Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonlinear Model Predictive Control for Agile Guidance of Fixed-Wing sUAS

We present an onboard receding-horizon optimization-based nonlinear guidance controller for path-following control of a fixed-wing small uninhabited aircraft in uncertain flow fields. We formulate two instances of the path-following optimal control problem as Model Predictive Contouring Control problems, and solve them in real-time using the ACADOS toolkit. We compare their performance to an industry-standard lookahead guidance method with hardware experiments. Our formulations lend themselves nicely to practitioners, as system identification of the employed kinematic model is straightforward. We demonstrate that our controllers are able to utilize the full control envelope, resulting in accurate path following. Finally, we utilize a state-of-the-art avionics stack and custom autopilot firmware to achieve real-time onboard solutions to the optimal control problems. Experimental test flights demonstrate the feasibility and effectiveness of the proposed approach on a fielded fixed-wing aircraft system.
Modèles de Markov cachés

Les modeles de Markov caches (MMC) connaissent aujourd'hui un grand succes dans divers domaines d'application. Ils ont ete initialement introduits dans la reconnaissance vocale par Baker (1975) et Rabiner (1989), et plus tard dans des domaines tels que l'analyse de sequences biologiques par R. Durbin et Mitchison (1998), l'ingenierie financiere par Weigend et Shi (1997) et bien d'autres. Ils sont utilises pour modeliser des sequences d'observations qualitatives ou quantitatives. La plupart des methodes d'utilisation et de developpement des MMC ont ete developpees dans le cadre de la reconnaissance vocale. Par la suite ces memes techniques ont ete appliquees et adaptees a d'autres domaines. Notre objectif dans ce memoire est de presenter une vue d'ensemble de la theorie des MMC a temps discret. Nous exposons les trois problemes classiques et developpons differents algorithmes susceptibles de les resoudre en effectuant de l'inference sur les etats du processus. Les differents algorithmes dont nous traitons sont : l'algorithme Forward-Backward developpe par Rabiner et Juang (1986) pour le probleme d'evaluation de l'etat le plus probable de generer une observation particuliere, ou "symbole", a un certain instant defini (evaluation), l'algorithme de Viterbi (1967) pour le probleme de calcul de la trajectoire d'etats la plus probable de generer une sequence d'observations (decodage) et finalement l'algorithme de Baum-Welch traite par Baum et Eagon (1967) pour la construction d'un modele adapte aux sequences d'etats ou d'observations a modeliser (apprentissage). Nous illustrons ensuite ces algorithmes en les appliquants a des exemples plus demonstratifs. ______________________________________________________________________________ MOTS-CLES DE L’AUTEUR : Etats, sequences, symboles observables, processus de Markov a temps discret, MMC, algorithme Forward-Backward, algorithme de Viterbi, algorithme de Baulm-Welch, inference.
A Hybrid Analytical-Machine Learning Approach for LEO Satellite Orbit Prediction

A hybrid analytical-machine learning (ML) framework for improved low Earth orbit (LEO) satellite orbit prediction is developed. The framework assumes the following three stages. (i) LEO satellite first pass: A terrestrial receiver with knowledge of its position produces carrier phase measurements from received LEO satellite signals, enabling it to estimate the time of arrival. The LEO satellite's states are initialized with simplified general perturbations 4 (SGP4)-propagated two-line element (TLE) data, and are subsequently estimated via an extended Kalman filter (EKF) during the period of satellite visibility. (ii) LEO satellite not in view: a nonlinear autoregressive with exogenous inputs (NARX) neural network is trained on the estimated ephemeris and is used to propagate the LEO satellite orbit for the period where the satellite is not in view. (iii) LEO satellite second pass: a terrestrial receiver with no knowledge of its position uses the ML-predicted LEO ephemeris along with its carrier phase measurements from received LEO signals to estimate its own position via an EKF. Experimental results with with signals from an Orbcomm satellite are presented to demonstrate the efficacy of the proposed framework. It is shown that during the satellite's second pass, the ML-predicted ephemeris error is reduced by nearly 90% from that of an SGP4 propagation. In addition, it is shown that if the receiver was to use the SGP4-predicted satellite ephemeris to localize itself, the EKF's initial position error of 2.2 km increases to 6.7 km, while the proposed framework reduces the position error to 448 m.
Reasoning with conceptual graphs and evidential networks for multi-entity maritime threat assessment

