation angle cases have a better performance with respect to anti-jitter and may perform better compared to smaller elevation angle situations in the case of larger standard deviation of jitter. This work studies for the first time the transceiver jitter effects in ultraviolet communications and provides guidelines for experimental system design., Comment: 5 pages, 2 figures, comments are welcome!

Transcranial ultrasound imaging is currently limited by attenuation and aberration induced by the skull. First used in contrast-enhanced ultrasound (CEUS), highly echoic microbubbles allowed for the development of novel imaging modalities such as ultrasound localization microscopy (ULM). Herein, we develop an inverse problem approach to aberration correction (IPAC) that leverages the sparsity of microbubble signals. We propose to use the \textit{a priori} knowledge of the medium based upon microbubble localization and wave propagation to build a forward model to link the measured signals directly to the aberration function. A standard least-squares inversion is then used to retrieve the aberration function. We first validated IPAC on simulated data of a vascular network using plane wave as well as divergent wave emissions. We then evaluated the reproducibility of IPAC \textit{in vivo} in 5 mouse brains. We showed that aberration correction improved the contrast of CEUS images by 4.6 dB. For ULM images, IPAC yielded sharper vessels, reduced vessel duplications, and improved the resolution from 21.1 $\mu$m to 18.3 $\mu$m. Aberration correction also improved hemodynamic quantification for velocity magnitude and flow direction.

Our online lives generate a wealth of behavioral records -'digital footprints'- which are stored and leveraged by technology platforms. This data can be used to create value for users by personalizing services. At the same time, however, it also poses a threat to people's privacy by offering a highly intimate window into their private traits (e.g., their personality, political ideology, sexual orientation). Prior work has proposed a potential remedy: The cloaking of users' footprints. That is, platforms could allow users to hide portions of their digital footprints from predictive algorithms to avoid undesired inferences. While such an approach has been shown to offer privacy protection in the moment, there are two open questions. First, it remains unclear how well cloaking performs over time. As people constantly leave new digital footprints, the algorithm might regain the ability to predict previously cloaked traits. Second, cloaking digital footprints to avoid one undesirable inference may degrade the performance of models for other, desirable inferences (e.g., those driving desired personalized content). In the light of these research gaps, our contributions are twofold: 1) We propose a novel cloaking strategy that conceals 'metafeatures' (automatically generated higher-level categories) and compares its effectiveness against existing cloaking approaches, and 2) we test the spill-over effects of cloaking one trait on the accuracy of inferences on other traits. A key finding is that the effectiveness of cloaking degrades over times, but the rate at which it degrades is significantly smaller when cloaking metafeatures rather than individual footprints. In addition, our findings reveal the expected trade-off between privacy and personalization: Cloaking an undesired trait also partially conceals other desirable traits.

Paraphasias are speech errors that are often characteristic of aphasia and they represent an important signal in assessing disease severity and subtype. Traditionally, clinicians manually identify paraphasias by transcribing and analyzing speech-language samples, which can be a time-consuming and burdensome process. Identifying paraphasias automatically can greatly help clinicians with the transcription process and ultimately facilitate more efficient and consistent aphasia assessment. Previous research has demonstrated the feasibility of automatic paraphasia detection by training an automatic speech recognition (ASR) model to extract transcripts and then training a separate paraphasia detection model on a set of hand-engineered features. In this paper, we propose a novel, sequence-to-sequence (seq2seq) model that is trained end-to-end (E2E) to perform both ASR and paraphasia detection tasks. We show that the proposed model outperforms the previous state-of-the-art approach for both word-level and utterance-level paraphasia detection tasks and provide additional follow-up evaluations to further understand the proposed model behavior.

Various methods have been proposed to enhance image quality in ultrafast ultrasound. Coherent compounding can improve image quality using multiple steered diverging transmits when motion occurring between transmits is corrected for. Harmonic imaging, a standard technique in conventional focused echocardiography, has been adapted for ultrafast imaging, reducing clutter. Coherence-based approaches have also been shown to increase contrast in clinical settings by enhancing signals from coherent echoes and reducing clutter. Herein, we introduce a simple, unified framework that combines motion-correction, harmonic imaging, and angular-coherence, showing for the first time that their benefits can be combined in real-time. Validation was conducted through in vitro testing on a spinning disk model and in vivo on 4 volunteers. In vitro results confirmed the unified framework capability to achieve high contrast in large-motion contexts up to 17 cm/s. In vivo testing highlighted proficiency in generating images of high quality during low and high tissue velocity phases of the cardiac cycle. Specifically, during ventricular filling, the unified framework increased the gCNR from 0.47 to 0.87 when compared against coherent compounding.

