Search

The increasing sophistication of encryption-based ransomware has demanded innovative approaches to detection and mitigation, prompting the development of a hierarchical framework grounded in probabilistic cryptographic analysis. By focusing on the statistical characteristics of encryption patterns, the proposed methodology introduces a layered approach that combines advanced clustering algorithms with machine learning to isolate ransomware-induced anomalies. Through comprehensive testing across diverse ransomware families, the framework demonstrated exceptional accuracy, effectively distinguishing malicious encryption operations from benign activities while maintaining low false positive rates. The system's design integrates dynamic feedback mechanisms, enabling adaptability to varying cryptographic complexities and operational environments. Detailed entropy-based evaluations revealed its sensitivity to subtle deviations in encryption workflows, offering a robust alternative to traditional detection methods reliant on static signatures or heuristics. Computational benchmarks confirmed its scalability and efficiency, achieving consistent performance even under high data loads and complex cryptographic scenarios. The inclusion of real-time clustering and anomaly evaluation ensures rapid response capabilities, addressing critical latency challenges in ransomware detection. Performance comparisons with established methods highlighted its improvements in detection efficacy, particularly against advanced ransomware employing extended key lengths and unique cryptographic protocols.

In this work, we generalize the concept of bisimulation metric in order to metrize the behaviour of continuous-time processes. Similarly to what is done for discrete-time systems, we follow two approaches and show that they coincide: as a fixpoint of a functional and through a real-valued logic. The whole discrete-time approach relies entirely on the step-based dynamics: the process jumps from state to state. We define a behavioural pseudometric for processes that evolve continuously through time, such as Brownian motion or involve jumps or both., Comment: arXiv admin note: substantial text overlap with arXiv:2312.16729

We introduce a new multimodal optimization approach called Natural Variational Annealing (NVA) that combines the strengths of three foundational concepts to simultaneously search for multiple global and local modes of black-box nonconvex objectives. First, it implements a simultaneous search by using variational posteriors, such as, mixtures of Gaussians. Second, it applies annealing to gradually trade off exploration for exploitation. Finally, it learns the variational search distribution using natural-gradient learning where updates resemble well-known and easy-to-implement algorithms. The three concepts come together in NVA giving rise to new algorithms and also allowing us to incorporate "fitness shaping", a core concept from evolutionary algorithms. We assess the quality of search on simulations and compare them to methods using gradient descent and evolution strategies. We also provide an application to a real-world inverse problem in planetary science.

Super-Resolution Microscopy (SRM) is emerging as a powerful and innovative tool for imaging, characterizing, and understanding the structure of Extracellular Vesicles (EVs). By addressing the need for single-particle analysis with the high resolution required to study the composition and organization of these nanoparticles, SRM provides unique insights into EV biology. However, its application is accompanied by significant challenges, ranging from experimental setup to data analysis. This review outlines the fundamentals of SRM and its position within the broader field of EV research. We then explore its applications in evaluating (i) the morphological structure of EVs, (ii) their molecular composition, and (iii) their roles in biological systems. By offering practical guidance and an overview of critical parameters for standardization, this review aims at providing researchers with the tools and insights necessary to effectively apply SRM to EV investigation.

In the rapidly evolving landscape of GameFi, a fusion of gaming and decentralized finance (DeFi), there exists a critical need to enhance player engagement and economic interaction within gaming ecosystems. Our GameFi ecosystem aims to fundamentally transform this landscape by integrating advanced embodied AI agents into GameFi platforms. These AI agents, developed using cutting-edge large language models (LLMs), such as GPT-4 and Claude AI, are capable of proactive, adaptive, and contextually rich interactions with players. By going beyond traditional scripted responses, these agents become integral participants in the game's narrative and economic systems, directly influencing player strategies and in-game economies. We address the limitations of current GameFi platforms, which often lack immersive AI interactions and mechanisms for community engagement or creator monetization. Through the deep integration of AI agents with blockchain technology, we establish a consensus-driven, decentralized GameFi ecosystem. This ecosystem empowers creators to monetize their contributions and fosters democratic collaboration among players and creators. Furthermore, by embedding DeFi mechanisms into the gaming experience, we enhance economic participation and provide new opportunities for financial interactions within the game. Our approach enhances player immersion and retention and advances the GameFi ecosystem by bridging traditional gaming with Web3 technologies. By integrating sophisticated AI and DeFi elements, we contribute to the development of more engaging, economically robust, and community-centric gaming environments. This project represents a significant advancement in the state-of-the-art in GameFi, offering insights and methodologies that can be applied throughout the gaming industry., Comment: 11 pages, 4 figures