Hybrid threat events are rare and cannot be modelled solely based on data. Instead they require a focus on discovery of emergent knowledge through information sharing across agencies and systems. That requires a shared conceptualisation of the problem and entities involved. It also means that uncertain and possibly conflicting information describing multiple entities and their relationships needs to be reasoned about. In this paper we discuss the relationship between uncertain conceptual graphs and belief functions. We put forward a fusion process which allows for taking advantage of evidential reasoning capabilities in a multi-entity context. We show how information from conceptual graphs can be fed into or represented as an evidential networks and how the inference results obtained from valuation networks can be used to generate a probability distribution on conceptual graphs. This is demonstrated on a multi-entity threat assessment situation where a hybrid threat is formed by several possibly cooperating vessels.
Nonlinear growth of structure in cosmological simulations

' ' . ' . ' ( Upcoming cosmological observations (South Pole Telescope, Atacama Cosmol~ ogy Telescope, Baryon Oscillation Spectroscopic Survey, and Planck) will allow for accurately. probing structures and their growth, some into highly nonlinear regimes. These observations, in combination with already very accurate measurements of the expansion rate of the universe, will not only constrain cosmological parameters to a percent level, but will also answer what is the theory . of gravity on the largest scales. In order to obtain theoretical predictions for different measurables (like the distribution of masses, spatial· correlations), large numerical simulations have to be carried out. In this context, their main goal is to quantify how are such measurables affected by a change of cosmological parameters. The promised high accuracy of observations make the simul.ation task very demanding, as the theoretical predictions have to be at least as accurate as the observations. ) . In this thesis, we study the formation and evolution of dark matter halos I in ACDM models.o~er a wide range of cosmologicalepochs, from redshift z=20 to the present. First, we focus on the halo mass function, likely a key probe of cosmological growth of structure. By performing a large suite ( 60. simulations) of nested-box N-body simulations with careful convergence and error controls, we determine the mass function and its evolution with excellent statistical and I systematic errors, reaching a few percent over most of the considered redshift and mass range. Our results are consistent with a 'universal' form for the mass function, and are 1 in a good agreement with the Warren et al. analytic fit. Next, we. study the· structure of halos and ra~ificatidn of different halo mass definitions. This analysis is important for connecting structure formation theory with . observations, and also impacts the widely used approaches of assigning visible galaxies to dark matter halos the halo occupancy distribution models. We find that the vast majority of halos (80-85%) appear as isolated objects, allowing for an accurate mapping between the two main mass definitions (friends~of-friends · and spherical overdensity). Based on results from Monte Carfo realizations of . ideal Navarro-Frenk-White halos and N-body simulations we \)rovide a mass mapping formula. Furthermore, investigation of non-isolated, bridged halos, reveals that the fraction of these -halos and their satellite mass distribution is cosmology dependent, and can be expressed in a cosmology universal form. 1 Third, we turn to the spatial distribution of. halos, which serves as a 'biased' mass tracer. While this bias is scale dependent, at large distances it asymptotes
On the Observability of Gaussian Models using Discrete Density Approximations

This paper proposes a novel method for testing observability in Gaussian models using discrete density approximations (deterministic samples) of (multivariate) Gaussians. Our notion of observability is defined by the existence of the maximum a posteriori estimator. In the first step of the proposed algorithm, the discrete density approximations are used to generate a single representative design observation vector to test for observability. In the second step, a number of carefully chosen design observation vectors are used to obtain information on the properties of the estimator. By using measures like the variance and the so-called local variance, we do not only obtain a binary answer to the question of observability but also provide a quantitative measure.
FTC: A Universal Sensor for Fault Injection Attack Detection

