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Understanding the relationships between geometric structures and semantic concepts is crucial for building accurate models of complex environments. In indoors, certain spatial constraints, such as the relative positioning of planes, remain consistent despite variations in layout. This paper explores how these invariant relationships can be captured in a graph SLAM framework by representing high-level concepts like rooms and walls, linking them to geometric elements like planes through an optimizable factor graph. Several efforts have tackled this issue with add-hoc solutions for each concept generation and with manually-defined factors. This paper proposes a novel method for metric-semantic factor graph generation which includes defining a semantic scene graph, integrating geometric information, and learning the interconnecting factors, all based on Graph Neural Networks (GNNs). An edge classification network (G-GNN) sorts the edges between planes into same room, same wall or none types. The resulting relations are clustered, generating a room or wall for each cluster. A second family of networks (F-GNN) infers the geometrical origin of the new nodes. The definition of the factors employs the same F-GNN used for the metric attribute of the generated nodes. Furthermore, share the new factor graph with the S-Graphs+ algorithm, extending its graph expressiveness and scene representation with the ultimate goal of improving the SLAM performance. The complexity of the environments is increased to N-plane rooms by training the networks on L-shaped rooms. The framework is evaluated in synthetic and simulated scenarios as no real datasets of the required complex layouts are available., Comment: Submitted to ICRA 2025

Having prior knowledge of an environment boosts the localization and mapping accuracy of robots. Several approaches in the literature have utilized architectural plans in this regard. However, almost all of them overlook the deviations between actual as-built environments and as-planned architectural designs, introducing bias in the estimations. To address this issue, we present a novel localization and mapping method denoted as deviations-informed Situational Graphs or diS-Graphs that integrates prior knowledge from architectural plans even in the presence of deviations. It is based on Situational Graphs (S-Graphs) that merge geometric models of the environment with 3D scene graphs into a multi-layered jointly optimizable factor graph. Our diS-Graph extracts information from architectural plans by first modeling them as a hierarchical factor graph, which we will call an Architectural Graph (A-Graph). While the robot explores the real environment, it estimates an S-Graph from its onboard sensors. We then use a novel matching algorithm to register the A-Graph and S-Graph in the same reference, and merge both of them with an explicit model of deviations. Finally, an alternating graph optimization strategy allows simultaneous global localization and mapping, as well as deviation estimation between both the A-Graph and the S-Graph. We perform several experiments in simulated and real datasets in the presence of deviations. On average, our diS-Graphs outperforms the baselines by a margin of approximately 43% in simulated environments and by 7% in real environments, while being able to estimate deviations up to 35 cm and 15 degrees.

To establish general principles of optimal control of active matter, we study the elementary problem of moving an active particle by a trap with minimum work input. We show analytically that (open-loop) optimal protocols are not affected by activity, but work fluctuations are always increased. For closed-loop protocols, which rely on initial measurements of the self-propulsion, the average work has a minimum for a finite persistence time. Using these insights, we derive an optimal cyclic active information engine, which is found to have a higher precision and information efficiency when operated with a run-and-tumble particle than for an active Ornstein-Uhlenbeck particle and, we argue, than for any other type of active particle., Comment: 7 pages, 3 figures

As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, this paper presents the BIOSCAN-5M Insect dataset to the machine learning community and establish several benchmark tasks. BIOSCAN-5M is a comprehensive dataset containing multi-modal information for over 5 million insect specimens, and it significantly expands existing image-based biological datasets by including taxonomic labels, raw nucleotide barcode sequences, assigned barcode index numbers, and geographical information. We propose three benchmark experiments to demonstrate the impact of the multi-modal data types on the classification and clustering accuracy. First, we pretrain a masked language model on the DNA barcode sequences of the BIOSCAN-5M dataset, and demonstrate the impact of using this large reference library on species- and genus-level classification performance. Second, we propose a zero-shot transfer learning task applied to images and DNA barcodes to cluster feature embeddings obtained from self-supervised learning, to investigate whether meaningful clusters can be derived from these representation embeddings. Third, we benchmark multi-modality by performing contrastive learning on DNA barcodes, image data, and taxonomic information. This yields a general shared embedding space enabling taxonomic classification using multiple types of information and modalities. The code repository of the BIOSCAN-5M Insect dataset is available at https://github.com/zahrag/BIOSCAN-5M.