The gut-brain axis has emerged as a key player in the regulation of brain function and cognitive health. Gut microbiota dysbiosis has been observed in preclinical models of Alzheimer's disease and patients. Manipulating the composition of the gut microbiota enhances or delays neuropathology and cognitive deficits in mouse models. Accordingly, the health status of the animal facility may strongly influence these outcomes. In the present study, we longitudinally analysed the faecal microbiota composition and amyloid pathology of 5XFAD mice housed in a specific opportunistic pathogen-free (SOPF) and a conventional facility. The composition of the microbiota of 5XFAD mice after aging in conventional facility showed marked differences compared to WT littermates that were not observed when the mice were bred in SOPF facility. The development of amyloid pathology was also enhanced by conventional housing. We then transplanted faecal microbiota (FMT) from both sources into wild-type (WT) mice and measured memory performance, assessed in the novel object recognition test, in transplanted animals. Mice transplanted with microbiota from conventionally bred 5XFAD mice showed impaired memory performance, whereas FMT from mice housed in SOPF facility did not induce memory deficits in transplanted mice. Finally, 18 weeks of housing SOPF-born animals in a conventional facility resulted in the reappearance of specific microbiota compositions in 5XFAD vs WT mice. In conclusion, these results show a strong impact of housing conditions on microbiota-associated phenotypes and question the relevance of breeding preclinical models in specific pathogen-free (SPF) facilities.

Gene expression and DNA methylation are two interconnected biological processes and understanding their relationship is important in advancing understanding in diverse areas, including disease pathogenesis, environmental adaptation, developmental biology, and therapeutic responses. Differential analysis, including the identification of differentially methylated cytosine-guanine dinucleotide (CpG) sites (DMCs) and differentially expressed genes (DEGs) between two conditions, such as healthy and affected samples, can aid understanding of biological processes and disease progression. Typically, gene expression and DNA methylation data are analysed independently to identify DMCs and DEGs which are further analysed to explore relationships between them. Such approaches ignore the inherent dependencies and biological structure within these related data. A joint mixture model is proposed that integrates information from the two data types at the modelling stage to capture their inherent dependency structure, enabling simultaneous identification of DMCs and DEGs. The model leverages a joint likelihood function that accounts for the nested structure in the data, with parameter estimation performed using an expectation-maximisation algorithm. Performance of the proposed method, idiffomix, is assessed through a thorough simulation study and application to a publicly available breast cancer dataset. Several genes, identified as non-differentially expressed when the data types were modelled independently, had high likelihood of being differentially expressed when associated methylation data were integrated into the analysis. The idiffomix approach highlights the advantage of an integrated analysis via a joint mixture model over independent analyses of the two data types; genome-wide and cross-omics information is simultaneously utilised providing a more comprehensive view., Comment: 29 pages 6 figures

Successful realization of Bell tests has settled an 80-year-long debate, proving the existence of correlations which cannot be explained by a local realistic model. Recent experimental progress allowed to rule out any possible loopholes in these tests, and opened up the possibility of applications in cryptography envisaged more than three decades ago. A prominent example of such an application is device-independent quantum key distribution, which has recently been demonstrated. One remaining gap in all existing experiments, however, is that access to perfect randomness is assumed. To tackle this problem, the concept of randomness amplification has been introduced, allowing to generate such randomness from a weak source -- a task impossible in classical physics. In this work, we demonstrate the amplification of imperfect randomness coming from a physical source. It is achieved by building on two recent developments: The first is a theoretical protocol implementing the concept of randomness amplification within an experimentally realistic setup, which however requires a combination of the degree of Bell inequality violation (S-value) and the amount of data not attained previously. The second is experimental progress enabling the execution of a loophole-free Bell test with superconducting circuits, which offers a platform to reach the necessary combination. Our experiment marks an important step in achieving the theoretical physical limits of privacy and randomness generation.

