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Preserving instance continuity and length in segmentation through connectivity-aware loss computation
Authors:
Karol Szustakowski,
Luk Frank,
Julia Esser,
Jan Gründemann,
Marie Piraud
Abstract:
In many biomedical segmentation tasks, the preservation of elongated structure continuity and length is more important than voxel-wise accuracy. We propose two novel loss functions, Negative Centerline Loss and Simplified Topology Loss, that, applied to Convolutional Neural Networks (CNNs), help preserve connectivity of output instances. Moreover, we discuss characteristics of experiment design, s…
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In many biomedical segmentation tasks, the preservation of elongated structure continuity and length is more important than voxel-wise accuracy. We propose two novel loss functions, Negative Centerline Loss and Simplified Topology Loss, that, applied to Convolutional Neural Networks (CNNs), help preserve connectivity of output instances. Moreover, we discuss characteristics of experiment design, such as downscaling and spacing correction, that help obtain continuous segmentation masks. We evaluate our approach on a 3D light-sheet fluorescence microscopy dataset of axon initial segments (AIS), a task prone to discontinuity due to signal dropout. Compared to standard CNNs and existing topology-aware losses, our methods reduce the number of segmentation discontinuities per instance, particularly in regions with missing input signal, resulting in improved instance length calculation in downstream applications. Our findings demonstrate that structural priors embedded in the loss design can significantly enhance the reliability of segmentation for biological applications.
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Submitted 3 September, 2025;
originally announced September 2025.
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Nonparametric regression for cost-effectiveness analyses with observational data -- a tutorial
Authors:
Jonas Esser,
Mateus Maia,
Judith Bosmans,
Johanna van Dongen
Abstract:
Healthcare decision-making often requires selecting among treatment options under budget constraints, particularly when one option is more effective but also more costly. Cost-effectiveness analysis (CEA) provides a framework for evaluating whether the health benefits of a treatment justify its additional costs. A key component of CEA is the estimation of treatment effects on both health outcomes…
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Healthcare decision-making often requires selecting among treatment options under budget constraints, particularly when one option is more effective but also more costly. Cost-effectiveness analysis (CEA) provides a framework for evaluating whether the health benefits of a treatment justify its additional costs. A key component of CEA is the estimation of treatment effects on both health outcomes and costs, which becomes challenging when using observational data, due to potential confounding. While advanced causal inference methods exist for use in such circumstances, their adoption in CEAs remains limited, with many studies relying on overly simplistic methods such as linear regression or propensity score matching. We believe that this is mainly due to health economists being generally unfamiliar with superior methodology. In this paper, we address this gap by introducing cost-effectiveness researchers to modern nonparametric regression models, with a particular focus on Bayesian Additive Regression Trees (BART). We provide practical guidance on how to implement BART in CEAs, including code examples, and discuss its advantages in producing more robust and credible estimates from observational data.
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Submitted 28 July, 2025; v1 submitted 4 July, 2025;
originally announced July 2025.
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Three Approaches to the Automation of Laser System Alignment and Their Resource Implications: A Case Study
Authors:
David A. Robb,
Donald Risbridger,
Ben Mills,
Ildar Rakhmatulin,
Xianwen Kong,
Mustafa Erden,
M. J. Daniel Esser,
Richard M. Carter,
Mike J. Chantler
Abstract:
The alignment of optical systems is a critical step in their manufacture. Alignment normally requires considerable knowledge and expertise of skilled operators. The automation of such processes has several potential advantages, but requires additional resource and upfront costs. Through a case study of a simple two mirror system we identify and examine three different automation approaches. They a…
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The alignment of optical systems is a critical step in their manufacture. Alignment normally requires considerable knowledge and expertise of skilled operators. The automation of such processes has several potential advantages, but requires additional resource and upfront costs. Through a case study of a simple two mirror system we identify and examine three different automation approaches. They are: artificial neural networks; practice-led, which mimics manual alignment practices; and design-led, modelling from first principles. We find that these approaches make use of three different types of knowledge 1) basic system knowledge (of controls, measurements and goals); 2) behavioural skills and expertise, and 3) fundamental system design knowledge. We demonstrate that the different automation approaches vary significantly in human resources, and measurement sampling budgets. This will have implications for practitioners and management considering the automation of such tasks.
