Search

Phenotyping consists in applying algorithms to identify individuals associated with a specific, potentially complex, trait or condition, typically out of a collection of Electronic Health Records (EHRs). Because a lot of the clinical information of EHRs are lying in texts, phenotyping from text takes an important role in studies that rely on the secondary use of EHRs. However, the heterogeneity and highly specialized aspect of both the content and form of clinical texts makes this task particularly tedious, and is the source of time and cost constraints in observational studies. To facilitate the development, evaluation and reproductibility of phenotyping pipelines, we developed an open-source Python library named medkit. It enables composing data processing pipelines made of easy-to-reuse software bricks, named medkit operations. In addition to the core of the library, we share the operations and pipelines we already developed and invite the phenotyping community for their reuse and enrichment. medkit is available at https://github.com/medkit-lib/medkit

We introduce a learning-based approach to optimize a joint constellation for a multi-user MIMO broadcast channel ($T$ Tx antennas, $K$ users, each with $R$ Rx antennas), with perfect channel knowledge. The aim of the optimizer (MAX-MIN) is to maximize the minimum mutual information between the transmitter and each receiver, under a sum-power constraint. The proposed optimization method do neither impose the transmitter to use superposition coding (SC) or any other linear precoding, nor to use successive interference cancellation (SIC) at the receiver. Instead, the approach designs a joint constellation, optimized such that its projection into the subspace of each receiver $k$, maximizes the minimum mutual information $I(W_k;Y_k)$ between each transmitted binary input $W_k$ and the output signal at the intended receiver $Y_k$. The rates obtained by our method are compared to those achieved with linear precoders.

As Large Language Models (LLMs), including ChatGPT and analogous systems, continue to advance, their robust natural language processing capabilities and diverse applications have garnered considerable attention. Nonetheless, despite the increasing acknowledgment of the convergence of Artificial Intelligence (AI) and Software Engineering (SE), there is a lack of studies involving the impact of this convergence on the practices and perceptions of software developers. Understanding how software developers perceive and engage with AI tools, such as ChatGPT, is essential for elucidating the impact and potential challenges of incorporating AI-driven tools in the software development process. In this paper, we conducted a survey with 207 software developers to understand the impact of ChatGPT on software quality, productivity, and job satisfaction. Furthermore, the study delves into developers' expectations regarding future adaptations of ChatGPT, concerns about potential job displacement, and perspectives on regulatory interventions., Comment: 31 pages, 9 figures

In August 2023, IT experts and scientists came together for a workshop to discuss the possibilities of building a computer cluster fully on renewable energies, as a test-case at Havana University in Cuba. The discussion covered the scientific needs for a computer cluster for particle physics at the InSTEC institute at Havana University, the possibilities to use solar energy, new developments in computing technologies, and computer cluster operation as well as operational needs for computing in particle physics. This computer cluster on renewable energies at the InSTEC institute is seen as a prototype for a large-scale computer cluster on renewable energies for scientific computing in the Caribbean, hosted in Cuba. The project is called "Humboldt Highway", to remember Alexander von Humboldt's achievements in bringing cultures of the American and European continents closer together by exchange and travel. In this spirit, we propose a project that enables and intensifies the scientific exchange between research laboratories and universities in Europe and the Caribbean, in particular Cuba.

This paper presents the methodology and key results which enabled to establish the so-called Ancillary Service Matrix (ASM) presenting the ability to deliver the different ancillary services of each of the 6 demonstrators of the XFLEX HYDRO research project combined with the applicable technologies studied in this analysis. These technologies include i) the variable speed technology with Doubly Fed Induction Machine (DFIM) or Full Size Frequency Converters (FSFC), ii) the Smart Power Plant Supervisor (SPPS) enabling to extend the operating range of the hydraulic units in turbine mode based on a better knowledge of the hydro unit wear and tear and associated costs over the full unit operating range, iii) the hydraulic short circuit (HSC) operation leading to simultaneous operation of pump and turbines of Pumped Storage Power Plants (PSPP) and iv) the Hydro-Battery-Hybrid (HBH) applied at Run-of-River demonstrator. The demonstrators considered for this study includes 4 pumped storage power plants, 1 conventional hydro storage plant and 1 run-of-the-river plant. For each demonstrator a 1D simulation model was developed and validated and was further enhanced to include the model of control system enabling to address the various ancillary services. The systematic 1D numerical simulation of ancillary service contribution of each demonstrator and related technologies enabled to quantify the magnitude of active power response to contribute to the different grid services. The results have been scored between 0 and 5 for each ancillary service, allowing to populate the Ancillary Service Matrix which is summarizing the results in a graphical and synthetic way. The analysis of the score of the Ancillary Services Matrix enables the reader to draw several key conclusions about the benefits unlocked by the implementation of these technologies which are summarized in the paper., Comment: 25 pages, Proceedings of HYDRO 2023, International Conference, October 16-18, 2023, Edinburgh, Scotland