Background: Despite the recent advances in computational fluid dynamics (CFD) techniques applied to blood flow within the left atrium (LA), the relationship between atrial geometry, flow patterns, and blood stasis within the left atrial appendage (LAA) remains unclear. A better understanding of this relationship would have important clinical implications, as thrombi originating in the LAA are a common cause of stroke in patients with atrial fibrillation (AF). Aim: To identify the most representative atrial flow patterns on a patient-specific basis and study their influence on LAA blood stasis by varying the flow split ratio and some common atrial modeling assumptions. Methods: Three recent techniques were applied to nine patient-specific computational fluid dynamics (CFD) models of patients with AF: a kinematic atrial model to isolate the influence of wall motion because of AF, projection on a universal LAA coordinate system, and quantification of stagnant blood volume (SBV). Results: We identified three different atrial flow patterns based on the position of the center of the main circulatory flow. The results also illustrate how atrial flow patterns are highly affected by the flow split ratio, increasing the SBV within the LAA. As the flow split ratio is determined by the patient's lying position, the results suggest that the most frequent position adopted while sleeping may have implications for the medium- and long-term risks of stroke., Comment: Accepted manuscript, 21 pages, 10 figures, 5 tables

Boolean networks can be viewed as functions on the set of binary strings of a given length, described via logical rules. They were introduced as dynamic models into biology, in particular as logical models of intracellular regulatory networks involving genes, proteins, and metabolites. Since genes can have several modes of action, depending on their expression levels, binary variables are often not sufficiently rich, requiring the use of multi-valued networks instead. The steady state analysis of Boolean networks is computationally complex, and increasing the number of variable values beyond $2$ adds substantially to this complexity, and no general methods are available beyond simulation. The main contribution of this paper is to give an algorithm to compute the steady states of a multi-valued network that has a complexity that, in many cases, is essentially the same as that for the case of binary values. Our approach is based on a representation of multi-valued networks using multi-valued logic functions, providing a biologically intuitive representation of the network. Furthermore, it uses tools to compute lattice points in rational polytopes, tapping a rich area of algebraic combinatorics as a source for combinatorial algorithms for Boolean network analysis. An implementation of the algorithm is provided., Comment: 21 pages

While the mechanical behavior of noble nanoporous metals has been the subject of numerous studies, less is known about their recently developed refractory-based counterparts. Here we report on the mechanical properties, deformation mechanisms and topological changes of nanoporous tantalum, a prototypical refractory metal, by means of atomistic simulations of compression tests. An open-source multi-cpu and gpu-capable software is presented and used for the generation of computational samples. The stress strain curves show a non-linear elastic response, with early yielding. The plastic regime is first characterized by a linear hardening followed by an exponential hardening at large strains, associated with a high degree of densification. Plasticity is dominated by dislocation activity, with twinning and vacancy formation appearing as complementary deformation mechanisms. In order to study the mechanical response from a topological perspective, we track the evolution of the genus throughout the tests, finding direct correlations with each regime of the stress strain curves. The results are in agreement with previous studies of plasticity in nanoporous metals and highlight the importance of using topological metrics, for gaining insights into complex aspects of the deformation of nanoporous metals.