We present a novel usage of Transformers to make image classification interpretable. Unlike mainstream classifiers that wait until the last fully connected layer to incorporate class information to make predictions, we investigate a proactive approach, asking each class to search for itself in an image. We realize this idea via a Transformer encoder-decoder inspired by DEtection TRansformer (DETR). We learn "class-specific" queries (one for each class) as input to the decoder, enabling each class to localize its patterns in an image via cross-attention. We name our approach INterpretable TRansformer (INTR), which is fairly easy to implement and exhibits several compelling properties. We show that INTR intrinsically encourages each class to attend distinctively; the cross-attention weights thus provide a faithful interpretation of the prediction. Interestingly, via "multi-head" cross-attention, INTR could identify different "attributes" of a class, making it particularly suitable for fine-grained classification and analysis, which we demonstrate on eight datasets. Our code and pre-trained models are publicly accessible at the Imageomics Institute GitHub site: https://github.com/Imageomics/INTR., Comment: Accepted to International Conference on Learning Representations 2024 (ICLR 2024)

Speech disfluencies, such as filled pauses or repetitions, are disruptions in the typical flow of speech. Stuttering is a speech disorder characterized by a high rate of disfluencies, but all individuals speak with some disfluencies and the rates of disfluencies may by increased by factors such as cognitive load. Clinically, automatic disfluency detection may help in treatment planning for individuals who stutter. Outside of the clinic, automatic disfluency detection may serve as a pre-processing step to improve natural language understanding in downstream applications. With this wide range of applications in mind, we investigate language, acoustic, and multimodal methods for frame-level automatic disfluency detection and categorization. Each of these methods relies on audio as an input. First, we evaluate several automatic speech recognition (ASR) systems in terms of their ability to transcribe disfluencies, measured using disfluency error rates. We then use these ASR transcripts as input to a language-based disfluency detection model. We find that disfluency detection performance is largely limited by the quality of transcripts and alignments. We find that an acoustic-based approach that does not require transcription as an intermediate step outperforms the ASR language approach. Finally, we present multimodal architectures which we find improve disfluency detection performance over the unimodal approaches. Ultimately, this work introduces novel approaches for automatic frame-level disfluency and categorization. In the long term, this will help researchers incorporate automatic disfluency detection into a range of applications.

Ultrasound Localization Microscopy (ULM) relies on the injection of microbubbles (MBs) to obtain highly resolved density maps of blood circulation in vivo, with a resolution that can reach 10 {\mu}m ~ {\lambda}/10 in the rodent brain. Static mean velocity maps can be extracted but are intrinsically biased by potential significant changes in the number of MBs detected during the cardiac cycle. Dynamic ULM (DULM) is a technique developed for non-invasive pulsatility measurements in the brain of rodents, leading to temporally resolved velocity and density cine-loops. It was previously based on external triggers such as the electrocardiogram (ECG), limiting its use to datasets acquired specifically for DULM applications while also increasing the required acquisition time. This study presents a new motion matching method using tissue Doppler that eliminates the need for ECG-gating in DULM experiments. DULM can now be performed on any ULM datasets, recovering pertinent temporal information, and improving the robustness of the mean velocity estimates., Comment: 11 pages, 6 figures, 4 tables