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Submitted 17 September, 2024;
originally announced September 2024.
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The first spectroscopic IR reverberation programme on Mrk 509
Authors:
J. A. J. Mitchell,
M. J. Ward,
D. Kynoch,
J. V. Hernández Santisteban,
K. Horne,
J. -U. Pott,
J. Esser,
P. Mercatoris,
C. Packham,
G. J. Ferland,
A. Lawrence,
T. Fischer,
A. J. Barth,
C. Villforth,
H. Winkler
Abstract:
Near IR spectroscopic reverberation of Active Galactic Nuclei (AGN) potentially allows the infrared (IR) broad line region (BLR) to be reverberated alongside the disc and dust continua, while the spectra can also reveal details of dust astro-chemistry. Here, we describe results of a short pilot study (17 near-IR spectra over a 183 d period) for Mrk 509. The spectra give a luminosity-weighted dust…
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Near IR spectroscopic reverberation of Active Galactic Nuclei (AGN) potentially allows the infrared (IR) broad line region (BLR) to be reverberated alongside the disc and dust continua, while the spectra can also reveal details of dust astro-chemistry. Here, we describe results of a short pilot study (17 near-IR spectra over a 183 d period) for Mrk 509. The spectra give a luminosity-weighted dust radius of $\langle R_{\mathrm{d,lum}} \rangle = 186 \pm 4$ light-days for blackbody (large grain dust), consistent with previous (photometric) reverberation campaigns, whereas carbon and silicate dust give much larger radii. We develop a method of calibrating spectral data in objects where the narrow lines are extended beyond the slit width. We demonstrate this by showing our resultant photometric band light curves are consistent with previous results, with a hot dust lag at >40 d in the K band, clearly different from the accretion disc response at <20 d in the z band. We place this limit of 40 d by demonstrating clearly that the modest variability that we do detect in the H and K band does not reverberate on time-scales of less than 40 d. We also extract the Pa$β$ line light curve, and find a lag which is consistent with the optical BLR H$β$ line of $\sim$70-90 d. This is important as direct imaging of the near-IR BLR is now possible in a few objects, so we need to understand its relation to the better studied optical BLR.
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Submitted 10 April, 2024;
originally announced April 2024.
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Seemingly unrelated Bayesian additive regression trees for cost-effectiveness analyses in healthcare
Authors:
Jonas Esser,
Mateus Maia,
Andrew C. Parnell,
Judith Bosmans,
Hanneke van Dongen,
Thomas Klausch,
Keefe Murphy
Abstract:
In recent years, theoretical results and simulation evidence have shown Bayesian additive regression trees to be a highly-effective method for nonparametric regression. Motivated by cost-effectiveness analyses in health economics, where interest lies in jointly modelling the costs of healthcare treatments and the associated health-related quality of life experienced by a patient, we propose a mult…
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In recent years, theoretical results and simulation evidence have shown Bayesian additive regression trees to be a highly-effective method for nonparametric regression. Motivated by cost-effectiveness analyses in health economics, where interest lies in jointly modelling the costs of healthcare treatments and the associated health-related quality of life experienced by a patient, we propose a multivariate extension of BART which is applicable in regression analyses with several dependent outcome variables. Our framework allows for continuous or binary outcomes and overcomes some key limitations of existing multivariate BART models by allowing each individual response to be associated with different ensembles of trees, while still handling dependencies between the outcomes. In the case of continuous outcomes, our model is essentially a nonparametric version of seemingly unrelated regression. Likewise, our proposal for binary outcomes is a nonparametric generalisation of the multivariate probit model. We give suggestions for easily interpretable prior distributions, which allow specification of both informative and uninformative priors. We provide detailed discussions of MCMC sampling methods to conduct posterior inference. Our methods are implemented in the R package "subart". We showcase their performance through extensive simulation experiments and an application to an empirical case study from health economics. By also accommodating propensity scores in a manner befitting a causal analysis, we find substantial evidence for a novel trauma care intervention's cost-effectiveness.
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Submitted 26 February, 2025; v1 submitted 2 April, 2024;
originally announced April 2024.