Magnetic Resonance Fingerprinting (MRF) is an emerging technology with the potential to revolutionize radiology and medical diagnostics. In comparison to traditional magnetic resonance imaging (MRI), MRF enables the rapid, simultaneous, non-invasive acquisition and reconstruction of multiple tissue parameters, paving the way for novel diagnostic techniques. In the original matching approach, reconstruction is based on the search for the best matches between in vivo acquired signals and a dictionary of high-dimensional simulated signals (fingerprints) with known tissue properties. A critical and limiting challenge is that the size of the simulated dictionary increases exponentially with the number of parameters, leading to an extremely costly subsequent matching. In this work, we propose to address this scalability issue by considering probabilistic mixtures of high-dimensional elliptical distributions, to learn more efficient dictionary representations. Mixture components are modelled as flexible ellipitic shapes in low dimensional subspaces. They are exploited to cluster similar signals and reduce their dimension locally cluster-wise to limit information loss. To estimate such a mixture model, we provide a new incremental algorithm capable of handling large numbers of signals, allowing us to go far beyond the hardware limitations encountered by standard implementations. We demonstrate, on simulated and real data, that our method effectively manages large volumes of MRF data with maintained accuracy. It offers a more efficient solution for accurate tissue characterization and significantly reduces the computational burden, making the clinical application of MRF more practical and accessible.

Satellite optical images, upon their on-ground receipt, offer a distorted view of the observed scene. Their restoration, classically including denoising, deblurring, and sometimes super-resolution, is required before their exploitation. Moreover, quantifying the uncertainty related to this restoration could be valuable by lowering the risk of hallucination and avoiding propagating these biases in downstream applications. Deep learning methods are now state-of-the-art for satellite image restoration. However, they require to train a specific network for each sensor and they do not provide the associated uncertainties. This paper proposes a generic method involving a single network to restore images from several sensors and a scalable way to derive the uncertainties. We focus on deep regularization (DR) methods, which learn a deep prior on target images before plugging it into a model-based optimization scheme. First, we introduce VBLE-xz, which solves the inverse problem in the latent space of a variational compressive autoencoder, estimating the uncertainty jointly in the latent and in the image spaces. It enables scalable posterior sampling with relevant and calibrated uncertainties. Second, we propose the denoiser-based method SatDPIR, adapted from DPIR, which efficiently computes accurate point estimates. We conduct a comprehensive set of experiments on very high resolution simulated and real Pleiades images, asserting both the performance and robustness of the proposed methods. VBLE-xz and SatDPIR achieve state-of-the-art results compared to direct inversion methods. In particular, VBLE-xz is a scalable method to get realistic posterior samples and accurate uncertainties, while SatDPIR represents a compelling alternative to direct inversion methods when uncertainty quantification is not required.

Solvation free energy is an important design parameter in reaction kinetics and separation processes, making it a critical property to predict during process development. In previous research, directed message passing neural networks (D-MPNN) have successfully been used to predict solvation free energies and enthalpies in organic solvents. However, solvent mixtures provide greater flexibility for optimizing solvent interactions than monosolvents. This work aims to extend our previous models to mixtures. To handle mixtures in a permutation invariant manner we propose a pooling function; MolPool. With this pooling function, the machine learning models can learn and predict properties for an arbitrary number of molecules. The novel SolProp-mix software that applies MolPool to D-MPNN was compared to state-of-the-art architectures for predicting mixture properties and validated with our new database of COSMOtherm calculations; BinarySolv-QM. To improve predictions towards experimental accuracy, the network was then fine-tuned on experimental data in monosolvents. To demonstrate the benefit of this transfer learning methodology, experimental datasets of solvation free energies in binary (BinarySolv-Exp) and ternary (TernarySolv-Exp) solvent mixtures were compiled from data on vapor-liquid equilibria and activity coefficients. The neural network performed better than COSMOtherm calculations with an MAE of 0.25 kcal/mol and an RMSE of 0.37 kcal/mol for non-aqueous mixed solvents. Additionally, the ability to capture trends for a varying mixture composition was validated successfully. Our model's ability to accurately predict mixture properties from the combination of in silico data and pure component experimental data is promising given the scarcity of experimental data for mixtures in many fields.

