Daily Papers

There will be a paradigm shift in chemical and biological research, to be enabled by autonomous, closed-loop, real-time self-directed decision-making experimentation. Spectrum-to-structure correlation, which is to elucidate molecular structures with spectral information, is the core step in understanding the experimental results and to close the loop. However, current approaches usually divide the task into either database-dependent retrieval and database-independent generation and neglect the inherent complementarity between them. In this study, we proposed Vib2Mol, a general deep learning model designed to flexibly handle diverse spectrum-to-structure tasks according to the available prior knowledge by bridging the retrieval and generation. It achieves state-of-the-art performance, even for the most demanding Raman spectra, over previous models in predicting reaction products and sequencing peptides as well as analyzing experimental spectra and integrating multi-modal spectral data. Vib2Mol enables vibrational spectroscopy a real-time guide for autonomous scientific discovery workflows.

Identifying a small molecule from its mass spectrum is the primary open problem in computational metabolomics. This is typically cast as information retrieval: an unknown spectrum is matched against spectra predicted computationally from a large database of chemical structures. However, current approaches to spectrum prediction model the output space in ways that force a tradeoff between capturing high resolution mass information and tractable learning. We resolve this tradeoff by casting spectrum prediction as a mapping from an input molecular graph to a probability distribution over molecular formulas. We discover that a large corpus of mass spectra can be closely approximated using a fixed vocabulary constituting only 2% of all observed formulas. This enables efficient spectrum prediction using an architecture similar to graph classification - GrAFF-MS - achieving significantly lower prediction error and orders-of-magnitude faster runtime than state-of-the-art methods.

Advancements in space telescopes have opened new avenues for gathering vast amounts of data on exoplanet atmosphere spectra. However, accurately extracting chemical and physical properties from these spectra poses significant challenges due to the non-linear nature of the underlying physics. This paper presents novel machine learning models developed by the AstroAI team for the Ariel Data Challenge 2023, where one of the models secured the top position among 293 competitors. Leveraging Normalizing Flows, our models predict the posterior probability distribution of atmospheric parameters under different atmospheric assumptions. Moreover, we introduce an alternative model that exhibits higher performance potential than the winning model, despite scoring lower in the challenge. These findings highlight the need to reevaluate the evaluation metric and prompt further exploration of more efficient and accurate approaches for exoplanet atmosphere spectra analysis. Finally, we present recommendations to enhance the challenge and models, providing valuable insights for future applications on real observational data. These advancements pave the way for more effective and timely analysis of exoplanet atmospheric properties, advancing our understanding of these distant worlds.

With the advent of new spectroscopic surveys from ground and space, observing up to hundreds of millions of galaxies, spectra classification will become overwhelming for standard analysis techniques. To prepare for this challenge, we introduce a family of deep learning tools to classify features in one-dimensional spectra. As the first application of these Galaxy Spectra neural Networks (GaSNets), we focus on tools specialized at identifying emission lines from strongly lensed star-forming galaxies in the eBOSS spectra. We first discuss the training and testing of these networks and define a threshold probability, PL, of 95% for the high quality event detection. Then, using a previous set of spectroscopically selected strong lenses from eBOSS, confirmed with HST, we estimate a completeness of ~80% as the fraction of lenses recovered above the adopted PL. We finally apply the GaSNets to ~1.3M spectra to collect a first list of ~430 new high quality candidates identified with deep learning applied to spectroscopy and visually graded as highly probable real events. A preliminary check against ground-based observations tentatively shows that this sample has a confirmation rate of 38%, in line with previous samples selected with standard (no deep learning) classification tools and follow-up by Hubble Space Telescope. This first test shows that machine learning can be efficiently extended to feature recognition in the wavelength space, which will be crucial for future surveys like 4MOST, DESI, Euclid, and the Chinese Space Station Telescope (CSST).