Ultrasound Localization Microscopy (ULM) has recently enabled the mapping of the cerebral vasculature in vivo with a resolution ten times smaller than the wavelength used, down to ten microns. However, with frame rates up to 20.000 frames per second, this method requires large amount of data to be acquired, transmitted, stored, and processed. The transfer rate is, as of today, one of the main limiting factors of this technology. Herein, we introduce a novel reconstruction framework to decrease this quantity of data to be acquired and the complexity of the required hardware by randomly subsampling the channels of a linear probe. Method performance evaluation as well as parameters optimization were conducted in silico using the SIMUS simulation software in an anatomically realistic phantom and then compared to in vivo acquisitions in a rat brain after craniotomy. Results show that reducing the number of active elements deteriorates the signal-to-noise ratio and could lead to false microbubbles detections but has limited effect on localization accuracy. In simulation, the false positive rate on microbubble detection deteriorates from 3.7% for 128 channels in receive and 7 steered angles to 11% for 16 channels and 7 angles. The average localization accuracy ranges from 10.6 um and 9.93 um for 16 channels/3 angles and 128 channels/13 angles respectively. These results suggest that a compromise can be found between the number of channels and the quality of the reconstructed vascular network and demonstrate feasibility of performing ULM with a reduced number of channels in receive, paving the way for low-cost devices enabling high-resolution vascular mapping., Comment: 15 pages, 9 figures

The development of neurologically active drugs faces a challenge in treating brain diseases due to the blood-brain barrier's impermeability. High-intensity focused ultrasound can open the barrier in a targeted manner, expanding treatment options. However, this procedure risks brain damage and off-target effects without proper monitoring. Current monitoring methods have limitations. We present Equivalent Time Active Cavitation Imaging, a novel ultrasound modality that characterizes the ultrasound pressure field during treatment. This system utilizes a unique plane wave sequence and an algorithm to filter the microbubble signal for pressure field mapping. We conducted pressure measurements in vitro for comparison with hydrophones and in vivo during blood-brain barrier opening in mice. Our modality successfully spatiotemporally characterizes the pressure field with an active imaging setup, demonstrating good correlation with hydrophone measurements. Experimental in vivo results are promising, establishing the feasibility of this monitoring method. In conclusion, this proof of concept represents a significant step toward a new ultrasound modality for monitoring blood-brain barrier opening using focused ultrasound. This approach offers a safer and more precise monitoring method, opening new possibilities for treating brain diseases., Comment: 21 pages, 9 figures

Heavy tails is a common feature of filtering distributions that results from the nonlinear dynamical and observation processes as well as the uncertainty from physical sensors. In these settings, the Kalman filter and its ensemble version - the ensemble Kalman filter (EnKF) - that have been designed under Gaussian assumptions result in degraded performance. t-distributions are a parametric family of distributions whose tail-heaviness is modulated by a degree of freedom $\nu$. Interestingly, Cauchy and Gaussian distributions correspond to the extreme cases of a t-distribution for $\nu = 1$ and $\nu = \infty$, respectively. Leveraging tools from measure transport (Spantini et al., SIAM Review, 2022), we present a generalization of the EnKF whose prior-to-posterior update leads to exact inference for t-distributions. We demonstrate that this filter is less sensitive to outlying synthetic observations generated by the observation model for small $\nu$. Moreover, it recovers the Kalman filter for $\nu = \infty$. For nonlinear state-space models with heavy-tailed noise, we propose an algorithm to estimate the prior-to-posterior update from samples of joint forecast distribution of the states and observations. We rely on a regularized expectation-maximization (EM) algorithm to estimate the mean, scale matrix, and degree of freedom of heavy-tailed \textit{t}-distributions from limited samples (Finegold and Drton, arXiv preprint, 2014). Leveraging the conditional independence of the joint forecast distribution, we regularize the scale matrix with an $l1$ sparsity-promoting penalization of the log-likelihood at each iteration of the EM algorithm. By sequentially estimating the degree of freedom at each analysis step, our filter can adapt its prior-to-posterior update to the tail-heaviness of the data. We demonstrate the benefits of this new ensemble filter on challenging filtering problems., Comment: 28 pages, 9 figures