We demonstrate sub-Doppler cooling of calcium atoms using a two-photon transition from the ${^1}S_0$ ground state to the upper $4s5s~{^1}S_0$ state via the ${^1}P_1$ intermediate state. We achieve temperatures as low as $260~\mu\text{K}$ in a magneto-optical trap (MOT), well below the Doppler limit ($T_{\text{D}} = 0.8~\text{mK}$) of the ${^1}P_1$ state. We characterize temperature, lifetime and confinement of the MOT over a range of experimental parameters, observing no reduction in lifetime due to coupling to the higher state. We perform theoretical simulations of the cooling scheme and observe good agreement with the experimental results. The two-photon cooling scheme presented in this work provides an alternative to the standard Doppler cooling applied to alkaline-earth atoms, based on a sequence of two magneto-optical traps. The advantages of our scheme are the possibility of varying the effective linewidth of the ${^1}P_1$ state, a higher transfer efficiency (close to 100$\%$), and a more straightforward experimental implementation., Comment: 8 pages 4+1 figures

We propose an expert-elicitation method for learning non-parametric joint prior distributions using normalizing flows. Normalizing flows are a class of generative models that enable exact, single-step density evaluation and can capture complex density functions through specialized deep neural networks. Building on our previously introduced simulation-based framework, we adapt and extend the methodology to accommodate non-parametric joint priors. Our framework thus supports the development of elicitation methods for learning both parametric and non-parametric priors, as well as independent or joint priors for model parameters. To evaluate the performance of the proposed method, we perform four simulation studies and present an evaluation pipeline that incorporates diagnostics and additional evaluation tools to support decision-making at each stage of the elicitation process.

Structured prediction involves learning to predict complex structures rather than simple scalar values. The main challenge arises from the non-Euclidean nature of the output space, which generally requires relaxing the problem formulation. Surrogate methods build on kernel-induced losses or more generally, loss functions admitting an Implicit Loss Embedding, and convert the original problem into a regression task followed by a decoding step. However, designing effective losses for objects with complex structures presents significant challenges and often requires domain-specific expertise. In this work, we introduce a novel framework in which a structured loss function, parameterized by neural networks, is learned directly from output training data through Contrastive Learning, prior to addressing the supervised surrogate regression problem. As a result, the differentiable loss not only enables the learning of neural networks due to the finite dimension of the surrogate space but also allows for the prediction of new structures of the output data via a decoding strategy based on gradient descent. Numerical experiments on supervised graph prediction problems show that our approach achieves similar or even better performance than methods based on a pre-defined kernel.

With the rapid advancements in medical data acquisition and production, increasingly richer representations exist to characterize medical information. However, such large-scale data do not usually meet computing resource constraints or algorithmic complexity, and can only be processed after compression or reduction, at the potential loss of information. In this work, we consider specific Gaussian mixture models (HD-GMM), tailored to deal with high dimensional data and to limit information loss by providing component-specific lower dimensional representations. We also design an incremental algorithm to compute such representations for large data sets, overcoming hardware limitations of standard methods. Our procedure is illustrated in a magnetic resonance fingerprinting study, where it achieves a 97% dictionary compression for faster and more accurate map reconstructions.

Nearly fifty years ago, Roberts (1978) postulated that Earth's magnetic field, which is generated by turbulent motions of liquid metal in its outer core, likely results from a subcritical dynamo instability characterised by a dominant balance between Coriolis, pressure and Lorentz forces. Here we numerically explore the generation of subcritical geomagnetic fields using techniques from optimal control and dynamical systems theory to uncover the nonlinear dynamical landscape underlying dynamo action. Through nonlinear optimisation, via direct-adjoint looping, we identify the minimal seed - the smallest magnetic field that attracts to a nonlinear dynamo solution. Additionally, using the Newton-hookstep algorithm, we converge stable and unstable travelling wave solutions to the governing equations. By combining these two techniques, complex nonlinear pathways between attracting states are revealed, providing insight into a potential subcritical origin of the geodynamo. This paper showcases these methods on the widely studied benchmark of Christensen et al. (2001), laying the foundations for future studies in more extreme and realistic parameter regimes. We show that the minimal seed reaches a nonlinear dynamo solution by first attracting to an unstable travelling wave solution, which acts as an edge state separating a hydrodynamic solution from a magnetohydrodynamic one. Furthermore, by carefully examining the choice of cost functional, we establish a robust optimisation procedure that can systematically locate dynamo solutions on short time horizons with no prior knowledge of its structure., Comment: 21 pages, 8 figures