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Expected Performance of the EUSO-SPB2 Fluorescence Telescope
Authors:
G. Filippatos,
M. Battisti,
M. Bertaina,
F. Bisconti,
J. Esser,
C. Heaton,
G. Osteria,
F. Sarazin,
L. Wiencke
Abstract:
The Extreme Universe Space Observatory Supper Pressure Balloon 2 (EUSO-SPB2) is under development, and will prototype instrumentation for future satellite-based missions, including the Probe of Extreme Multi-Messenger Astrophysics (POEMMA). EUSO-SPB2 will consist of two telescopes. The first is a Cherenkov telescope (CT) being developed to identify and estimate the background sources for future be…
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The Extreme Universe Space Observatory Supper Pressure Balloon 2 (EUSO-SPB2) is under development, and will prototype instrumentation for future satellite-based missions, including the Probe of Extreme Multi-Messenger Astrophysics (POEMMA). EUSO-SPB2 will consist of two telescopes. The first is a Cherenkov telescope (CT) being developed to identify and estimate the background sources for future below-the-limb very high energy (E>10 PeV) astrophysical neutrino observations, as well as above-the-limb cosmic ray induced signals (E>1 PeV). The second is a fluorescence telescope (FT) being developed for detection of Ultra High Energy Cosmic Rays (UHECRs). In preparation for the expected launch in 2023, extensive simulations tuned by preliminary laboratory measurements have been preformed to understand the FT capabilities. The energy threshold has been estimated at $10^{18.2}$ eV, and results in a maximum detection rate at $10^{18.6}$ eV when taking into account the shape of the UHECR spectrum. In addition, onboard software has been developed based on the simulations as well as experience with previous EUSO missions. This includes a level 1 trigger to be run on the computationally limited flight hardware, as well as a deep learning based prioritization algorithm in order to accommodate the balloon's telemetry budget. These techniques could also be used later for future, space-based missions.
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Submitted 14 December, 2021;
originally announced December 2021.
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Design, analysis and control of the series-parallel hybrid RH5 humanoid robot
Authors:
Julian Esser,
Shivesh Kumar,
Heiner Peters,
Vinzenz Bargsten,
Jose de Gea Fernandez,
Carlos Mastalli,
Olivier Stasse,
Frank Kirchner
Abstract:
Last decades of humanoid research has shown that humanoids developed for high dynamic performance require a stiff structure and optimal distribution of mass--inertial properties. Humanoid robots built with a purely tree type architecture tend to be bulky and usually suffer from velocity and force/torque limitations. This paper presents a novel series-parallel hybrid humanoid called RH5 which is 2…
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Last decades of humanoid research has shown that humanoids developed for high dynamic performance require a stiff structure and optimal distribution of mass--inertial properties. Humanoid robots built with a purely tree type architecture tend to be bulky and usually suffer from velocity and force/torque limitations. This paper presents a novel series-parallel hybrid humanoid called RH5 which is 2 m tall and weighs only 62.5 kg capable of performing heavy-duty dynamic tasks with 5 kg payloads in each hand. The analysis and control of this humanoid is performed with whole-body trajectory optimization technique based on differential dynamic programming (DDP). Additionally, we present an improved contact stability soft-constrained DDP algorithm which is able to generate physically consistent walking trajectories for the humanoid that can be tracked via a simple PD position control in a physics simulator. Finally, we showcase preliminary experimental results on the RH5 humanoid robot.
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Submitted 26 January, 2021;
originally announced January 2021.
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Optical continuum photometric reverberation mapping of the Seyfert-1 galaxy Mrk509
Authors:
F. Pozo Nuñez,
N. Gianniotis,
J. Blex,
T. Lisow,
R. Chini,
K. L. Polsterer,
J. -U. Pott,
J. Esser,
G. Pietrzyński
Abstract:
We present the results of a two year optical continuum photometric reverberation mapping campaign carried out on the nucleus of the Seyfert-1 galaxy Mrk509. Specially designed narrow-band filters were used in order to mitigate the line and pseudo-continuum contamination of the signal from the broad line region, while allowing for high-accuracy flux-calibration over a large field of view. We obtain…
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We present the results of a two year optical continuum photometric reverberation mapping campaign carried out on the nucleus of the Seyfert-1 galaxy Mrk509. Specially designed narrow-band filters were used in order to mitigate the line and pseudo-continuum contamination of the signal from the broad line region, while allowing for high-accuracy flux-calibration over a large field of view. We obtained light curves with a sub-day time sampling and typical flux uncertainties of $1\%$. The high photometric precision allowed us to measure inter-band continuum time delays of up to $\sim 2$ days across the optical range. The time delays are consistent with the relation $τ\propto λ^{4/3}$ predicted for an optically thick and geometrically thin accretion disk model. The size of the disk is, however, a factor of 1.8 larger than predictions based on the standard thin-disk theory. We argue that, for the particular case of Mrk509, a larger black hole mass due to the unknown geometry scaling factor can reconcile the difference between the observations and theory.
