We present a neural-network emulator for the thermal and chemical evolution in Population III star formation. The emulator accurately reproduces the thermochemical evolution over a wide density range spanning 21 orders of magnitude (10$^{-3}$-10$^{18}$ cm$^{-3}$), tracking six primordial species: H, H$_2$, e$^{-}$, H$^{+}$, H$^{-}$, and H$_2^{+}$. To handle the broad dynamic range, we partition the density range into five subregions and train separate deep operator networks (DeepONets) in each region. When applied to randomly sampled thermochemical states, the emulator achieves relative errors below 10% in over 90% of cases for both temperature and chemical abundances (except for the rare species H$_2^{+}$). The emulator is roughly ten times faster on a CPU and more than 1000 times faster for batched predictions on a GPU, compared with conventional numerical integration. Furthermore, to ensure robust predictions under many iterations, we introduce a novel timescale-based update method, where a short-timestep update of each variable is computed by rescaling the predicted change over a longer timestep equal to its characteristic variation timescale. In one-zone collapse calculations, the results from the timescale-based method agree well with traditional numerical integration even with many iterations at a timestep as short as 10$^{-4}$ of the free-fall time. This proof-of-concept study suggests the potential for neural network-based chemical emulators to accelerate hydrodynamic simulations of star formation.

The analysis of spatial data from biological imaging technology, such as imaging mass spectrometry (IMS) or imaging mass cytometry (IMC), is challenging because of a competitive sampling process which convolves signals from molecules in a single pixel. To address this, we develop a scalable Bayesian framework that leverages natural sparsity in spatial signal patterns to recover relative rates for each molecule across the entire image. Our method relies on the use of a heavy-tailed variant of the graphical lasso prior and a novel hierarchical variational family, enabling efficient inference via automatic differentiation variational inference. Simulation results show that our approach outperforms state-of-the-practice point estimate methodologies in IMS, and has superior posterior coverage than mean-field variational inference techniques. Results on real IMS data demonstrate that our approach better recovers the true anatomical structure of known tissue, removes artifacts, and detects active regions missed by the standard analysis approach.

Microbiome sample representation to input into LLMs is essential for downstream tasks such as phenotype prediction and environmental classification. While prior studies have explored embedding-based representations of each microbiome sample, most rely on simple averaging over sequence embeddings, often overlooking the biological importance of taxa abundance. In this work, we propose an abundance-aware variant of the Set Transformer to construct fixed-size sample-level embeddings by weighting sequence embeddings according to their relative abundance. Without modifying the model architecture, we replicate embedding vectors proportional to their abundance and apply self-attention-based aggregation. Our method outperforms average pooling and unweighted Set Transformers on real-world microbiome classification tasks, achieving perfect performance in some cases. These results demonstrate the utility of abundance-aware aggregation for robust and biologically informed microbiome representation. To the best of our knowledge, this is one of the first approaches to integrate sequence-level abundance into Transformer-based sample embeddings.

ABSTRACT Standard Bayesian retrievals for exoplanet atmospheric parameters from transmission spectroscopy, while well understood and widely used, are generally computationally expensive. In the era of the JWST and other upcoming observatories, machine learning approaches have emerged as viable alternatives that are both efficient and robust. In this paper we present a systematic study of several existing machine learning regression techniques and compare their performance for retrieving exoplanet atmospheric parameters from transmission spectra. The regression methods tested here include partial least squares (PLS), support vector machines (SVM), k nearest neighbors (KNN), decision trees (DT), random forests (RF), voting (VOTE), stacking (STACK), and extreme gradient boosting (XGB). We also investigate the impact of different preprocessing methods of the training data on the model performance. We quantify the model uncertainties across the entire dynamical range of planetary parameters. The best performing combination of ML model and preprocessing scheme is validated on a the case study of JWST observation of WASP-39b. INTRODUCTION Over the last three decades, the study of extrasolar system planets has shifted from discovery to inference with particular interest in the characterization of their chemical compositions and temperature profiles. The chemical inventory of an exoplanet atmosphere is impacted by the planet formation processes, evolutionary modifications, and its interactions with the local space environment, thus allowing us to place constraints on the existing evolutionary models from the retrieved atmospheric composition. Transit spectroscopy is currently the most widely used observational technique to study the chemical composition of transiting exoplanets (Schneider 1994; Charbonneau et al. 2000). During transit, the planet atmosphere is observed in transmitted light when a planet passes in front of its host star, i.e., the primary eclipse, and in emitted and/or reflected light when a planet travels behind its host star, referred to as the secondary eclipse.

Neural Radiance Field (NeRF)-based segmentation methods focus on object semantics and rely solely on RGB data, lacking intrinsic material properties. This limitation restricts accurate material perception, which is crucial for robotics, augmented reality, simulation, and other applications. W e introduce UnMix-NeRF, a framework that integrates spectral unmixing into NeRF, enabling joint hy-perspectral novel view synthesis and unsupervised material segmentation. Our method models spectral reflectance via diffuse and specular components, where a learned dictionary of global endmembers represents pure material signatures, and per-point abundances capture their distribution. F or material segmentation, we use spectral signature predictions along learned endmembers, allowing unsupervised material clustering. Additionally, UnMix-NeRF enables scene editing by modifying learned endmember dictionaries for flexible material-based appearance manipulation.