This article focuses on the prediction of the vibration frequency response of handheld probes. A novel approach that involves machine learning and readily available data from probes was explored. Vibration probes are efficient and affordable devices that provide information about testing airborne sound insulation in building acoustics. However, fixing a probe to a vibrating surface downshifts sensor resonances and underestimates levels. Therefore, the calibration response of the sensor included in a probe differs from the frequency response of that same probe. Simulation techniques of complex mechanical systems may describe this issue, but they include hardly obtainable parameters, ultimately restricting the model. Thus, this study discusses an alternative method, which comprises different parts. Firstly, the vibration frequency responses of 85 probes were measured and labelled according to six features. Then, Linear Regression, Decision Tree Regression and Artificial Neural Networks algorithms were analysed. It was revealed that decision tree regression is the more appropriate technique for this data. The best decision tree models, in terms of scores and model structure, were fine-tuned. Eventually, the final suggested model employs only four out of the six original features. A trade-off solution that involved a simple structure, an interpretable model and accurate predictions was accomplished. It showed a maximum average deviation from test measurements ranging from 0.6 dB in low-frequency to 3 dB in high-frequency while remaining at a low computational load. This research developed an original and reliable prediction tool that provides the vibration frequency response of handheld probes.

In this paper we introduce two conceptual algorithms for minimising abstract convex functions. Both algorithms rely on solving a proximal-type subproblem with an abstract Bregman distance based proximal term. We prove their convergence when the set of abstract linear functions forms a linear space. This latter assumption can be relaxed to only require the set of abstract linear functions to be closed under the sum, which is a classical assumption in abstract convexity. We provide numerical examples on the minimisation of nonconvex functions with the presented algorithms., Comment: 14 pages, 6 figures

Motivated by the question of how biological systems maintain homeostasis in changing environments, Shinar and Feinberg introduced in 2010 the concept of absolute concentration robustness (ACR). A biochemical system exhibits ACR in some species if the steady-state value of that species does not depend on initial conditions. Thus, a system with ACR can maintain a constant level of one species even as the environment changes. Despite a great deal of interest in ACR in recent years, the following basic question remains open: How can we determine quickly whether a given biochemical system has ACR? Although various approaches to this problem have been proposed, we show that they are incomplete. Accordingly, we present new methods for deciding ACR, which harness computational algebra. We illustrate our results on several biochemical signaling networks., Comment: 39 pages; substantial revision based on reviewer comments

Generative models are used as an alternative data augmentation technique to alleviate the data scarcity problem faced in the medical imaging field. Diffusion models have gathered special attention due to their innovative generation approach, the high quality of the generated images and their relatively less complex training process compared with Generative Adversarial Networks. Still, the implementation of such models in the medical domain remains at early stages. In this work, we propose exploring the use of diffusion models for the generation of high quality full-field digital mammograms using state-of-the-art conditional diffusion pipelines. Additionally, we propose using stable diffusion models for the inpainting of synthetic lesions on healthy mammograms. We introduce MAM-E, a pipeline of generative models for high quality mammography synthesis controlled by a text prompt and capable of generating synthetic lesions on specific regions of the breast. Finally, we provide quantitative and qualitative assessment of the generated images and easy-to-use graphical user interfaces for mammography synthesis., Comment: 10 pages + 2 pages of references, 6 figures

Understanding biodiversity is a global challenge, in which DNA barcodes - short snippets of DNA that cluster by species - play a pivotal role. In particular, invertebrates, a highly diverse and under-explored group, pose unique taxonomic complexities. We explore machine learning approaches, comparing supervised CNNs, fine-tuned foundation models, and a DNA barcode-specific masking strategy across datasets of varying complexity. While simpler datasets and tasks favor supervised CNNs or fine-tuned transformers, challenging species-level identification demands a paradigm shift towards self-supervised pretraining. We propose BarcodeBERT, the first self-supervised method for general biodiversity analysis, leveraging a 1.5 M invertebrate DNA barcode reference library. This work highlights how dataset specifics and coverage impact model selection, and underscores the role of self-supervised pretraining in achieving high-accuracy DNA barcode-based identification at the species and genus level. Indeed, without the fine-tuning step, BarcodeBERT pretrained on a large DNA barcode dataset outperforms DNABERT and DNABERT-2 on multiple downstream classification tasks. The code repository is available at https://github.com/Kari-Genomics-Lab/BarcodeBERT, Comment: Main text: 5 pages, Total: 9 pages, 2 figures, accepted at the 4th Workshop on Self-Supervised Learning: Theory and Practice (NeurIPS 2023)