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Submitted 21 December, 2019;
originally announced December 2019.
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The first spectroscopic dust reverberation programme on active galactic nuclei: the torus in NGC 5548
Authors:
H. Landt,
M. J. Ward,
D. Kynoch,
C. Packham,
G. J. Ferland,
A. Lawrence,
J. -U. Pott,
J. Esser,
K. Horne,
D. A. Starkey,
D. Malhotra,
M. M. Fausnaugh,
B. M. Peterson,
R. J. Wilman,
R. A. Riffel,
T. Storchi-Bergmann,
A. J. Barth,
C. Villforth,
H. Winkler
Abstract:
We have recently initiated the first spectroscopic dust reverberation programme on active galactic nuclei (AGN) in the near-infrared. Spectroscopy enables measurement of dust properties, such as flux, temperature and covering factor, with higher precision than photometry. In particular, it enables measurement of both luminosity-based dust radii and dust response times. Here we report results from…
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We have recently initiated the first spectroscopic dust reverberation programme on active galactic nuclei (AGN) in the near-infrared. Spectroscopy enables measurement of dust properties, such as flux, temperature and covering factor, with higher precision than photometry. In particular, it enables measurement of both luminosity-based dust radii and dust response times. Here we report results from a one-year campaign on NGC 5548. The hot dust responds to changes in the irradiating flux with a lag time of ~70 light-days, similar to what was previously found in photometric reverberation campaigns. The mean and rms spectra are similar, implying that the same dust component dominates both the emission and the variations. The dust lag time is consistent with the luminosity-based dust radius only if we assume a wavelength-independent dust emissivity-law, i.e. a blackbody, which is appropriate for grains of large sizes (of a few microns). For such grains the dust temperature is ~1450 K. Therefore, silicate grains have most likely evaporated and carbon is the main chemical component. But the hot dust is not close to its sublimation temperature, contrary to popular belief. This is further supported by our observation of temperature variations largely consistent with a heating/cooling process. Therefore, the inner dust-free region is enlarged and the dusty torus rather a "dusty wall", whose inner radius is expected to be luminosity-invariant. The dust-destruction mechanism that enlarges the dust-free region seems to partly affect also the dusty region. We observe a cyclical decrease in dust mass with implied dust reformation times of ~5-6 months.
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Submitted 5 August, 2019;
originally announced August 2019.
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Analyzing temporal variations of AGN emission line profiles in the context of (dusty) cloud structure formation in the broad line region
Authors:
J. Esser,
J. -U. Pott,
H. Landt,
W. D. Vacca
Abstract:
The formation processes and the exact appearance of the dust torus and broad line region (BLR) of active galactic nuclei (AGN) are under debate. Theoretical studies show a possible connection between the dust torus and BLR through a common origin in the accretion disk. However observationally the dust torus and BLR are typically studied separately. NGC~4151 is possibly one of the best suited Seyfe…
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The formation processes and the exact appearance of the dust torus and broad line region (BLR) of active galactic nuclei (AGN) are under debate. Theoretical studies show a possible connection between the dust torus and BLR through a common origin in the accretion disk. However observationally the dust torus and BLR are typically studied separately. NGC~4151 is possibly one of the best suited Seyfert~1 galaxies for simultaneous examinations because of its high number of both photometric and spectroscopic observations in the past. Here we compare changes of the dust radius to shape variations of broad emission lines (BEL). While the radius of the dust torus decreased by almost a factor of two from 2004 to 2006 shape variations can be seen in the red wing of BELs of NGC~4151. These simultaneous changes are discussed in a dust and BEL formation scheme. We also use the BEL shape variations to assess possible cloud distributions, especially in azimuthal direction, which could be responsible for the observed variations. Our findings can best be explained in the framework of a dust inflated accretion disk. The changes in the BELs suggest that this dusty cloud formation does not happen continuously, and over the whole accretion disk, but on the contrary in spatially confined areas over rather short amount of times. We derive limits to the azimuthal extension of the observed localized BEL flux enhancement event.
