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Epithelial cells form diverse structures from squamous spherical organoids to densely packed pseudostratified tissues. Quantification of cellular properties in these contexts requires high-resolution deep imaging and computational techniques to achieve truthful three-dimensional (3D) structural features. Here, we describe a detailed step-by-step protocol for sample preparation, imaging and deep-learning-assisted cell segmentation to achieve accurate quantification of fluorescently labelled individual cells in 3D within live tissues. We share the lessons learned through troubleshooting 3D imaging of Drosophila wing discs, including considerations on the choice of microscopy modality and settings (objective, sample mounting) and available segmentation methods. In addition, we include a computational pipeline alongside custom code to assist replication of the protocol. While we focus on the segmentation of cell outlines from membrane labelling, this protocol applies to a wide variety of samples, and we believe it be valuable for studying other tissues that demand complex analysis in 3D.

Ontology matching (OM) plays a key role in enabling data interoperability and knowledge sharing, but it remains challenging due to the need for large training datasets and limited vocabulary processing in machine learning approaches. Recently, methods based on Large Language Model (LLMs) have shown great promise in OM, particularly through the use of a retrieve-then-prompt pipeline. In this approach, relevant target entities are first retrieved and then used to prompt the LLM to predict the final matches. Despite their potential, these systems still present limited performance and high computational overhead. To address these issues, we introduce MILA, a novel approach that embeds a retrieve-identify-prompt pipeline within a prioritized depth-first search (PDFS) strategy. This approach efficiently identifies a large number of semantic correspondences with high accuracy, limiting LLM requests to only the most borderline cases. We evaluated MILA using the biomedical challenge proposed in the 2023 and 2024 editions of the Ontology Alignment Evaluation Initiative. Our method achieved the highest F-Measure in four of the five unsupervised tasks, outperforming state-of-the-art OM systems by up to 17%. It also performed better than or comparable to the leading supervised OM systems. MILA further exhibited task-agnostic performance, remaining stable across all tasks and settings, while significantly reducing LLM requests. These findings highlight that high-performance LLM-based OM can be achieved through a combination of programmed (PDFS), learned (embedding vectors), and prompting-based heuristics, without the need of domain-specific heuristics or fine-tuning.

Point defects dictate the properties of many functional materials. The standard approach to modelling the thermodynamics of defects relies on a static description, where the change in Gibbs free energy is approximated by the internal energy. This approach has a low computational cost, but ignores contributions from atomic vibrations and structural configurations that can be accessed at finite temperatures. We train a machine learning force field (MLFF) to explore dynamic defect behaviour using $\mathrm{Te_i^{+1}}$ and $\textit{V}{\mathrm{_{Te}^{+2}}}$ in CdTe as exemplars. We consider the different entropic contributions (e.g., electronic, spin, vibrational, orientational, and configurational) and compare methods to compute the defect free energies, ranging from a harmonic treatment to a fully anharmonic approach based on thermodynamic integration. We find that metastable configurations are populated at room temperature and thermal effects increase the predicted concentration of $\mathrm{Te_i^{+1}}$ by two orders of magnitude -- and can thus significantly affect the predicted properties. Overall, our study underscores the importance of finite-temperature effects and the potential of MLFFs to model defect dynamics at both synthesis and device operating temperatures.

Cognitive and neurological impairments are very common, but only a small proportion of affected individuals are diagnosed and treated, partly because of the high costs associated with frequent screening. Detecting pre-illness stages and analyzing the progression of neurological disorders through effective and efficient intelligent systems can be beneficial for timely diagnosis and early intervention. We propose using Large Language Models to extract features from free dialogues to detect cognitive decline. These features comprise high-level reasoning content-independent features (such as comprehension, decreased awareness, increased distraction, and memory problems). Our solution comprises (i) preprocessing, (ii) feature engineering via Natural Language Processing techniques and prompt engineering, (iii) feature analysis and selection to optimize performance, and (iv) classification, supported by automatic explainability. We also explore how to improve Chatgpt's direct cognitive impairment prediction capabilities using the best features in our models. Evaluation metrics obtained endorse the effectiveness of a mixed approach combining feature extraction with Chatgpt and a specialized Machine Learning model to detect cognitive decline within free-form conversational dialogues with older adults. Ultimately, our work may facilitate the development of an inexpensive, non-invasive, and rapid means of detecting and explaining cognitive decline.

We lift the Lefschetz number from an algebraic invariant of maps between spaces to an invariant of morphisms of data over the spaces., Comment: 21 pages. All comments are welcome!