The coldest Y spectral type brown dwarfs are similar in mass and temperature to cool and warm (sim200 -- 400 K) giant exoplanets. We can therefore use their atmospheres as proxies for planetary atmospheres, testing our understanding of physics and chemistry for these complex, cool worlds. At these cold temperatures, their atmospheres are cold enough for water clouds to form, and chemical timescales increase, increasing the likelihood of disequilibrium chemistry compared to warmer classes of planets. JWST observations are revolutionizing the characterization of these worlds with high signal-to-noise, moderate resolution near- and mid-infrared spectra. The spectra have been used to measure the abundances of prominent species like water, methane, and ammonia; species that trace chemical reactions like carbon monoxide; and even isotopologues of carbon monoxide and ammonia. Here, we present atmospheric retrieval results using both published fixed-slit (GTO program 1230) and new averaged time series observations (GO program 2327) of the coldest known Y dwarf, WISE 0855-0714 (using NIRSpec G395M spectra), which has an effective temperature of sim 264 K. We present a detection of deuterium in an atmosphere outside of the solar system via a relative measurement of deuterated methane (CH_{3}D) and standard methane. From this, we infer the D/H ratio of a substellar object outside the solar system for the first time. We also present a well-constrained part-per-billion abundance of phosphine (PH_{3}). We discuss our interpretation of these results and the implications for brown dwarf and giant exoplanet formation and evolution.

Half of the JWST high-contrast imaging objects will only have photometric data {{as of Cycle 2}}. However, to better understand their atmospheric chemistry which informs formation origin, spectroscopic data are preferred. Using HIP 65426 b, we investigate to what extent planet properties and atmospheric chemical abundance can be retrieved with only JWST photometric data points (2.5-15.5 mum) in conjunction with ground-based archival low-resolution spectral data (1.0-2.3 mum). We find that the data is consistent with an atmosphere with solar metallicity and C/O ratios at 0.40 and 0.55. We rule out 10x solar metallicity and an atmosphere with C/O = 1.0. We also find strong evidence of silicate clouds but no sign of an enshrouding featureless {{dust}} extinction. This work offers guidance and cautionary tales on analyzing data in the absence of medium-to-high resolution spectral data.

Recent space-borne and ground-based observations provide photometric measurements as time series. The effect of interstellar dust extinction in the near-infrared range is only 10% of that measured in the V band. However, the sensitivity of the light curve shape to the physical parameters in the near-infrared is much lower. So, interpreting these types of data sets requires new approaches like the different large-scale surveys, which create similar problems with big data. Using a selected data set, we provide a method for applying routines implemented in R to extract most information of measurements to determine physical parameters, which can also be used in automatic classification schemes and pipeline processing. We made a multivariate classification of 131 Cepheid light curves (LC) in J, H, and K colors, where all the LCs were represented in 20D parameter space in these colors separately. Performing a Principal Component Analysis (PCA), we got an orthogonal coordinate system and squared Euclidean distances between LCs, with 6 significant eigenvalues, reducing the 20-dimension to 6. We also estimated the optimal number of partitions of similar objects and found it to be equal to 7 in each color; their dependence on the period, absolute magnitude, amplitude, and metallicity are also discussed. We computed the Spearman rank correlations, showing that periods and absolute magnitudes correlate with the first three PCs significantly. The first two PC are also found to have a relationship with the amplitude, but the metallicity effects are only marginal. The method shown can be generalized and implemented in unsupervised classification schemes and analysis of mixed and biased samples. The analysis of our Classical Cepheid near-infrared LC sample showed that the J, H, K curves are insufficient for determination of stellar metallicity, with mass being the key factor shaping them.

The binding energies of the five bound rotational levels J=0-4 in the highest vibrational level v=14 in the X^1Sigma_g^+ ground electronic state of H_2 were measured in a three-step ultraviolet-laser experiment. Two-photon UV-photolysis of H_2S produced population in these high-lying bound states, that were subsequently interrogated at high precision via Doppler-free spectroscopy of the F^1Sigma_g^+ - X^1Sigma_g^+ system. A third UV-laser was used for detection through auto-ionizing resonances. The experimentally determined binding energies were found to be in excellent agreement with calculations based on non-adiabatic perturbation theory, also including relativistic and quantum electrodynamical contributions. The s-wave scattering length of the H + H system is derived from the binding energy of the last bound J=0 level via a direct semi-empirical approach, yielding a value of a_s = 0.2724(5) a_0, in good agreement with a result from a previously followed theoretical approach. The subtle effect of the malpha^4 relativity contribution to a_s was found to be significant. In a similar manner a value for the p-wave scattering volume is determined via the J=1 binding energy yielding a_p = -134.0000(6) a_0^3. The binding energy of the last bound state in H_2, the (v=14, J=4) level, is determined at 0.023(4) cm^{-1}, in good agreement with calculation. The effect of the hyperfine substructure caused by the two hydrogen atoms at large internuclear separation, giving rise to three distinct dissociation limits, is discussed.