The Pampilhosa da Serra Space Observatory (PASO) is located in the center of the continental Portuguese territory, in the heart of a certified Dark Sky destination by the Starlight Foundation (Aldeias do Xisto) and has been an instrumental asset to advance science, education and astrotourism certifications. PASO hosts astronomy and Space Situational Awareness (SSA) activities including a node of the Portuguese Space Surveillance \& Tracking (SST) infrastructure network, such as a space radar currently in test phase using GEM radiotelescope, a double Wide Field of View Telescope system, a EUSST optical sensor telescope. These instruments allow surveillance of satellite and space debris in LEO, MEO and GEO orbits. The WFOV telescope offers spectroscopy capabilities enabling light curve analysis and cosmic sources monitoring. Instruments for Space Weather are being considered for installation to monitor solar activities and expand the range of SSA services., Comment: 9 pages, 2 figures, Keywords: Dark Sky, radioastronomy, space, space debris, space situational awareness; Draft from Talk presented at Astronomy and Satellite Constellations: Pathways Forward, IAU Symposium 385, October 2023, Ed. C. Walker, D.Turnshek, P.Grimley, D.Galadi-Enriquez & M.Aub\'e, International Astronomical Union Proceedings Series, Cambridge University Press, 2024

Development of small pixels for high resolution image sensors implies a lot of challenges. A high level of performance should be guaranteed whereas the overall size must be reduced and so the degree of freedom in design and process. One key parameter of this constant improvement is the knowledge and the control of the crosstalk between pixels. In this paper, we present an advance in crosstalk characterization method based on the design of specific color patterns and the measurement of quantum efficiency. In a first part, we describe the color patterns designed to isolate one pixel or to simulate un-patterned colored pixels. These patterns have been implemented on test-chip and characterized. The second part deals with the characterization setup for quantum efficiency. Indeed, the use of spectral measurements allows us to discriminate pixels based on the color filter placed on top of them and to probe the crosstalk as a function of the depth in silicon, thanks to the photon absorption length variation with the wavelength. In the last part, results are presented showing the impact of color filters patterning, i.e. pixels in a Bayer pattern versus un-patterned pixels. The crosstalk directions and amplitudes are also analyzed in relation to pixel layout.

In this paper we present two design generations of metasurface-based planar microlenses implemented on Front-Side Illumination SPAD pixels. This kind of microlens is an alternative to conventional reflow microlens. It offers more degrees of freedom in term of design, especially the capability to design off-axis microlens to gather light around the SPAD photodiode. The two generations of microlenses have been fabricated on STMicroelectronics SPAD and characterized. We validated the sensitivity improvement offered by extended metasurface-based microlens. We also confirmed the impact of lithography capability on metasurface performances, highlighting the

Newly calculated multichannel quantum defect theory parameters and channel fractions are presented for the singlet and triplet S, P and D series and singlet F series of strontium. These results correct those reported in Vaillant C L, Jones M P A and Potvliege R M 2014 J. Phys. B: At. Mol. Opt. Phys. 47 155001.

Maneuvering a spacecraft in the cislunar space is a complex problem, since it is highly perturbed by the gravitational influence of both the Earth and the Moon, and possibly also the Sun. Trajectories minimizing the needed fuel are generally preferred in order to decrease the mass of the payload. A classical method to constrain maneuvers is mathematically modelling them using the Two Point Boundary Value Problem (TPBVP), defining spacecraft positions at the start and end of the trajectory. Solutions to this problem can then be obtained with optimization techniques like the nonlinear least squares conjugated with the Theory of Functional Connections (TFC) to embed the constraints, which recently became an effective method for deducing orbit transfers. In this paper, we propose a tangential velocity (TV) type of constraints to design orbital maneuvers. We show that the technique presented in this paper can be used to transfer a spacecraft (e.g. from the Earth to the Moon) and perform rendezvous maneuvers (e.g. a swing-by with the Moon). In comparison with the TPBVP, solving the TV constraints via TFC offers several advantages, leading to a significant reduction in computational time. Hence, it proves to be an efficient technique to design these maneuvers., Comment: Submitted to Scientific Reports