Misinformation is a complex societal issue, and mitigating solutions are difficult to create due to data deficiencies. To address this problem, we have curated the largest collection of (mis)information datasets in the literature, totaling 75. From these, we evaluated the quality of all of the 36 datasets that consist of statements or claims. We assess these datasets to identify those with solid foundations for empirical work and those with flaws that could result in misleading and non-generalizable results, such as insufficient label quality, spurious correlations, or political bias. We further provide state-of-the-art baselines on all these datasets, but show that regardless of label quality, categorical labels may no longer give an accurate evaluation of detection model performance. We discuss alternatives to mitigate this problem. Overall, this guide aims to provide a roadmap for obtaining higher quality data and conducting more effective evaluations, ultimately improving research in misinformation detection. All datasets and other artifacts are available at https://misinfo-datasets.complexdatalab.com/.

The vast size of Large Language Models (LLMs) has prompted a search to optimize inference. One effective approach is dynamic inference, which adapts the architecture to the sample-at-hand to reduce the overall computational cost. We empirically examine two common dynamic inference methods for natural language generation (NLG): layer skipping and early exiting. We find that a pre-trained decoder-only model is significantly more robust to layer removal via layer skipping, as opposed to early exit. We demonstrate the difficulty of using hidden state information to adapt computation on a per-token basis for layer skipping. Finally, we show that dynamic computation allocation on a per-sequence basis holds promise for significant efficiency gains by constructing an oracle controller. Remarkably, we find that there exists an allocation which achieves equal performance to the full model using only 23.3% of its layers on average.

Recent work has shown promising results for learning end-to-end robot policies using imitation learning. In this work we address the question of how far can we push imitation learning for challenging dexterous manipulation tasks. We show that a simple recipe of large scale data collection on the ALOHA 2 platform, combined with expressive models such as Diffusion Policies, can be effective in learning challenging bimanual manipulation tasks involving deformable objects and complex contact rich dynamics. We demonstrate our recipe on 5 challenging real-world and 3 simulated tasks and demonstrate improved performance over state-of-the-art baselines. The project website and videos can be found at aloha-unleashed.github.io.

In Deep Reinforcement Learning models trained using gradient-based techniques, the choice of optimizer and its learning rate are crucial to achieving good performance: higher learning rates can prevent the model from learning effectively, while lower ones might slow convergence. Additionally, due to the non-stationarity of the objective function, the best-performing learning rate can change over the training steps. To adapt the learning rate, a standard technique consists of using decay schedulers. However, these schedulers assume that the model is progressively approaching convergence, which may not always be true, leading to delayed or premature adjustments. In this work, we propose dynamic Learning Rate for deep Reinforcement Learning (LRRL), a meta-learning approach that selects the learning rate based on the agent's performance during training. LRRL is based on a multi-armed bandit algorithm, where each arm represents a different learning rate, and the bandit feedback is provided by the cumulative returns of the RL policy to update the arms' probability distribution. Our empirical results demonstrate that LRRL can substantially improve the performance of deep RL algorithms.

This report summarizes what has happened in the mini-workshops entitled ''My Earth in 180 minutes'' organized during the lunch break at the SF2A 2024 conference in Marseille. The project showcased an innovative serious game designed to raise awareness of greenhouse gas (GHG) emissions in astronomical research laboratories. Participants, organized into teams, simulate strategies to reduce their carbon footprints by 50\%, focusing on key astronomical activities such as space instrumentation, data analysis, and laboratory work. The sessions highlight the challenges of achieving significant emissions reductions without disrupting core research activities, such as telescope observations. While the serious game facilitates important discussions on sustainable practices, the results point to the need for broader engagement, adaptation to different cultural contexts, and institutional support. The project highlights the importance of integrating climate action into the academic environment and suggests potential future directions for expanding its impact., Comment: SF2A 2024, Jun 2024, Marseille, France