The role of type Ia supernovae (SN Ia), mainly the Delay Time Distributions (DTDs) determined by the binary systems, and the yields of elements created by different explosion mechanisms, are studied by using the MulChem chemical evolution model applied to our Galaxy. We explored 15 DTDs and 12 tables of elemental yields produced by different SN Ia explosion mechanisms, doing a total of 180 models. Chemical abundances for $\alpha$-elements (O, Mg, Si, Ca) and Fe derived from these models are compared with recent solar region observational data of $\alpha$-elements over Fe relative abundances, [X/Fe], as a function of [Fe/H] and age. A multidimensional maximum likelihood analysis shows that 52 models are able to fit all these datasets simultaneously, considering the 1$\sigma$ confidence level. The combination of STROLG1 DTD and LN20181 SN Ia yields provides the best fit. The exponential model with very prompt events is a possible DTD, but a combination of several channels is more probable. The SN Ia yields that include MCh or Near MCh correspond to 39 (75%) of the 52 best models. Regarding the DTD, 31 (60%) of the 52 most probable models correspond to the SD scenario, while the remaining 21 (40%) are based on the DD scenario. Our results also show that the relatively large dispersion of the observational data may be explained by the stellar migration from other radial regions, and/or perhaps a combination of DTDs and explosion channels., Comment: 26 pages, 28 figures. Accepted for publication in MNRAS

We have selected galaxies with very high levels of H$\alpha$ emission (EQW(H$\alpha$)$>$700 \AA.) in their central regions from the final data release of the MaNGA survey . Our study focuses on 14 very well-resolved nearby galaxies with stellar masses in the range $9.5 < \log M_*/(M_{\odot}) < 11.5$. We investigate a variety of procedures for selecting galaxy regions that are likely to harbour excess populations of young massive stars, finding that selection in the 2-dimensional space of extinction-corrected H$\alpha$ EQW and [SIII]/[SII] line ratio produces the best results. By comparing stacked spectra covering these regions with stacked spectra covering normal starburst regions with 100\AA$<$EQW(H$\alpha$)$<$200\AA, we obtain the following main results: 1) Clear signatures of excess Wolf Rayet stars are found in half of the H$\alpha$ excess regions, 2) Galaxy regions containing excess Wolf Rayet stars are more often associated with the presence of high-ionization emission lines characteristic of accreting black holes. Excess [NeIII] is detected in 4 out of 8 of the WR regions and there are tentative [FeX] detections in 2 galaxies. 3) Regions of the galaxy with excess Wolf Rayet stars are located where the interstellar medium has larger ionized gas turbulent velocities and higher neutral gas overdensities. We make a first attempt to constrain changes in the high mass end of the stellar initial mass function (IMF) using the HR-pyPopStar evolutionary population synthesis models that include high wavelength-resolution theoretical atmosphere libraries for Wolf Rayet stars., Comment: accepted for publication in MNRAS

We address several questions in reduced versus extended networks via the elimination or addition of intermediate complexes in the framework of chemical reaction networks with mass-action kinetics. We clarify and extend advances in the literature concerning multistationarity in this context. We establish general results about MESSI systems, which we use to compute the circuits of multistationarity for significant biochemical networks., Comment: 36 pages, 6 figures. References added

Recent works on SLAM extend their pose graphs with higher-level semantic concepts like Rooms exploiting relationships between them, to provide, not only a richer representation of the situation/environment but also to improve the accuracy of its estimation. Concretely, our previous work, Situational Graphs (S-Graphs+), a pioneer in jointly leveraging semantic relationships in the factor optimization process, relies on semantic entities such as Planes and Rooms, whose relationship is mathematically defined. Nevertheless, there is no unique approach to finding all the hidden patterns in lower-level factor-graphs that correspond to high-level concepts of different natures. It is currently tackled with ad-hoc algorithms, which limits its graph expressiveness. To overcome this limitation, in this work, we propose an algorithm based on Graph Neural Networks for learning high-level semantic-relational concepts that can be inferred from the low-level factor graph. Given a set of mapped Planes our algorithm is capable of inferring Room entities relating to the Planes. Additionally, to demonstrate the versatility of our method, our algorithm can infer an additional semantic-relational concept, i.e. Wall, and its relationship with its Planes. We validate our method in both simulated and real datasets demonstrating improved performance over two baseline approaches. Furthermore, we integrate our method into the S-Graphs+ algorithm providing improved pose and map accuracy compared to the baseline while further enhancing the scene representation.