Attempts to probe the atmospheres of rocky planets around M dwarfs present both promise and peril. While their favorable planet-to-star radius ratios enable searches for even thin secondary atmospheres, their high activity levels and high-energy outputs threaten atmosphere survival. Here, we present the 0.6--2.85\,mum transmission spectrum of the 1.1\,rm R_oplus, sim340\,K rocky planet TRAPPIST-1\,c obtained over two JWST NIRISS/SOSS transit observations. Each of the two spectra displays 100--500\,ppm signatures of stellar contamination. Despite being separated by 367\,days, the retrieved spot and faculae properties are consistent between the two visits, resulting in nearly identical transmission spectra. Jointly retrieving for stellar contamination and a planetary atmosphere reveals that our spectrum can rule out hydrogen-dominated, lesssim300times solar metallicity atmospheres with effective surface pressures down to 10\,mbar at the 3-sigma level. For high-mean molecular weight atmospheres, where O_2 or N_2 is the background gas, our spectrum disfavors partial pressures of more than sim10\,mbar for H_2O, CO, NH_3 and CH_4 at the 2-sigma level. Similarly, under the assumption of a 100\% H_2O, NH_3, CO, or CH_4 atmosphere, our spectrum disfavors thick, >1\,bar atmospheres at the 2-sigma level. These non-detections of spectral features are in line with predictions that even heavier, CO_2-rich, atmospheres would be efficiently lost on TRAPPIST-1\,c given the cumulative high-energy irradiation experienced by the planet. Our results further stress the importance of robustly accounting for stellar contamination when analyzing JWST observations of exo-Earths around M dwarfs, as well as the need for high-fidelity stellar models to search for the potential signals of thin secondary atmospheres.

Recent advancements in artificial intelligence have sparked interest in scientific assistants that could support researchers across the full spectrum of scientific workflows, from literature review to experimental design and data analysis. A key capability for such systems is the ability to process and reason about scientific information in both visual and textual forms - from interpreting spectroscopic data to understanding laboratory setups. Here, we introduce MaCBench, a comprehensive benchmark for evaluating how vision-language models handle real-world chemistry and materials science tasks across three core aspects: data extraction, experimental understanding, and results interpretation. Through a systematic evaluation of leading models, we find that while these systems show promising capabilities in basic perception tasks - achieving near-perfect performance in equipment identification and standardized data extraction - they exhibit fundamental limitations in spatial reasoning, cross-modal information synthesis, and multi-step logical inference. Our insights have important implications beyond chemistry and materials science, suggesting that developing reliable multimodal AI scientific assistants may require advances in curating suitable training data and approaches to training those models.

This study introduces a line list for the abundance analysis of F and G type stars across the 4080-9675 A wavelength range. A systematic search employing lower excitation potentials, accurate log gf values, and an updated multiplet table led to the identification of 592 lines across 33 species (25 elements), including C, O, Mg (ionized), Al, P, S, Cu, Zr (neutral), and La. To determine the uncertainties in log gf values, we assessed solar abundance using a very high-resolution (R=1000000) disk-integrated solar spectrum. These lines were confirmed to be blend-free in the solar spectrum. The line list was further validated by analyzing the metal-poor star HD 218209 (G6V), which is notable for its well-documented and reliable abundance in literature. The abundances were obtained using the equivalent width (EW) method and further refined by applying the spectrum synthesis method. A comparative analysis with the Gaia ESO line list v.6, provided by the Gaia ESO collaboration, revealed additional neutral and ionized Fe lines. This extensively refined line list will facilitate precise stellar parameter determinations and accurate abundance analyses of spectra within the PolarBASE spectral library.