Over the past two decades, fault-injection methods have evolved into very effective attacks to cause integrity or con-fidentiality violations in integrated circuits or electronic systems. Fault-injection attacks (FIAs) can be carried out using clock-glitch, voltage glitch, laser, optical instruments, electromagnetic (EM) emanation, and more. One promising solution to detect FIAs is to use on-chip sensors to capture the attacks' effect. However, having different types and techniques of FIAs enforces using the custom-designed sensors for each type of attack, which is challenging and introduces a large overhead. To address this, in this paper, we propose to develop a universal Fault-to- Time Converter (FTC) sensor that can effectively detect all the above-mentioned FIAs while requiring minimal overhead. The FTC sensor converts the effect of faults injected by an FIA method into “time” that is measurable. Then, the “time” difference can be analyzed further to identify whether an attack has been carried out successfully. Our FTC sensor implementation in FPGA platforms demonstrates that the design can effectively differentiate various FIA attack scenarios with its encoded output. The FTC sensor can also be extended to cover other fault attacks that have a similar impact on the victim device (i.e., affecting circuit timing).
BORIS/CTCFL-mediated chromatin accessibility alterations promote a pro-invasive transcriptional signature in melanoma cells

Melanoma is the deadliest form of skin cancer, due to its tendency to metastasize early. Brother of Regulator of Imprinted Sites (BORIS), also known as CCCTC binding factor-Like (CTCFL), is a transcription regulator that becomes ectopically expressed in melanoma. We recently showed that BORIS contributes to melanoma phenotype switching by altering the gene expression program of proliferative melanoma cells in favor of a more invasive phenotype. However, how BORIS alters the transcriptome remains unclear. Here, ATAC-seq was used to study BORIS-mediated chromatin accessibility alterations in proliferative melanoma cells. Genes that gained promoter accessibility following ectopic BORIS expression, were enriched for melanoma-specific invasive genes as well as invasion-associated biological processes, while promoters of genes associated with proliferation show reduce accessibility. Integration of ATAC-Seq and RNA-Seq data demonstrates that increased chromatin accessibility is associated with transcriptional upregulation of genes involved in tumor progression processes, and the aberrant activation of oncogenic transcription factors, while reduced chromatin accessibility and downregulated genes, were associated with repressed activity of tumor suppressors. Together, these findings indicate that BORIS mediates transcriptional reprogramming in melanoma cells by altering chromatin accessibility and gene expression, shifting the cellular transcription landscape of proliferative melanoma cells towards a pro-invasive genetic signature. Significance We recently reported that BORIS contributes to melanoma phenotype switching by altering the transcriptional landscape of melanoma cells from a proliferative to an invasive state. In this study, using ATAC-Seq, we demonstrate that ectopic BORIS expression in proliferative melanoma cells leads to increased chromatin accessibility at promoters of upregulated invasion-associated genes. Importantly, by integrating the ATAC-Seq data with RNA-Seq data, we were able to identify key cancer-associated transcription factors that become aberrantly activated or repressed following ectopic BORIS expression. Taken together, this study sheds light on the mechanisms by which BORIS mediates phenotype switching in melanoma cells.
Guidelines for standardising the application of discriminant analysis of principal components to genotype data