Bayesian Optimal Experimental Design (BOED) is a powerful tool to reduce the cost of running a sequence of experiments. When based on the Expected Information Gain (EIG), design optimization corresponds to the maximization of some intractable expected {\it contrast} between prior and posterior distributions. Scaling this maximization to high dimensional and complex settings has been an issue due to BOED inherent computational complexity. In this work, we introduce an {\it expected posterior} distribution with cost-effective sampling properties and provide a tractable access to the EIG contrast maximization via a new EIG gradient expression. Diffusion-based samplers are used to compute the dynamics of the expected posterior and ideas from bi-level optimization are leveraged to derive an efficient joint sampling-optimization loop, without resorting to lower bound approximations of the EIG. The resulting efficiency gain allows to extend BOED to the well-tested generative capabilities of diffusion models. By incorporating generative models into the BOED framework, we expand its scope and its use in scenarios that were previously impractical. Numerical experiments and comparison with state-of-the-art methods show the potential of the approach.

We provide a unified framework in which the three emotions at the heart of narrative tension (curiosity, suspense and surprise) are formalized. This framework is built on nonmonotonic reasoning which allows us to compactly represent the default behavior of the world and to simulate the affective evolution of an agent receiving a story. After formalizing the notions of awareness, curiosity, surprise and suspense, we explore the properties induced by our definitions and study the computational complexity of detecting them. We finally propose means to evaluate these emotions' intensity for a given agent listening to a story.

In this study, we propose a novel approach to uncover subgroup-specific and subgroup-common latent factors addressing the challenges posed by the heterogeneity of neurological and mental disorders, which hinder disease understanding, treatment development, and outcome prediction. The proposed approach, sparse Group Factor Analysis (GFA) with regularised horseshoe priors, was implemented with probabilistic programming and can uncover associations (or latent factors) among multiple data modalities differentially expressed in sample subgroups. Synthetic data experiments showed the robustness of our sparse GFA by correctly inferring latent factors and model parameters. When applied to the Genetic Frontotemporal Dementia Initiative (GENFI) dataset, which comprises patients with frontotemporal dementia (FTD) with genetically defined subgroups, the sparse GFA identified latent disease factors differentially expressed across the subgroups, distinguishing between "subgroup-specific" latent factors within homogeneous groups and "subgroup common" latent factors shared across subgroups. The latent disease factors captured associations between brain structure and non-imaging variables (i.e., questionnaires assessing behaviour and disease severity) across the different genetic subgroups, offering insights into disease profiles. Importantly, two latent factors were more pronounced in the two more homogeneous FTD patient subgroups (progranulin (GRN) and microtubule-associated protein tau (MAPT) mutation), showcasing the method's ability to reveal subgroup-specific characteristics. These findings underscore the potential of sparse GFA for integrating multiple data modalities and identifying interpretable latent disease factors that can improve the characterization and stratification of patients with neurological and mental health disorders., Comment: 38 pages, 14 figures

Mediation analysis aims to identify and estimate the effect of an exposure on an outcome that is mediated through one or more intermediate variables. In the presence of multiple intermediate variables, two pertinent methodological questions arise: estimating mediated effects when mediators are correlated, and performing high-dimensional mediation analysis when the number of mediators exceeds the sample size. This paper presents a two-step procedure for high-dimensional mediation analysis. The first step selects a reduced number of candidate mediators using an ad-hoc lasso penalty. The second step applies a procedure we previously developed to estimate the mediated and direct effects, accounting for the correlation structure among the retained candidate mediators. We compare the performance of the proposed two-step procedure with state-of-the-art methods using simulated data. Additionally, we demonstrate its practical application by estimating the causal role of DNA methylation in the pathway between smoking and rheumatoid arthritis using real data.