Large sky spectroscopic surveys have reached the scale of photometric surveys in terms of sample sizes and data complexity. These huge datasets require efficient, accurate, and flexible automated tools for data analysis and science exploitation. We present the Galaxy Spectra Network/GaSNet-II, a supervised multi-network deep learning tool for spectra classification and redshift prediction. GaSNet-II can be trained to identify a customized number of classes and optimize the redshift predictions for classified objects in each of them. It also provides redshift errors, using a network-of-networks that reproduces a Monte Carlo test on each spectrum, by randomizing their weight initialization. As a demonstration of the capability of the deep learning pipeline, we use 260k Sloan Digital Sky Survey spectra from Data Release 16, separated into 13 classes including 140k galactic, and 120k extragalactic objects. GaSNet-II achieves 92.4% average classification accuracy over the 13 classes (larger than 90% for the majority of them), and an average redshift error of approximately 0.23% for galaxies and 2.1% for quasars. We further train/test the same pipeline to classify spectra and predict redshifts for a sample of 200k 4MOST mock spectra and 21k publicly released DESI spectra. On 4MOST mock data, we reach 93.4% accuracy in 10-class classification and an average redshift error of 0.55% for galaxies and 0.3% for active galactic nuclei. On DESI data, we reach 96% accuracy in (star/galaxy/quasar only) classification and an average redshift error of 2.8% for galaxies and 4.8% for quasars, despite the small sample size available. GaSNet-II can process ~40k spectra in less than one minute, on a normal Desktop GPU. This makes the pipeline particularly suitable for real-time analyses of Stage-IV survey observations and an ideal tool for feedback loops aimed at night-by-night survey strategy optimization.

In this work, we present the ChemNLP library that can be used for 1) curating open access datasets for materials and chemistry literature, developing and comparing traditional machine learning, transformers and graph neural network models for 2) classifying and clustering texts, 3) named entity recognition for large-scale text-mining, 4) abstractive summarization for generating titles of articles from abstracts, 5) text generation for suggesting abstracts from titles, 6) integration with density functional theory dataset for identifying potential candidate materials such as superconductors, and 7) web-interface development for text and reference query. We primarily use the publicly available arXiv and Pubchem datasets but the tools can be used for other datasets as well. Moreover, as new models are developed, they can be easily integrated in the library. ChemNLP is available at the websites: https://github.com/usnistgov/chemnlp and https://jarvis.nist.gov/jarvischemnlp.

The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of molecular structures. However, decoding a molecular structure from its mass spectrum is exceptionally challenging, even when performed by human experts. As a result, the vast majority of acquired MS/MS spectra remain uninterpreted, thereby limiting our understanding of the underlying (bio)chemical processes. Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym -- the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. Our benchmark comprises the largest publicly available collection of high-quality labeled MS/MS spectra and defines three MS/MS annotation challenges: de novo molecular structure generation, molecule retrieval, and spectrum simulation. It includes new evaluation metrics and a generalization-demanding data split, therefore standardizing the MS/MS annotation tasks and rendering the problem accessible to the broad machine learning community. MassSpecGym is publicly available at https://github.com/pluskal-lab/MassSpecGym.

We present a web-based software tool, the Virtual Quantum Optics Laboratory (VQOL), that may be used for designing and executing realistic simulations of quantum optics experiments. A graphical user interface allows one to rapidly build and configure a variety of different optical experiments, while the runtime environment provides unique capabilities for visualization and analysis. All standard linear optical components are available as well as sources of thermal, coherent, and entangled Gaussian states. A unique aspect of VQOL is the introduction of non-Gaussian measurements using detectors modeled as deterministic devices that "click" when the amplitude of the light falls above a given threshold. We describe the underlying theoretical models and provide several illustrative examples. We find that VQOL provides a a faithful representation of many experimental quantum optics phenomena and may serve as both a useful instructional tool for students as well as a valuable research tool for practitioners.

Isotopic substitution in molecular systems can affect fundamental molecular properties including the energy position and spacing of electronic, vibrational and rotational levels, thus modifying the dynamics associated to their coherent superposition. In extreme ultraviolet spectroscopy, the photoelectron leaving the molecule after the absorption of a single photon can trigger an ultrafast nuclear motion in the cation, which can lead, eventually, to molecular fragmentation. This dynamics depends on the mass of the constituents of the cation, thus showing, in general, a significant isotopic dependence. In time-resolved attosecond photoelectron interferometry, the absorption of the extreme ultraviolet photon is accompanied by the exchange of an additional quantum of energy (typically in the infrared spectral range) with the photoelectron-photoion system, offering the opportunity to investigate in time the influence of isotopic substitution on the characteristics of the photoionisation dynamics. Here we show that attosecond photoelectron interferometry is sensitive to isotopic substitution by investigating the two-color photoionisation spectra measured in a mixture of methane (CH_4) and deuteromethane (CD_4). The isotopic dependence manifests itself in the modification of the amplitude and contrast of the oscillations of the photoelectron peaks generated in the two-color field with the two isotopologues. The observed effects are interpreted considering the differences in the time evolution of the nuclear autocorrelation functions in the two molecules.