Discriminant analysis of principal components (DAPC) has become a popular method for visualising population structure due to its simplicity, computational speed, and freedom from demographic assumptions. Despite the popularity of DAPC, there has been little discussion on best practise. In this work, I provide guidelines for standardising the use of DAPC in studies of population genetic structure. An often-overlooked fact is that DAPC generates a model describing the genetic differences among a set of populations defined by a researcher. I demonstrate that appropriate parameterisation of this model is critical for obtaining biologically meaningful results. I show that the number of leading PC axes used as predictors of among population differences, paxes, should not exceed the k – 1 biologically informative PC axes that are expected for k effective populations in a genotype dataset. This k – 1 criterion for paxes selection is more appropriate compared to the widely used proportional variance criterion, which often results in a choice of paxes ≫ k – 1. DAPC parameterised with no more than the leading k – 1 PC axes is: (1) more parsimonious; (2) captures maximal among-population variation on biologically relevant predictors; (3) less sensitive to unintended interpretations of population structure; and (4) more generally applicable to independent sample sets. Assessing model fit should be routine practise and can aid interpretation of population structure when implementing DAPC. Additionally, it is imperative that researchers clearly articulate their study goals, that is, testing a priori expectations versus studying de novo inferred populations. Distinguishing between these goals is important because it dictates whether a researcher’s results can be treated as a test of the hypothesis that significant genetic differences exist among populations. Defining populations a priori (before observing the genotype data) constitutes a true hypothesis test, but populations defined de novo (after observing the genotype data) cannot be used to test this hypothesis due to issues with circularity. The discussion and practical recommendations provided in this work provide the molecular ecology community a roadmap for applying DAPC to their genotype datasets.
A comparison of o-the-shelf IR engines for question answering

Common question answering (QA) systems are based on the extraction of answers from large document collections. The task of the IR component in QA is to retrieve relevant segments in order to reduce the search space. The performance (especially in terms of recall) of this component is crucial for such QA systems. We compared seven off-theshelf IR engines using the test set from the CLEF 2003 competition on Dutch question answering. Open source IR engines Amberfish: http://www.etymon. com/tr.html GPL, C/C++, plain text, semi-structured/XML (with nested fields), wild-card search, phrase search, boolean queries, relevance ranking Lucene: http://jakarta.apache.org/lucene/docs/index.html Apache License, Java, plain/semi-structured documents, snowball stemmers, phrase search, boolean queries, relevance ranking Managing Gigabytes (MG): http://www.cs. mu.oz. au/mg/ GPL, C, plain text, images, boolean or ranked queries Swish-e: http://swish-e.org/ GPL, C, plain/semi-structured documents, snowball stemmers, wild card search, phrase search, fuzzy search (soundex, metaphone), flexible configuration (input/output, tokenisation etc), boolean queries, relevance ranking, Perl bindings Xapian: http://www.xapian. org/ GPL, C++, plain text, snowball stemmers, phrase search, proximity search, relevance feedback, wide range of boolean operators, relevance ranking, Perl/SWIG bindings Zebra: http://www.indexdata. dk/zebra/ GPL, C, structured (XML), phrase search, boolean queries, relevance ranking, wild-card search, Z39.50 protocoll, client-server implementaton Zettair: http://www.seg. rmit.edu. au/zettair/ BSD-style license, C, plain, semi-structured (TREC), phrase search, boolean queries, relevance ranking, summary function Joost QA with dependency relations IR results (CLEF 2003 data, 200 retrieved documents) documents paragraphs sentences MRR (in %) doc answer doc answer doc answer Swish-e 26.02 54.01 28.62 43.52 23.85 32.87 Zettair 32.10 52.69 29.90 42.09 28.32 31.04 Xapian 28.25 50.49 30.11 41.41 25.14 28.90 Zebra 26.50 45.06 27.79 37.53 25.47 30.67 Lucene 29.74 47.87 30.14 36.48 27.82 29.61 Amberfish 21.05 44.31 20.67 28.05 21.15 23.06 MG 20.86 39.98 20.98 22.53 21.18 15.44 . number of paragraphs required to obtain >= x% recall 30 40 50 60 65 70 75 80 85 90 Zettair: 1 2 4 8 13 20 34 87 Swish-e: 1 2 4 7 12 19 35 112 Lucene: 2 3 5 10 15 24 43 114 Xapian: 1 2 4 11 17 37 71 MG: 5 8 14 25 36 57 99 Amberfish: 3 6 11 23 32 57 128 Zebra: 2 3 6 18 36 79 191 Evaluation methodology Performance is measured in terms of mean reciprocal ranks (MRR).
Two Forms of Sexual Dimorphism in Gene Expression in Drosophila melanogaster: Their Coincidence and Evolutionary Genetics