Lead-halide perovskites (LHPs) have shot to prominence as efficient energy conversion materials that can be processed using cost-effective fabrication methods. A widely-quoted reason for their exceptional performance is their ability to tolerate defects, enabling long charge-carrier lifetimes despite high defect densities. Realizing defect tolerance in broader classes of materials would have a substantial impact on the semiconductor industry. Significant effort has been made over the past decade to unravel the underlying origins of defect tolerance to design stable alternatives to LHPs comprised of nontoxic elements. However, it has become clear that understanding defect tolerance in LHPs is far from straightforward. This review discusses the models proposed for defect tolerance in halide perovskites, evaluating the experimental and theoretical support for these models, as well as their limitations. We cover attempts to apply these models to identify materials beyond the lead-halide system that could also exhibit defect tolerance, and the successes and pitfalls encountered over the past decade. Finally, a discussion is made of some of the important missing pieces of information required for a deeper understanding and predictive models that enable the inverse design of defect tolerant semiconductors., Comment: 64 pages, 4 figures, 3 boxes, 1 table

We theoretically investigate the magnetic response on a three-dimensional superconducting nanobridge system, which is compound of two parallel parallelepiped (samples) connected through a nanobridge of size $\mathbf{L}$ and thickness $\mathbf{x}$, which mediates interactions between them. This study is conducted in the presence of a magnetic field $\mathbf{H}$ and the transport of a direct current $\mathbf{J}$. We use the well-know time dependent Ginzburg-Landau theory ($\mathbf{TDGL}$) for analyzed the possible effects on the density Gibbs free energy $\mathbf{F}$, magnetization $\mathbf{M}$, and superconducting electronic Cooper pair density $|\psi|^{2}$. We are interested in studying two cases: varying the $\mathbf{L}$ and $\mathbf{x}$ of the nanobridge in the absence of induced $\mathbf{J}$, and including the induction of external $\mathbf{J}$ for fixed $\mathbf{L}$ and $\mathbf{x}$. We find that $\mathbf{L}$ and $\mathbf{x}$ play an essential role in stabilizing (controlling) vortex states in the nanobridge, and the presence of induced $\mathbf{J}$ ($\mathbf{J}>0$ and $\mathbf{J}<0$), with a fixed $\mathbf{L}$ and $\mathbf{x}$, causes the movement of vortex states in the nanobridge just when $\mathbf{J}$ is induced at both faces of superconducting nanobridge system., Comment: 11 pages, 10 figures

We consider experimentally and computationally the phenomenon of the reverse Janssen effect, involving the counterintuitive finding that the force on the base of a column containing granular particles may be larger than the weight of the granular material itself. This finding is in contrast to the common Janssen effect, for which the force on the base is smaller than the particle weight, illustrating one of the best-known differences between granular and liquid systems. We find that the reverse Janssen effect is strongly influenced by the pouring protocol: under Earth's gravitational field, we find that the reverse Janssen effect is strongly and consistently influenced by the pouring height, as well as by (to somewhat lesser degree) pouring flux. Pouring grains from the height measured in tens of particle diameters leads to a reverse Janssen effect that is an order of magnitude stronger than the one found for small pouring heights of few particle diameters. This influence of the particles' delivery protocol allows for the development of a better understanding of the general features of the reverse Janssen effect and of the comparison between experiments and simulations reported in this and previous works.

We present a numerical experiment that demonstrates the possibility to capture topological phase transitions via an x-ray absorption spectroscopy scheme. We consider a Chern insulator whose topological phase is tuned via a second-order hopping. We perform time-dynamics simulations of the out-of-equilibrium laser-driven electron motion that enables us to model a realistic attosecond spectroscopy scheme. In particular, we use an ultrafast scheme with a circularly polarized IR pump pulse and an attosecond x-ray probe pulse. A laser-induced dichroism-type spectrum shows a clear signature of the topological phase transition. We are able to connect these signatures with the Berry structure of the system. This work extend the applications of attosecond absorption spectroscopy to systems presenting a non-trivial topological phase.

New technologies such as Machine Learning (ML) gave great potential for evaluating industry workflows and automatically generating key performance indicators (KPIs). However, despite established standards for measuring the efficiency of industrial machinery, there is no precise equivalent for workers' productivity, which would be highly desirable given the lack of a skilled workforce for the next generation of industry workflows. Therefore, an ML solution combining data from manufacturing processes and workers' performance for that goal is required. Additionally, in recent times intense effort has been devoted to explainable ML approaches that can automatically explain their decisions to a human operator, thus increasing their trustworthiness. We propose to apply explainable ML solutions to differentiate between expert and inexpert workers in industrial workflows, which we validate at a quality assessment industrial workstation. Regarding the methodology used, input data are captured by a manufacturing machine and stored in a NoSQL database. Data are processed to engineer features used in automatic classification and to compute workers' KPIs to predict their level of expertise (with all classification metrics exceeding 90 %). These KPIs, and the relevant features in the decisions are textually explained by natural language expansion on an explainability dashboard. These automatic explanations made it possible to infer knowledge from expert workers for inexpert workers. The latter illustrates the interest of research in self-explainable ML for automatically generating insights to improve productivity in industrial workflows., Comment: IEEE Industrial Electronics Magazine (2023)