Ultrasound Localization Microscopy can resolve the microvascular bed down to a few micrometers. To achieve such performance microbubble contrast agents must perfuse the entire microvascular network. Microbubbles are then located individually and tracked over time to sample individual vessels, typically over hundreds of thousands of images. To overcome the fundamental limit of diffraction and achieve a dense reconstruction of the network, low microbubble concentrations must be used, which lead to acquisitions lasting several minutes. Conventional processing pipelines are currently unable to deal with interference from multiple nearby microbubbles, further reducing achievable concentrations. This work overcomes this problem by proposing a Deep Learning approach to recover dense vascular networks from ultrasound acquisitions with high microbubble concentrations. A realistic mouse brain microvascular network, segmented from 2-photon microscopy, was used to train a three-dimensional convolutional neural network based on a V-net architecture. Ultrasound data sets from multiple microbubbles flowing through the microvascular network were simulated and used as ground truth to train the 3D CNN to track microbubbles. The 3D-CNN approach was validated in silico using a subset of the data and in vivo on a rat brain acquisition. In silico, the CNN reconstructed vascular networks with higher precision (81%) than a conventional ULM framework (70%). In vivo, the CNN could resolve micro vessels as small as 10 $\mu$m with an increase in resolution when compared against a conventional approach., Comment: Copyright 2021 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works

Large scientific collaborations, often with hundreds or thousands of members, are an excellent opportunity for a case study in best practices implemented while developing open source hardware. Using a publicly available design of timing equipment for gravitational wave detectors as a case study, we evaluated many facets of the open source hardware development, including practices, awareness, documentation, and longevity. Two diverse student teams, composed of high school and college students, participated in an end-to-end exercise of testing publicly-available documented hardware that originated from more than a decade ago. We found that the primary value of large collaborations lie in the ability to cultivate teamwork, provide a diverse set of role-models, and explore the possibilities of open hardware development of varying complexities. Learning from the experiences of the student groups, we make constructive recommendations where the open source hardware community can learn from the collaborations and vice versa.

Conventional ultrasound imaging relies on the computation of geometric time delay from multiple sensors to detect the position of a scatterer. In this paper, we present Ergodic Relay Ultrasound Imaging (ERUI), a method that utilizes an ergodic cavity down to a single ultrasonic sensor for ultrasound imaging. With the proposed method, the ergodic cavity creates a unique temporal signature that encodes the position of a scatterer. When compared to standard approaches, ERUI enables the generation of images of comparable quality while utilizing fewer detector elements. Our results suggest that ERUI has the potential to achieve image resolution similar to that of traditional imaging techniques, shifting the complexity from hardware to sofware. The demonstrated feasibility offers a promising path towards ultrasound probes with reduced costs and complexity for more portable scanning devices., Comment: 5 pages, 4 figures, Letter

We study the instantaneous inference of an unbounded planar flow from sparse noisy pressure measurements. The true flow field comprises one or more regularized point vortices of various strength and size. We interpret the true flow's measurements with a vortex estimator, also consisting of regularized vortices, and attempt to infer the positions and strengths of this estimator assuming little prior knowledge. The problem often has several possible solutions, many due to a variety of symmetries. To deal with this ill-posedness and to quantify the uncertainty, we develop the vortex estimator in a Bayesian setting. We use Markov-chain Monte Carlo and a Gaussian mixture model to sample and categorize the probable vortex states in the posterior distribution, tailoring the prior to avoid spurious solutions. Through experiments with one or more true vortices, we reveal many aspects of the vortex inference problem. With fewer sensors than states, the estimator infers a manifold of equally-possible states. Using one more sensor than states ensures that no cases of rank deficiency arise. Uncertainty grows rapidly with distance when a vortex lies outside of the vicinity of the sensors. Vortex size cannot be reliably inferred, but the position and strength of a larger vortex can be estimated with a much smaller one. In estimates of multiple vortices their individual signs are discernible because of the non-linear coupling in the pressure. When the true vortex state is inferred from an estimator of fewer vortices, the estimate approximately aggregates the true vortices where possible., Comment: 34 pages, 20 figures

The Robotics Major at the University of Michigan was successfully launched in the 2022-23 academic year as an innovative step forward to better serve students, our communities, and our society. Building on our guiding principle of "Robotics with Respect" and our larger Robotics Pathways model, the Michigan Robotics Major was designed to define robotics as a true academic discipline with both equity and excellence as our highest priorities. Understanding that talent is equally distributed but opportunity is not, the Michigan Robotics Major has embraced an adaptable curriculum that is accessible through a diversity of student pathways and enables successful and sustained career-long participation in robotics, AI, and automation professions. The results after our planning efforts (2019-22) and first academic year (2022-23) have been highly encouraging: more than 100 students declared Robotics as their major, completion of the Robotics major by our first two graduates, soaring enrollments in our Robotics classes, thriving partnerships with Historically Black Colleges and Universities. This document provides our original curricular proposal for the Robotics Undergraduate Program at the University of Michigan, submitted to the Michigan Association of State Universities in April 2022 and approved in June 2022. The dissemination of our program design is in the spirit of continued growth for higher education towards realizing equity and excellence. The most recent version of this document is also available on Google Docs through this link: https://ocj.me/robotics_major, Comment: 49 pages, approximately 25 figures