Phenotypic sexual dimorphism can be mediated by sex differences in gene expression. We examine two forms of sexual dimorphism in gene expression in Drosophila melanogaster: (i) sex-biased gene expression (SBGE) in which the sexes differ in the amount a gene is expressed and (ii) sexual dimorphism in isoform usage, i.e., sex-specific splicing (SSS). In whole body (but not head) expression, we find a negative association between SBGE and SSS, possibly suggesting these are alternate routes to resolving sexual antagonistic selection. Next, we evaluate whether expression dimorphism contributes to the heterogeneity among genes in rmf, the intersexual genetic correlation in body expression that constrains the extent to which a gene’s expression can evolve independently between the sexes. We find lower rmf values for genes with than without SSS. We find higher rmf values for male- than female-biased genes (except genes with extreme male-bias), even though male-biased genes are known to have greater evolutionary divergence in expression. Finally, we examine population genetic patterns in relation to SBGE and SSS because genes with expression dimorphism have likely experienced a history of sex differences in selection. SSS is associated with reduced values of Tajima’s D and elevated Direction of Selection (DoS) values, suggestive of higher rates of adaptive evolution. Though DoS is highly elevated for genes with extreme male bias, DoS otherwise tends to decline from female-biased to unbiased to male-biased genes. Collectively, the results indicate that SBGE and SSS are differentially distributed across the genome and are associated with different forms of selection.
The cost of sympatry: spatio-temporal patterns in leopard dietary and physiological responses to tiger competition in Rajaji Tiger Reserve, India

Apex predators have critical roles in maintaining the structure of ecosystem functioning by controlling intraguild subordinate populations. Such dominant-subordinate interactions involve agonistic interactions including direct (death/displacement) or indirect (physiological and/or health implications) impacts on the subordinates. As these indirect effects are often mediated through physiological processes, it is important to quantify such responses for better understanding of population parameters. We used a well-known sympatric large carnivore intraguild system involving tiger (Panthera tigris) and leopard (Panthera pardus) to understand the dietary and physiological responses under a spatio-temporal gradient of tiger competition pressures in Rajaji Tiger Reserve (RTR), a major source tiger population of the western Terai-Arc Landscape, India between 2015-2020. The park provided a natural experimental set-up for tiger competition with the eastern part (ERTR) having high tiger density and the western (WRTR) part with functionally no competition from tigers. We conducted systematic faecal sampling in the winters of 2015 and 2020 from ERTR and WRTR to assess diet and physiological measures. Analyses of leopard-confirmed faeces suggest a dietary-niche separation as a consequence of tiger competition. In 2020, we found increased occurrence of large-bodied prey species without tiger competition in WRTR. Physiological measures followed the dietary responses where leopards with large-sized prey in diet showed higher fT3M and lower fGCM measures in WRTR. In contrast, ERTR leopards showed lower levels of fT3M as well as fGCM in 2020, possibly due to intense competition from tigers. Overall, these pattens strongly indicate a physiological cost of sympatry where competition with dominant tigers resulted in elevated nutritional stress. The combination of the natural habitat providing unique experimental setup, spatio-temporal sampling strategy and multidisciplinary approaches provide critical conservation perspectives for leopards, particularly in the context of recent increase in tiger numbers across India. We recommend expansion of leopard monitoring and population estimation efforts to buffers, developing appropriate plans for human-leopard conflict mitigation and intensive efforts to understand leopard population dynamics patterns to ensure their persistence during the ongoing Anthropocene.