Galaxy clusters, which underwent a recent ($\leq3$ Gyr) major merger, offer a harsher environment due to the global hydrodynamical disturbance and the merger-shock heated ICM. However, the aftermath of such extreme cluster interactions on the member galaxy properties is not very well constrained. We explore the integrated star formation properties of galaxies through galaxy colours, as well as morphology buildup in three nearby ($0.04

The variational inequality problem in finite-dimensional Euclidean space is addressed in this paper, and two inexact variants of the extragradient method are proposed to solve it. Instead of computing exact projections on the constraint set, as in previous versions extragradient method, the proposed methods compute feasible inexact projections on the constraint set using a relative error criterion. The first version of the proposed method provided is a counterpart to the classic form of the extragradient method with constant steps. In order to establish its convergence we need to assume that the operator is pseudo-monotone and Lipschitz continuous, as in the standard approach. For the second version, instead of a fixed step size, the method presented finds a suitable step size in each iteration by performing a line search. Like the classical extragradient method, the proposed method does just two projections into the feasible set in each iteration. A full convergence analysis is provided, with no Lipschitz continuity assumption of the operator defining the variational inequality problem.

In the present paper, we formulate two versions of Frank--Wolfe algorithm or conditional gradient method to solve the DC optimization problem with an adaptive step size. The DC objective function consists of two components; the first is thought to be differentiable with a continuous Lipschitz gradient, while the second is only thought to be convex. The second version is based on the first and employs finite differences to approximate the gradient of the first component of the objective function. In contrast to past formulations that used the curvature/Lipschitz-type constant of the objective function, the step size computed does not require any constant associated with the components. For the first version, we established that the algorithm is well-defined of the algorithm and that every limit point of the generated sequence is a stationary point of the problem. We also introduce the class of weak-star-convex functions and show that, despite the fact that these functions are non-convex in general, the rate of convergence of the first version of the algorithm to minimize these functions is ${\cal O}(1/k)$. The finite difference used to approximate the gradient in the second version of the Frank-Wolfe algorithm is computed with the step-size adaptively updated using two previous iterations. Unlike previous applications of finite difference in the Frank-Wolfe algorithm, which provided approximate gradients with absolute error, the one used here provides us with a relative error, simplifying the algorithm analysis. In this case, we show that all limit points of the generated sequence for the second version of the Frank-Wolfe algorithm are stationary points for the problem under consideration, and we establish that the rate of convergence for the duality gap is ${\cal O}(1/\sqrt{k})$.

We introduce a generalized information criterion that contains other well-known information criteria, such as Bayesian information Criterion (BIC) and Akaike information criterion (AIC), as special cases. Furthermore, the proposed spectral information criterion (SIC) is also more general than the other information criteria, e.g., since the knowledge of a likelihood function is not strictly required. SIC extracts geometric features of the error curve and, as a consequence, it can be considered an automatic elbow detector. SIC provides a subset of all possible models, with a cardinality that often is much smaller than the total number of possible models. The elements of this subset are elbows of the error curve. A practical rule for selecting a unique model within the sets of elbows is suggested as well. Theoretical invariance properties of SIC are analyzed. Moreover, we test SIC in ideal scenarios where provides always the optimal expected results. We also test SIC in several numerical experiments: some involving synthetic data, and two experiments involving real datasets. They are all real-world applications such as clustering, variable selection, or polynomial order selection, to name a few. The results show the benefits of the proposed scheme. Matlab code related to the experiments is also provided. Possible future research lines are finally discussed.