Linking cavitation and anatomy was found to be important for predictable outcomes in Focused-Ultrasound Blood-Brain-Barrier-Opening and requires high resolution cavitation mapping. However, cavitation mapping techniques for planning and monitoring of therapeutic procedures either 1) do not leverage the full resolution capabilities of ultrasound imaging or 2) place strong constraints on the length of the therapeutic pulse. This study aimed to develop a high-resolution technique that could resolve vascular anatomy in the cavitation map. Herein, we develop BP-ETACI, derived from bandpass sampling and dual-frequency contrast imaging at 12.5 MHz to produce cavitation maps prior and during blood-brain barrier opening with long therapeutic bursts using a 1.5-MHz focused transducer in the brain of C57BL/6 mice. The BP-ETACI cavitation maps were found to correlate with the vascular anatomy in ultrasound localization microscopy vascular maps and in histological sections. Cavitation maps produced from non-blood-brain-barrier disrupting doses showed the same cavitation-bearing vasculature as maps produced over entire blood-brain-barrier opening procedures, allowing use for 1) monitoring FUS-BBBO, but also for 2) therapy planning and target verification. BP-ETACI is versatile, created high resolution cavitation maps in the mouse brain and is easily translatable to existing FUS-BBBO experiments. As such, it provides a means to further study cavitation phenomena in FUS-BBBO.

Ultrasound Localization Microscopy (ULM) has proven effective in resolving microvascular structures and local mean velocities at sub-diffraction-limited scales, offering high-resolution imaging capabilities. Dynamic ULM (DULM) enables the creation of angiography or velocity movies throughout cardiac cycles. Currently, these techniques rely on a Localization-and-Tracking (LAT) workflow consisting in detecting microbubbles (MB) in the frames before pairing them to generate tracks. While conventional LAT methods perform well at low concentrations, they suffer from longer acquisition times and degraded localization and tracking accuracy at higher concentrations, leading to biased angiogram reconstruction and velocity estimation. In this study, we propose a novel approach to address these challenges by reversing the current workflow. The proposed method, Tracking-and-Localization (TAL), relies on first tracking the MB and then performing localization. Through comprehensive benchmarking using both in silico and in vivo experiments and employing various metrics to quantify ULM angiography and velocity maps, we demonstrate that the TAL method consistently outperforms the reference LAT workflow. Moreover, when applied to DULM, TAL successfully extracts velocity variations along the cardiac cycle with improved repeatability. The findings of this work highlight the effectiveness of the TAL approach in overcoming the limitations of conventional LAT methods, providing enhanced ULM angiography and velocity imaging.

We report on electron spin resonance (ESR) spectroscopy of boron-vacancy (V$_\text{B}^-$) centers hosted in isotopically-engineered hexagonal boron nitride (hBN) crystals. We first show that isotopic purification of hBN with $^{15}$N yields a simplified and well-resolved hyperfine structure of V$_\text{B}^-$ centers, while purification with $^{10}$B leads to narrower ESR linewidths. These results establish isotopically-purified h$^{10}$B$^{15}$N crystals as the optimal host material for future use of V$_\text{B}^-$ spin defects in quantum technologies. Capitalizing on these findings, we then demonstrate optically-induced polarization of $^{15}$N nuclei in h$^{10}$B$^{15}$N, whose mechanism relies on electron-nuclear spin mixing in the V$_\text{B}^-$ ground state. This work opens up new prospects for future developments of spin-based quantum sensors and simulators on a two-dimensional material platform., Comment: 6 pages, 3 figure