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Submitted 4 December, 2018;
originally announced December 2018.
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Molecular insights into Neotropical bird-tick ecological associations and the role of birds in tick-borne disease ecology
Authors:
Matthew J. Miller,
Helen J. Esser,
Jose R. Loaiza,
Edward A. Herre,
Celestino Aguilar,
Diomedes Quintero,
Erick Alvarez,
Eldredge Bermingham
Abstract:
Ticks are important vectors of emerging zoonotic diseases. While adults of many tick species parasitize mammals, immature ticks are often found on wild birds. In the tropics, difficulties in species-level identification of immature ticks hinder studies of tick ecology and tick-borne disease transmission, including any potential role for birds. In Panama, we found immature ticks on 227 out of 3,498…
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Ticks are important vectors of emerging zoonotic diseases. While adults of many tick species parasitize mammals, immature ticks are often found on wild birds. In the tropics, difficulties in species-level identification of immature ticks hinder studies of tick ecology and tick-borne disease transmission, including any potential role for birds. In Panama, we found immature ticks on 227 out of 3,498 birds representing 93 host species, about 1/8th of the entire Panamanian terrestrial avifauna. Tick parasitism rates did not vary with temperature or rainfall, but parasitism rates did vary with host ecological traits: non-migratory residents, forest dwelling birds, bark insectivores, terrestrial foragers and lowland species were most likely to be infested with ticks. Using a molecular library developed from adult ticks specifically for this study, we identified 130 immature ticks obtained from wild birds, corresponding to eleven tick species, indicating that a substantial portion of the Panamanian avifauna is parasitized by a variety of tick species. Furthermore, we found evidence that immature ticks show taxonomic or ecological specificity to avian hosts. Finally, our data indicate that Panamanian birds are not parasitized regularly by the tick species responsible for most known tick-borne diseases. However, they are frequent hosts of other tick species known to carry a variety of rickettsial parasites of unknown pathogenicity. Given the broad interaction between tick and avian biodiversity in the Neotropics, future work on emerging tropical tick-borne disease should explicitly consider wild birds as vertebrate hosts.
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Submitted 24 November, 2014;
originally announced November 2014.
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Properties of optically selected BL Lac candidates from the SDSS
Authors:
S. D. Kügler,
K. Nilsson,
J. Heidt,
J. Esser,
T. Schultz
Abstract:
\textbf{Context.} Deep optical surveys open the avenue for find large numbers of BL Lac objects that are hard to identify because they lack the unique properties classifying them as such. While radio or X-ray surveys typically reveal dozens of sources, recent compilations based on optical criteria alone have increased the number of BL Lac candidates considerably. However, these compilations are su…
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\textbf{Context.} Deep optical surveys open the avenue for find large numbers of BL Lac objects that are hard to identify because they lack the unique properties classifying them as such. While radio or X-ray surveys typically reveal dozens of sources, recent compilations based on optical criteria alone have increased the number of BL Lac candidates considerably. However, these compilations are subject to biases and may contain a substantial number of contaminating sources. \textbf{Aims.} In this paper we extend our analysis of 182 optically selected BL Lac object candidates from the SDSS with respect to an earlier study. The main goal is to determine the number of bona fide BL Lac objects in this sample. \textbf{Methods.} We examine their variability characteristics, determine their broad-band radio-UV SEDs, and search for the presence of a host galaxy. In addition we present new optical spectra for 27 targets with improved S/N with respect to the SDSS spectra. \textbf{Results.} At least 59% of our targets have shown variability between SDSS DR2 and our observations by more than 0.1-0.27 mag de- pending on the telescope used. A host galaxy was detected in 36% of our targets. The host galaxy type and luminosities are consistent with earlier studies of BL Lac host galaxies. Simple fits to broad-band SEDS for 104 targets of our sample derived synchrotron peak frequencies between $13.5 \leq \mathrm{log}_{10}(ν_{\mathrm{peak}}) \leq 16$ with a peak at $\mathrm{log}_{10} \sim 14.5$. Our new optical spectra do not reveal any new redshift for any of our objects. Thus the sample contains a large number of bona fide BL Lac objects and seems to contain a substantial fraction of intermediate-frequency peaked BL Lacs.