Human feedback is central to the alignment of Large Language Models (LLMs). However, open questions remain about methods (how), domains (where), people (who) and objectives (to what end) of feedback processes. To navigate these questions, we introduce PRISM, a dataset that maps the sociodemographics and stated preferences of 1,500 diverse participants from 75 countries, to their contextual preferences and fine-grained feedback in 8,011 live conversations with 21 LLMs. With PRISM, we contribute (i) wider geographic and demographic participation in feedback; (ii) census-representative samples for two countries (UK, US); and (iii) individualised ratings that link to detailed participant profiles, permitting personalisation and attribution of sample artefacts. We target subjective and multicultural perspectives on value-laden and controversial issues, where we expect interpersonal and cross-cultural disagreement. We use PRISM in three case studies to demonstrate the need for careful consideration of which humans provide what alignment data.

We introduce two novel complementary notions of the Lefschetz number for a functor from a finite acyclic category to itself and we prove a Lefschetz fixed-object theorem and a Lefschetz fixed-morphism theorem. In order to do so, we use the connection between these type of categories and simplicial structures, such as trisps or delta complexes. Through the use of a pair of functors that, when composed, form the barycentric subdivision, we are not only able to identify fixed objects but also fixed chains of morphisms., Comment: 8 pages with 3 figures

As the field of AI continues to evolve, a significant dimension of this progression is the development of Large Language Models and their potential to enhance multi-agent artificial intelligence systems. This paper explores the cooperative capabilities of Large Language Model-augmented Autonomous Agents (LAAs) using the well-known Meltin Pot environments along with reference models such as GPT4 and GPT3.5. Preliminary results suggest that while these agents demonstrate a propensity for cooperation, they still struggle with effective collaboration in given environments, emphasizing the need for more robust architectures. The study's contributions include an abstraction layer to adapt Melting Pot game scenarios for LLMs, the implementation of a reusable architecture for LLM-mediated agent development - which includes short and long-term memories and different cognitive modules, and the evaluation of cooperation capabilities using a set of metrics tied to the Melting Pot's "Commons Harvest" game. The paper closes, by discussing the limitations of the current architectural framework and the potential of a new set of modules that fosters better cooperation among LAAs.

Defects are a universal feature of crystalline solids, dictating the key properties and performance of many functional materials. Given their crucial importance yet inherent difficulty in measuring experimentally, computational methods (such as DFT and ML/classical force-fields) are widely used to predict defect behaviour at the atomic level and the resultant impact on macroscopic properties. Here we report doped, a Python package for the generation, pre-/post-processing, and analysis of defect supercell calculations. doped has been built to implement the defect simulation workflow in an efficient and user-friendly -- yet powerful and fully-flexible -- manner, with the goal of providing a robust general-purpose platform for conducting reproducible calculations of solid-state defect properties.

Histopathology is a gold standard for cancer diagnosis under a microscopic examination. However, histological tissue processing procedures result in artifacts, which are ultimately transferred to the digitized version of glass slides, known as whole slide images (WSIs). Artifacts are diagnostically irrelevant areas and may result in wrong deep learning (DL) algorithms predictions. Therefore, detecting and excluding artifacts in the computational pathology (CPATH) system is essential for reliable automated diagnosis. In this paper, we propose a mixture of experts (MoE) scheme for detecting five notable artifacts, including damaged tissue, blur, folded tissue, air bubbles, and histologically irrelevant blood from WSIs. First, we train independent binary DL models as experts to capture particular artifact morphology. Then, we ensemble their predictions using a fusion mechanism. We apply probabilistic thresholding over the final probability distribution to improve the sensitivity of the MoE. We developed DL pipelines using two MoEs and two multiclass models of state-of-the-art deep convolutional neural networks (DCNNs) and vision transformers (ViTs). DCNNs-based MoE and ViTs-based MoE schemes outperformed simpler multiclass models and were tested on datasets from different hospitals and cancer types, where MoE using DCNNs yielded the best results. The proposed MoE yields 86.15% F1 and 97.93% sensitivity scores on unseen data, retaining less computational cost for inference than MoE using ViTs. This best performance of MoEs comes with relatively higher computational trade-offs than multiclass models. The proposed artifact detection pipeline will not only ensure reliable CPATH predictions but may also provide quality control., Comment: Submitted to BMC Medical Informatics and Decision Making Journal