We investigate the exploration of rugged fitness landscapes by spatially structured populations with demes on the nodes of a graph, connected by migrations. In the rare migration regime, we find that finite structures can adapt more efficiently than very large ones, especially in high-dimensional fitness landscapes. Furthermore, we show that, in most landscapes, migration asymmetries associated with some suppression of natural selection allow the population to reach higher fitness peaks first. In this sense, suppression of selection can make early adaptation more efficient. However, the time it takes to reach the first fitness peak is then increased. We also find that suppression of selection tends to enhance finite-size effects. We extend our study to frequent migrations, suggesting that our conclusions hold in this regime. We then investigate the impact of spatial structure with rare migrations on long-term evolution by studying the steady state of the population. For this, we define an effective population size for the steady-state distribution. We find that suppression of selection is associated to reduced steady-state effective population sizes, and reduced average steady-state fitnesses., Comment: 53 pages, 28 figures

Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature correlations in amino acid usage due to the need to maintain complementary interaction interfaces. Thus, the problem of finding interacting pairs can be formulated as searching for a pairing of sequences that maximizes a sequence similarity or a coevolution score. Several methods have been developed to address this problem, applying different approximate optimization methods to different scores. We introduce DiffPaSS, a differentiable framework for flexible, fast, and hyperparameter-free optimization for pairing interacting biological sequences, which can be applied to a wide variety of scores. We apply it to a benchmark prokaryotic dataset, using mutual information and neighbor graph alignment scores. DiffPaSS outperforms existing algorithms for optimizing the same scores. We demonstrate the usefulness of our paired alignments for the prediction of protein complex structure. DiffPaSS does not require sequences to be aligned, and we also apply it to non-aligned sequences from T cell receptors., Comment: 25 pages, 16 figures

In this work, we present a novel approach to type design by using Fourier-type series to generate letterforms. We construct a Fourier-type series for functions in $L^2(S^1,\mathbb C)$ based on triangles of constant width instead of circles to model the curves and shapes that define individual characters. In order to compute the coefficients of the series, we construct an isomorphism $\mathcal R:L^2(S^1,\mathbb C)\to L^2(S^1,\mathbb C)$ and study its application to letterforms, thus presenting an alternative to the common use of B\'ezier curves. The proposed method demonstrates potential for creative experimentation in modern type design., Comment: 14 pages, 9 figures

Bacterial populations often have complex spatial structures, which can impact their evolution. Here, we study how spatial structure affects the evolution of antibiotic resistance in a bacterial population. We consider a minimal model of spatially structured populations where all demes (i.e., subpopulations) are identical and connected to each other by identical migration rates. We show that spatial structure can facilitate the survival of a bacterial population to antibiotic treatment, starting from a sensitive inoculum. Specifically, the bacterial population can be rescued if antibiotic resistant mutants appear and are present when drug is added, and spatial structure can impact the fate of these mutants and the probability that they are present. Indeed, the probability of fixation of neutral or deleterious mutations providing drug resistance is increased in smaller populations. This promotes local fixation of resistant mutants in the structured population, which facilitates evolutionary rescue by drug resistance in the rare mutation regime. Once the population is rescued by resistance, migrations allow resistant mutants to spread in all demes. Our main result that spatial structure facilitates evolutionary rescue by antibiotic resistance extends to more complex spatial structures, and to the case where there are resistant mutants in the inoculum.

Artificial Intelligence (AI) for health has the potential to significantly change and improve healthcare. However in most African countries, identifying culturally and contextually attuned approaches for deploying these solutions is not well understood. To bridge this gap, we conduct a qualitative study to investigate the best practices, fairness indicators, and potential biases to mitigate when deploying AI for health in African countries, as well as explore opportunities where artificial intelligence could make a positive impact in health. We used a mixed methods approach combining in-depth interviews (IDIs) and surveys. We conduct 1.5-2 hour long IDIs with 50 experts in health, policy, and AI across 17 countries, and through an inductive approach we conduct a qualitative thematic analysis on expert IDI responses. We administer a blinded 30-minute survey with case studies to 672 general population participants across 5 countries in Africa and analyze responses on quantitative scales, statistically comparing responses by country, age, gender, and level of familiarity with AI. We thematically summarize open-ended responses from surveys. Our results find generally positive attitudes, high levels of trust, accompanied by moderate levels of concern among general population participants for AI usage for health in Africa. This contrasts with expert responses, where major themes revolved around trust/mistrust, ethical concerns, and systemic barriers to integration, among others. This work presents the first-of-its-kind qualitative research study of the potential of AI for health in Africa from an algorithmic fairness angle, with perspectives from both experts and the general population. We hope that this work guides policymakers and drives home the need for further research and the inclusion of general population perspectives in decision-making around AI usage., Comment: added illustrative figures