We design a Universal Automatic Elbow Detector (UAED) for deciding the effective number of components in model selection problems. The relationship with the information criteria widely employed in the literature is also discussed. The proposed UAED does not require the knowledge of a likelihood function and can be easily applied in diverse applications, such as regression and classification, feature and/or order selection, clustering, and dimension reduction. Several experiments involving synthetic and real data show the advantages of the proposed scheme with benchmark techniques in the literature.

Among the list of one dimensional solvable Hamiltonians, we find the Hamiltonian with the Rosen--Morse II potential. The first objective is to analyze the scattering matrix corresponding to this potential. We show that it includes a series of poles corresponding to the types of redundant poles or anti-bound poles. In some cases, there are even bound states and this depends on the values of given parameters. Then, we perform different supersymmetric transformations on the original Hamiltonian either using the ground state (for those situations where there are bound states) wave functions, or other solutions that come from anti-bound states or redundant states. We study the properties of these transformations., Comment: 21 pages, 6 figures

Cu-exchanged zeolites rely on mobile solvated Cu+ cations for their catalytic activity, but the role of framework composition on transport is not fully understood. Ab initio molecular dynamics simulations can provide quantitative atomistic insight but are too computationally expensive to explore large length- and time-scales or diverse compositions. We report a machine-learning interatomic potential that accurately reproduces ab initio results and effectively generalizes to allow multi-nanosecond simulations of large supercells and diverse chemical compositions. Biased and unbiased simulations of [Cu(NH3)2]+ mobility show that aluminum pairing in eight-membered rings accelerates local hopping, and demonstrate that increased NH3 concentration enhances long-range diffusion. The probability of finding two [Cu(NH3)2]+ complexes in the same cage - key for SCR-NOx reaction - increases with Cu content and Al content, but does not correlate with the long-range mobility of Cu+. Supporting experimental evidence was obtained from reactivity tests of Cu-CHA catalysts with controlled chemical composition.

In this paper, we propose a solution for graph-based global robot simultaneous localization and mapping (SLAM) using architectural plans. Before the start of the robot operation, the previously available architectural plan of the building is converted into our proposed architectural graph (A-Graph). When the robot starts its operation, it uses its onboard LIDAR and odometry to carry out an online SLAM relying on our situational graph (S-Graph), which includes both, a representation of the environment with multiple levels of abstractions, such as walls or rooms, and their relationships, as well as the robot poses with their associated keyframes. Our novel graph-to-graph matching method is used to relate the aforementioned S-Graph and A-Graph, which are aligned and merged, resulting in our novel informed Situational Graph (iS-Graph). Our iS-Graph not only provides graph-based global robot localization, but it extends the graph-based SLAM capabilities of the S-Graph by incorporating into it the prior knowledge of the environment existing in the architectural plan, Comment: 4 Page Workshop paper for ICRA 2023. arXiv admin note: substantial text overlap with arXiv:2303.02076

Understanding material surfaces and interfaces is vital in applications like catalysis or electronics. By combining energies from electronic structure with statistical mechanics, ab initio simulations can in principle predict the structure of material surfaces as a function of thermodynamic variables. However, accurate energy simulations are prohibitive when coupled to the vast phase space that must be statistically sampled. Here, we present a bi-faceted computational loop to predict surface phase diagrams of multi-component materials that accelerates both the energy scoring and statistical sampling methods. Fast, scalable, and data-efficient machine learning interatomic potentials are trained on high-throughput density-functional theory calculations through closed-loop active learning. Markov-chain Monte Carlo sampling in the semi-grand canonical ensemble is enabled by using virtual surface sites. The predicted surfaces for GaN(0001), Si(111), and SrTiO3(001) are in agreement with past work and suggest that the proposed strategy can model complex material surfaces and discover previously unreported surface terminations., Comment: 30 pages main, 15 figures/tables, 5 pages supplementary