High-quality ultrafast ultrasound imaging is based on coherent compounding from multiple transmissions of plane waves (PW) or diverging waves (DW). However, compounding results in reduced frame rate, as well as destructive interferences from high-velocity tissue motion if motion compensation (MoCo) is not considered. While many studies have recently shown the interest of deep learning for the reconstruction of high-quality static images from PW or DW, its ability to achieve such performance while maintaining the capability of tracking cardiac motion has yet to be assessed. In this paper, we addressed such issue by deploying a complex-weighted convolutional neural network (CNN) for image reconstruction and a state-of-the-art speckle tracking method. The evaluation of this approach was first performed by designing an adapted simulation framework, which provides specific reference data, i.e. high quality, motion artifact-free cardiac images. The obtained results showed that, while using only three DWs as input, the CNN-based approach yielded an image quality and a motion accuracy equivalent to those obtained by compounding 31 DWs free of motion artifacts. The performance was then further evaluated on non-simulated, experimental in vitro data, using a spinning disk phantom. This experiment demonstrated that our approach yielded high-quality image reconstruction and motion estimation, under a large range of velocities and outperforms a state-of-the-art MoCo-based approach at high velocities. Our method was finally assessed on in vivo datasets and showed consistent improvement in image quality and motion estimation compared to standard compounding. This demonstrates the feasibility and effectiveness of deep learning reconstruction for ultrafast speckle-tracking echocardiography.

Optically-active spin defects in hexagonal boron nitride (hBN) are promising quantum systems for the design of two-dimensional quantum sensing units offering optimal proximity to the sample being probed. In this work, we first demonstrate that the electron spin resonance frequencies of boron vacancy centres (V$_\text{B}^-$) can be detected optically in the limit of few-atomic-layer thick hBN flakes despite the nanoscale proximity of the crystal surface that often leads to a degradation of the stability of solid-state spin defects. We then analyze the variations of the electronic spin properties of V$_\text{B}^-$ centres with the hBN thickness with a focus on (i) the zero-field splitting parameters, (ii) the optically-induced spin polarization rate and (iii) the longitudinal spin relaxation time. This work provides important insights into the properties of V$_\text{B}^-$ centres embedded in ultrathin hBN flakes, which are valuable for future developments of foil-based quantum sensing technologies., Comment: 7 pages, 3 figures

The assessment of myocardial fiber disarray is of major interest for the study of the progression of myocardial disease. However, time-resolved imaging of the myocardial structure remains unavailable in clinical practice. In this study, we introduce 3D Backscatter Tensor Imaging (3D-BTI), an entirely novel ultrasound-based imaging technique that can map the myocardial fibers orientation and its dynamics with a temporal resolution of 10 ms during a single cardiac cycle, non-invasively and in vivo in entire volumes. 3D-BTI is based on ultrafast volumetric ultrasound acquisitions, which are used to quantify the spatial coherence of backscattered echoes at each point of the volume. The capability of 3D-BTI to map the fibers orientation was evaluated in vitro in 5 myocardial samples. The helicoidal transmural variation of fiber angles was in good agreement with the one obtained by histological analysis. 3D-BTI was then performed to map the fiber orientation dynamics in vivo in the beating heart of an open-chest sheep at a volume rate of 90 volumes/s. Finally, the clinical feasibility of 3D-BTI was shown on a healthy volunteer. These initial results indicate that 3D-BTI could become a fully non-invasive technique to assess myocardial disarray at the bedside of patients.

The boron-vacancy spin defect ($\text{V}_\text{B}^{-}$) in hexagonal boron nitride (hBN) has a great potential as a quantum sensor in a two-dimensional material that can directly probe various external perturbations in atomic-scale proximity to the quantum sensing layer. Here, we apply first principles calculations to determine the coupling of the $\text{V}_\text{B}^{-}$ electronic spin to strain and electric fields. Our work unravels the interplay between local piezoelectric and elastic effects contributing to the final response to the electric fields. The theoretical predictions are then used to analyse optically detected magnetic resonance (ODMR) spectra recorded on hBN crystals containing different densities of $\text{V}_\text{B}^{-}$ centres. We prove that the orthorhombic zero-field splitting parameter results from local electric fields produced by surrounding charge defects. By providing calculations of the spin-strain and spin-electric field couplings, this work paves the way towards applications of $\text{V}_\text{B}^{-}$ centres for quantitative electric field imaging and quantum sensing under pressure., Comment: 9 pages, 5 figures