Blazars, a class of active galactic nuclei (AGN) powered by supermassive black holes, are known for their remarkable variability across multiple timescales and wavelengths. With advancements in both ground- and space-based telescopes, our understanding of AGN central engines has significantly improved. However, the mechanisms driving this variability remain elusive, and continue to fascinate both theorists and observers alike. The primary objective of this study is to constrain the X-ray variability properties of the TeV blazar PKS 2155-304. We conduct a comprehensive X-ray spectral and timing analysis, focusing on both long-term and intra-day variability. This analysis uses data from 22 epochs of XMM-Newton EPIC-pn observations, collected over 15 years (2000-2014). To investigate the variability of the source, we applied both timing and spectral analyses. For the timing analysis, we estimated fractional variability, variability amplitude, minimum variability timescales, flux distribution, and power spectral density (PSD). In the spectral analysis, we fitted the X-ray spectra using power-law, log-parabola, and broken power-law (BPL) models to determine the best-fitting parameters. Additionally, we studied the hardness ratio (HR). We observed moderate intra-day variability in most of the light curves. Seven out of the twenty-two observations showed a clear bimodal flux distribution, indicating the presence of two distinct flux states. Our analysis revealed a variable power-law PSD slope. Most HR plots did not show significant variation with flux, except for one observation (OBSID 0124930501), where HR increased with flux (Count/s). The fitted X-ray spectra favored the BPL model for the majority of observations. The findings of this work shed light on the intraday variability of blazars, providing insights into the non-thermal jet processes that drive the observed flux variations.

Knowledge of mixtures' phase equilibria is crucial in nature and technical chemistry. Phase equilibria calculations of mixtures require activity coefficients. However, experimental data on activity coefficients is often limited due to high cost of experiments. For an accurate and efficient prediction of activity coefficients, machine learning approaches have been recently developed. However, current machine learning approaches still extrapolate poorly for activity coefficients of unknown molecules. In this work, we introduce the SMILES-to-Properties-Transformer (SPT), a natural language processing network to predict binary limiting activity coefficients from SMILES codes. To overcome the limitations of available experimental data, we initially train our network on a large dataset of synthetic data sampled from COSMO-RS (10 Million data points) and then fine-tune the model on experimental data (20 870 data points). This training strategy enables SPT to accurately predict limiting activity coefficients even for unknown molecules, cutting the mean prediction error in half compared to state-of-the-art models for activity coefficient predictions such as COSMO-RS, UNIFAC, and improving on recent machine learning approaches.

The polarization of an X-ray beam that produces electrons with velocity components perpendicular to the beam generates an azimuthal distribution of the ejected electrons. We present methods for simulating and for analyzing the angular dependence of electron detections which enable us to derive simple analytical expressions for useful statistical properties of observable data. The derivations are verified by simulations. While we confirm the results of previous work on this topic, we provide an extension needed for analytical treatment of the full range of possible polarization amplitudes.

There is vast evidence from observations of multiple stellar populations (MPs) in globular clusters (GCs). To explore the issue theoretically, this work considers two subsolar metallicities, two ages, and two initial abundance patterns: a first population of standard alpha-enhanced metal mixture stars and a second stellar population displaying C-N and Na-O anticorrelations chemical abundance patterns, along with an enhanced helium fraction. Analysing the predictions for these extreme compositions, we provide insights into the observability of not-resolved MPs into individual stars of GCs. We use colours and spectrophotometric indices measurable with modern facilities (e.g. Euclid, LSST, DES, JWST).

We present a low-cost ultraviolet to infrared absolute quantum efficiency detector characterization system developed using commercial off-the-shelf components. The key components of the experiment include a light source,a regulated power supply, a monochromator, an integrating sphere, and a calibrated photodiode. We provide a step-by-step procedure to construct the photon and quantum efficiency transfer curves of imaging sensors. We present results for the GSENSE 2020 BSI CMOS sensor and the Sony IMX 455 BSI CMOS sensor. As a reference for similar characterizations, we provide a list of parts and associated costs along with images of our setup.