Transfer learning enables the sharing of common knowledge among models for a variety of downstream tasks, but traditional methods suffer in limited training data settings and produce narrow models incapable of effectively generalizing under distribution shifts. Foundation models have recently demonstrated impressive zero-shot inference capabilities and robustness under distribution shifts. However, zero-shot evaluation for these models has been predominantly confined to benchmarks with simple distribution shifts, limiting our understanding of their effectiveness under the more realistic shifts found in practice. Moreover, common fine-tuning methods for these models have yet to be evaluated against vision models in few-shot scenarios where training data is limited. To address these gaps, we present a new recipe for few-shot fine-tuning of the popular vision-language foundation model CLIP and evaluate its performance on challenging benchmark datasets with realistic distribution shifts from the WILDS collection. Our experimentation demonstrates that, while zero-shot CLIP fails to match performance of trained vision models on more complex benchmarks, few-shot CLIP fine-tuning outperforms its vision-only counterparts in terms of in-distribution and out-of-distribution accuracy at all levels of training data availability. This provides a strong incentive for adoption of foundation models within few-shot learning applications operating with real-world data. Code is available at https://github.com/mit-ll/robust-vision-language-finetuning, Comment: In proceedings of the 27th IEEE High Performance Extreme Computing Conference

This paper presents a new FDTD-based optical simulation model dedicated to describe the optical performances of CMOS image sensors taking into account diffraction effects. Following market trend and industrialization constraints, CMOS image sensors must be easily embedded into even smaller packages, which are now equipped with auto-focus and short-term coming zoom system. Due to miniaturization, the ray-tracing models used to evaluate pixels optical performances are not accurate anymore to describe the light propagation inside the sensor, because of diffraction effects. Thus we adopt a more fundamental description to take into account these diffraction effects: we chose to use Maxwell-Boltzmann based modeling to compute the propagation of light, and to use a software with an FDTD-based (Finite Difference Time Domain) engine to solve this propagation. We present in this article the complete methodology of this modeling: on one hand incoherent plane waves are propagated to approximate a product-use diffuse-like source, on the other hand we use periodic conditions to limit the size of the simulated model and both memory and computation time. After having presented the correlation of the model with measurements we will illustrate its use in the case of the optimization of a 1.75$\mu$m pixel.

In this paper, we present the results of rigorous electromagnetic broadband simulations applied to CMOS image sensors as well as experimental measurements. We firstly compare the results of 1D, 2D, and 3D broadband simulations in the visible range (380nm-720nm) of a 1.75$\mu$m CMOS image sensor, emphasizing the limitations of 1D and 2D simulations and the need of 3D modeling, particularly to rigorously simulate parameters like Quantum Efficiency. Then we illustrate broadband simulations by two proposed solutions that improve the spectral response of the sensor: an antireflective coating, and the reduction of the optical stack. We finally show that results from experimental measurements are in agreement with the simulated results.

A precise model library based on an equivalent circuit is presented and discussed. The model fully describes the light and bias behaviours of organic photodiodes realized on plastic substrates. The sub circuit modelling consists of a single SPICE LEVEL1 diode, a light power dependent series resistance, a shunt resistance. A combined light-power and voltage-controlled current source is also used to emulate the sensitivity behaviour of the photodiode. Moreover the model also permits designers to follow the technology deviations through the inclusion of worst-case corners. Finally a statistical model is included in order to allow designers run Monte Carlo simulations.

The complex classification of trans-Neptunian objects (TNOs) that are captured in mean-motion resonances (MMRs) and the constraint of their multiple origins are two significant open problems concerning the Solar System. The case-by-case study of the different MMRs and their characteristics provide information about their origin and dynamics, which helps us to understand the early stages of the Solar System evolution. In this paper, we study the dynamics of the detected TNOs close to a 3/1 MMR with Neptune. We initially use a semi-analytic three-body model to investigate the coplanar secular dynamics of these objects and find the stationary points. We then use surface sections and stability maps to analyse the non-averaged dynamics. These methods allow us to isolate the different stability regions and determine the extent of the chaotic regions. We show that stability maps are an extremely powerful tool for studying the resonant dynamics when they are computed in terms of the resonant angle. We then use these maps to study the non-planar three-body problem and the full dynamics in the presence of planetary perturbations. We confirm that TNOs near the 3/1 MMR regions can exist at very high inclinations. In the framework of the three-body problem, many of these objects can also be stable outside the 3/1 MMR owing to a Kozai secular resonance. However, when we take into account the perturbations of the four giant planets, the Kozai regions disappear and only the 3/1 MMR region remains, with eccentricities $e \lesssim 0.5$., Comment: 17 pages, 17 figures, 1 table