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Submitted 29 September, 2014;
originally announced September 2014.
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Modified Scaling Relation for the Random-Field Ising Model
Authors:
U. Nowak,
K. D. Usadel,
J. Esser
Abstract:
We investigate the low-temperature critical behavior of the three dimensional random-field Ising ferromagnet. By a scaling analysis we find that in the limit of temperature $T \to 0$ the usual scaling relations have to be modified as far as the exponent $α$ of the specific heat is concerned. At zero temperature, the Rushbrooke equation is modified to $α+ 2 β+ γ= 1$, an equation which we expect t…
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We investigate the low-temperature critical behavior of the three dimensional random-field Ising ferromagnet. By a scaling analysis we find that in the limit of temperature $T \to 0$ the usual scaling relations have to be modified as far as the exponent $α$ of the specific heat is concerned. At zero temperature, the Rushbrooke equation is modified to $α+ 2 β+ γ= 1$, an equation which we expect to be valid also for other systems with similar critical behavior. We test the scaling theory numerically for the three dimensional random field Ising system with Gaussian probability distribution of the random fields by a combination of calculations of exact ground states with an integer optimization algorithm and Monte Carlo methods. By a finite size scaling analysis we calculate the critical exponents $ν\approx 1.0$, $β\approx 0.05$, $\barγ \approx 2.9$ $γ\approx 1.5$ and $α\approx -0.55$.
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Submitted 19 August, 1997;
originally announced August 1997.
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Exact Ground State Properties of Disordered Ising-Systems
Authors:
J. Esser,
U. Nowak,
K. D. Usadel
Abstract:
Exact ground states are calculated with an integer optimization algorithm for two and three dimensional site-diluted Ising antiferromagnets in a field (DAFF) and random field Ising ferromagnets (RFIM). We investigate the structure and the size-distribution of the domains of the ground state and compare it to earlier results from Monte Carlo simulations for finite temperature. Although DAFF and R…
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Exact ground states are calculated with an integer optimization algorithm for two and three dimensional site-diluted Ising antiferromagnets in a field (DAFF) and random field Ising ferromagnets (RFIM). We investigate the structure and the size-distribution of the domains of the ground state and compare it to earlier results from Monte Carlo simulations for finite temperature. Although DAFF and RFIM are thought to be in the same universality class we found essential differences between these systems as far as the domain properties are concerned. For the DAFF the ground states consist of fractal domains with a broad size distribution that can be described by a power law with exponential cut-off. For the RFIM the limiting case of the size distribution and structure of the domains for strong random fields is the size distribution and structure of the clusters of the percolation problem with a field dependent lower cut-off. The domains are fractal and in three dimensions nearly all spins belong to two large infinite domains of up- and down spins - the system is in a two-domain state.
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Submitted 2 December, 1996;
originally announced December 1996.
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Dynamics of Domains in Diluted Antiferromagnets
Authors:
U. Nowak,
J. Esser,
K. D. Usadel
Abstract:
We investigate the dynamics of two-dimensional site-diluted Ising antiferromagnets. In an external magnetic field these highly disordered magnetic systems have a domain structure which consists of fractal domains with sizes on a broad range of length scales. We focus on the dynamics of these systems during the relaxation from a long-range ordered initial state to the disordered fractal-domain st…
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We investigate the dynamics of two-dimensional site-diluted Ising antiferromagnets. In an external magnetic field these highly disordered magnetic systems have a domain structure which consists of fractal domains with sizes on a broad range of length scales. We focus on the dynamics of these systems during the relaxation from a long-range ordered initial state to the disordered fractal-domain state after applying an external magnetic field. The equilibrium state with applied field consists of fractal domains with a size distribution which follows a power law with an exponential cut-off. The dynamics of the system can be understood as a growth process of this fractal-domain state in such a way that the equilibrium distribution of domains develops during time. Following these ideas quantitatively we derive a simple description of the time dependence of the order parameter. The agreement with simulations is excellent.
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Submitted 16 April, 1996;
originally announced April 1996.