Dusty post-red giant branch (post-RGB) stars are low- and intermediate-mass stars where the RGB evolution was prematurely terminated by a poorly understood binary interaction. These binary stars are considered to be low-luminosity analogues of post-asymptotic giant branch (post-AGB) binary stars. In this study, we investigated the chemical composition of two dusty post-RGB binary stars, SZ Mon and DF Cyg, using multi-wavelength spectroscopic data from HERMES/Mercator (optical) and the APOGEE survey (near-infrared). Owing to challenges posed by existing spectral analysis tools for the study of evolved stars with complex atmospheres, we developed E-iSpec: a dedicated spectral analysis tool for evolved stars, to consistently determine atmospheric parameters, elemental abundances, and carbon isotopic ratios. Our abundance analysis revealed that observed depletion patterns and estimated depletion efficiencies resemble those found in post-AGB binary stars. However, the onset of chemical depletion in post-RGB targets occurs at higher condensation temperatures (T_{rm turn-off, post-RGB}approx1400 K), than in most post-AGB stars (T_{rm turn-off, post-AGB}approx1100 K). Additionally, our study resulted in the first estimates of carbon isotopic ratios for post-RGB stars (^{12}C/^{13}C_{rm SZ Mon}=8pm4, ^{12}C/^{13}C_{rm DF Cyg}=12pm3). We found that the observationally derived CNO abundances and the carbon isotopic ratios of our post-RGB binary targets are in good agreement with theoretical predictions from the ATON single star evolutionary models involving first dredge-up and moderately-deep extra mixing. This agreement emphasises that in post-RGB binary targets, the observed CNO abundances reflect the chemical composition expected from single star nucleosynthesis (i.e., convective and non-convective mixing processes) occurring during the RGB phase before it is terminated.

Computational catalysis is playing an increasingly significant role in the design of catalysts across a wide range of applications. A common task for many computational methods is the need to accurately compute the minimum binding energy - the adsorption energy - for an adsorbate and a catalyst surface of interest. Traditionally, the identification of low energy adsorbate-surface configurations relies on heuristic methods and researcher intuition. As the desire to perform high-throughput screening increases, it becomes challenging to use heuristics and intuition alone. In this paper, we demonstrate machine learning potentials can be leveraged to identify low energy adsorbate-surface configurations more accurately and efficiently. Our algorithm provides a spectrum of trade-offs between accuracy and efficiency, with one balanced option finding the lowest energy configuration, within a 0.1 eV threshold, 86.33% of the time, while achieving a 1331x speedup in computation. To standardize benchmarking, we introduce the Open Catalyst Dense dataset containing nearly 1,000 diverse surfaces and 85,658 unique configurations.

The PRObabilistic Value-Added Bright Galaxy Survey (PROVABGS) catalog will provide measurements of galaxy properties, such as stellar mass (M_*), star formation rate ({rm SFR}), stellar metallicity (Z_{rm MW}), and stellar age (t_{rm age, MW}), for >10 million galaxies of the DESI Bright Galaxy Survey. Full posterior distributions of the galaxy properties will be inferred using state-of-the-art Bayesian spectral energy distribution (SED) modeling of DESI spectroscopy and Legacy Surveys photometry. In this work, we present the SED model, Bayesian inference framework, and methodology of PROVABGS. Furthermore, we apply the PROVABGS SED modeling on realistic synthetic DESI spectra and photometry, constructed using the L-GALAXIES semi-analytic model. We compare the inferred galaxy properties to the true galaxy properties of the simulation using a hierarchical Bayesian framework to quantify accuracy and precision. Overall, we accurately infer the true M_*, {rm SFR}, Z_{rm MW}, and t_{rm age, MW} of the simulated galaxies. However, the priors on galaxy properties induced by the SED model have a significant impact on the posteriors. They impose a {rm SFR}{>}10^{-1} M_odot/{rm yr} lower bound on {rm SFR}, a {sim}0.3 dex bias on log Z_{rm MW} for galaxies with low spectral signal-to-noise, and t_{rm age, MW} < 8,{rm Gyr} upper bound on stellar age. This work also demonstrates that a joint analysis of spectra and photometry significantly improves the constraints on galaxy properties over photometry alone and is necessary to mitigate the impact of the priors. With the methodology presented and validated in this work, PROVABGS will maximize information extracted from DESI observations and provide a probabilistic value-added galaxy catalog that will extend current galaxy studies to new regimes and unlock cutting-edge probabilistic analyses.