The growing population of man-made objects with the build up of mega-constellations not only increases the potential danger to all space vehicles and in-space infrastructures (including space observatories), but above all poses a serious threat to astronomy and dark skies. Monitoring of this population requires precise satellite characterization, which is is a challenging task that involves analyzing observational data such as position, velocity, and light curves using optimization methods. In this study, we propose and analyze the application of two optimization procedures to determine the parameters associated with the dynamics of a satellite: one based on the Theory of Functional Connections (TFC) and another one based on the Nelder-Mead heuristic optimization algorithm. The TFC performs linear functional interpolation to embed the constraints of the problem into a functional. In this paper, we propose to use this functional to analytically embed the observational data of a satellite into its equations of dynamics. After that, any solution will always satisfy the observational data. The second procedure proposed in this research takes advantage of the Nealder-Mead algorithm, that does not require the gradient of the objective function, as alternative solution. The accuracy, efficiency, and dependency on the initial guess of each method is investigated, analyzed, and compared for several dynamical models. These methods can be used to obtain the physical parameters of a satellite from available observational data and for space debris characterization contributing to follow-up monitoring activities in space and astronomical observatories., Comment: Submitted to Acta Astronautica

Background Chronic kidney disease (CKD) induces muscle wasting and a reduction in the maximum voluntary force (MVF). Little is known about the neuromuscular fatigability in CKD patients, defined as the reduction of muscle force capacities during exercise. Neuromuscular fatigability is a crucial physical parameter of the daily living. The quantification of explosive force has been shown to be a sensitive means to assess neuromuscular fatigability. Thus, our study used explosive force estimates to assess neuromuscular fatigability in elderly CKD patients. Methods Inclusion criteria for CKD patients were age $\ge$ 60 years old and glomerular filtration rate (GFR) < 45 mL/ min/1.73 m 2 not on dialysis, and those for controls were GFR > 60 mL/min/1.73 m 2 , age and diabetes matched. The fatigability protocol focused on a handgrip task coupled with surface electromyography (sEMG). Scalars were extracted from the rate of force development (RFD): absolute and normalized time periods (50, 75, 100, 150 and 200 ms, RFD 50 , RFD 75 , RFD 100 , RFD 150 and RFD 200 , respectively), peak RFD (RFD peak in absolute; NRFD peak normalized), timeto-peak RFD (t-RFD peak) and the relative force at RFD peak (MVF-RFD peak). A statistical parametric mapping approach was performed on the force, impulse and RFD-time curves. The integrated sEMG with time at 0-30, 0-50, 0-100 and 0-200 ms time intervals relative to onset of sEMG activity was extracted and groups were compared separately for each sex. Results The cohort of 159 individuals had a median age of 69 (9 IQR) years and body mass index was 27.6 (6.2 IQR) kg/ m 2. Propensity-score-matched groups balanced CKD patients and controls by gender with 66 males and 34 females. In scalar analysis, CKD patients manifested a higher decrement than controls in the early phase of contraction, regarding the NRFD peak (P = 0.009; $\eta$ 2 p = 0.034) and RFD 75 and RFD 100 (for both P < 0.001; $\eta$ 2 p = 0.068 and 0.064). The onedimensional analysis confirmed that CKD males manifest higher and delayed neuromuscular fatigability, especially before 100 ms from onset of contraction. sEMG was lower in CKD patients than controls in the 0-100 ms (at rest: P = 0.049, Cohen's d = 0.458) and 0-200 ms (at rest: P = 0.016, Cohen's d = 0.496; during exercise: P = 0.006, Cohen's d = 0.421) time windows. Controls showed greater decrease of sEMG than CKD patients in the 0-30 ms (P = 0.020, Cohen's d = 0.533) and 0-50 ms (P = 0.010, Cohen's d = 0.640) time windows. As opposite to females, males showed almost the same differences between groups. Conclusions Our study is the first to show that CKD patients have higher fatigability than controls, which may be associated with an impaired motor-unit recruitment, highlighting a neural drive disturbance with CKD. Further studies are needed to confirm these findings., Comment: Journal of Cachexia, Sarcopenia and Muscle, In press