Hyperspectral unmixing aims at estimating material signatures (known as endmembers) and the corresponding proportions (referred to abundances), which is a critical preprocessing step in various hyperspectral imagery applications. This study develops a novel approach called sparsity and total variation (TV) constrained multilayer linear unmixing (STVMLU) for hyperspectral imagery. Specifically, based on a multilayer matrix factorization model, to improve the accuracy of unmixing, a TV constraint is incorporated to consider adjacent spatial similarity. Additionally, a L1/2-norm sparse constraint is adopted to effectively characterize the sparsity of the abundance matrix. For optimizing the STVMLU model, the method of alternating direction method of multipliers (ADMM) is employed, which allows for the simultaneous extraction of endmembers and their corresponding abundance matrix. Experimental results illustrate the enhanced performance of the proposed STVMLU when compared to other algorithms.

There is no much doubt that biotic interactions shape community assembly and ultimately the spatial co-variations between species. There is a hope that the signal of these biotic interactions can be observed and retrieved by investigating the spatial associations between species while accounting for the direct effects of the environment. By definition, biotic interactions can be both symmetric and asymmetric. Yet, most models that attempt to retrieve species associations from co-occurrence or co-abundance data internally assume symmetric relationships between species. Here, we propose and validate a machine-learning framework able to retrieve bidirectional associations by analyzing species community and environmental data. Our framework (1) models pairwise species associations as directed influences from a source to a target species, parameterized with two species-specific latent embeddings: the effect of the source species on the community, and the response of the target species to the community; and (2) jointly fits these associations within a multi-species conditional generative model with different modes of interactions between environmental drivers and biotic associations. Using both simulated and empirical data, we demonstrate the ability of our framework to recover known asymmetric and symmetric associations and highlight the properties of the learned association networks. By comparing our approach to other existing models such as joint species distribution models and probabilistic graphical models, we show its superior capacity at retrieving symmetric and asymmetric interactions. The framework is intuitive, modular and broadly applicable across various taxonomic groups.

In 2017, a game design thinktank called Project Horseshoe gathered a group of developers together to define the concept of cosiness in video games. Games, of course, have had non-violent elements since the medium was invented. Early life simulators such as 1985's Little Computer People, a low-stakes game in which the player interacts with a man living his unremarkable life in a house, could fit the bill; then there was the proliferation of social farming simulations after 1996's chibi-adorable Harvest Moon. But the resulting report, Coziness in Games: An Exploration of Safety, Softness, and Satisfied Needs, is probably the first organised effort to define a then-emerging genre. Cosy games (cozy in US spelling) don't have high-risk scenarios: "There is no impending loss of threat," they wrote.

We present COMPASS, a novel simulation-based inference framework that combines score-based diffusion models with transformer architectures to jointly perform parameter estimation and Bayesian model comparison across competing Galactic Chemical Evolution (GCE) models. COMPASS handles high-dimensional, incomplete, and variable-size stellar abundance datasets. Applied to high-precision elemental abundance measurements, COMPASS evaluates 40 combinations of nucleosynthetic yield tables. The model strongly favours Asymptotic Giant Branch yields from NuGrid and core-collapse SN yields used in the IllustrisTNG simulation, achieving near-unity cumulative posterior probability. Using the preferred model, we infer a steep high-mass IMF slope and an elevated Supernova Ia normalization, consistent with prior solar neighbourhood studies but now derived from fully amortized Bayesian inference. Our results demonstrate that modern SBI methods can robustly constrain uncertain physics in astrophysical simulators and enable principled model selection when analysing complex, simulation-based data.

Context. The outer Milky Way has a lower metallicity than our solar neighbourhood, but still many molecules are detected in the region. Molecular line ratios can serve as probes to better understand the chemistry and physics in these regions. Aims. We use interpretable machine learning to study 9 different molecular ratios, helping us understand the forward connection between the physics of these environments and the carbon and oxygen chemistries. Methods. Using a large grid of astrochemical models generated using UCLCHEM, we study the properties of molecular clouds of low oxygen and carbon initial abundance. We first try to understand the line ratios using a classical analysis. We then move on to using interpretable machine learning, namely Shapley Additive Explanations (SHAP), to understand the higher order dependencies of the ratios over the entire parameter grid. Lastly we use the Uniform Manifold Approximation and Projection technique (UMAP) as a reduction method to create intuitive groupings of models. Results. We find that the parameter space is well covered by the line ratios, allowing us to investigate all input parameters. SHAP analysis shows that the temperature and density are the most important features, but the carbon and oxygen abundances are important in parts of the parameter space. Lastly, we find that we can group different types of ratios using UMAP. Conclusions. We show the chosen ratios are mostly sensitive to changes in the carbon initial abundance, together with the temperature and density. Especially the CN/HCN and HNC/HCN ratio are shown to be sensitive to the initial carbon abundance, making them excellent probes for this parameter. Out of the ratios, only CS/SO shows a sensitivity to the oxygen abundance.