Astrochemical models of interstellar clouds, the sites of stars, and planet formation require information about spin-state chemistry to allow quantitative comparison with spectroscopic observations. In particular, it is important to know if full scrambling or H abstraction (also known as proton hopping) takes place in ion-neutral reactions. The reaction of Cl+ and HCl+ with H2 and isotopologues has been studied at cryogenic temperatures between 20 and 180 K using a 22 pole radio frequency ion trap. Isotopic exchange processes are used to probe the reaction mechanism of the HCl+ + H2 reaction. The results are compared with previous measurements and theoretical predictions. The rate coefficients for the Cl+ + H2 and HCl+ + H2 reactions are found to be constant in the range of temperatures studied, except for the DCl+ + D2 reaction, where a weak negative temperature dependence is observed, and reactions with D2 are found to be significantly slower than the Langevin rate. No isotopic exchange reactions are observed to occur for the H2Cl+ ion. The analysis of the products of the HCl+ + H2 isotopic system clearly indicates that the reaction proceeds via simple hydrogen atom abstraction.

Mechanistic Interpretability (MI) promises a path toward fully understanding how neural networks make their predictions. Prior work demonstrates that even when trained to perform simple arithmetic, models can implement a variety of algorithms (sometimes concurrently) depending on initialization and hyperparameters. Does this mean neuron-level interpretability techniques have limited applicability? We argue that high-dimensional neural networks can learn low-dimensional representations of their training data that are useful beyond simply making good predictions. Such representations can be understood through the mechanistic interpretability lens and provide insights that are surprisingly faithful to human-derived domain knowledge. This indicates that such approaches to interpretability can be useful for deriving a new understanding of a problem from models trained to solve it. As a case study, we extract nuclear physics concepts by studying models trained to reproduce nuclear data.

Supervised machine learning approaches have been increasingly used in accelerating electronic structure prediction as surrogates of first-principle computational methods, such as density functional theory (DFT). While numerous quantum chemistry datasets focus on chemical properties and atomic forces, the ability to achieve accurate and efficient prediction of the Hamiltonian matrix is highly desired, as it is the most important and fundamental physical quantity that determines the quantum states of physical systems and chemical properties. In this work, we generate a new Quantum Hamiltonian dataset, named as QH9, to provide precise Hamiltonian matrices for 999 or 2998 molecular dynamics trajectories and 130,831 stable molecular geometries, based on the QM9 dataset. By designing benchmark tasks with various molecules, we show that current machine learning models have the capacity to predict Hamiltonian matrices for arbitrary molecules. Both the QH9 dataset and the baseline models are provided to the community through an open-source benchmark, which can be highly valuable for developing machine learning methods and accelerating molecular and materials design for scientific and technological applications. Our benchmark is publicly available at https://github.com/divelab/AIRS/tree/main/OpenDFT/QHBench.

We here propose a machine learning approach for monitoring particle detectors in real-time. The goal is to assess the compatibility of incoming experimental data with a reference dataset, characterising the data behaviour under normal circumstances, via a likelihood-ratio hypothesis test. The model is based on a modern implementation of kernel methods, nonparametric algorithms that can learn any continuous function given enough data. The resulting approach is efficient and agnostic to the type of anomaly that may be present in the data. Our study demonstrates the effectiveness of this strategy on multivariate data from drift tube chamber muon detectors.

Low-mass X-ray binaries with a neutron star as the primary object show a complex array of phenomenology during outbursts. The observed variability in X-ray emission primarily arises from changes in the innermost regions of the accretion disk, neutron star surface, and corona. In this work, we present the results of a comprehensive X-ray spectral and timing analysis of the neutron star transient MAXI J1807+132 during its 2023 outburst using data from the NICER observatory. The outburst is marked by a very rapid rise in the count rate by about a factor of 20 in a day. The source undergoes full state transitions and displays hysteresis effect in the hardness and rms intensity diagrams. Spectral analysis with a three-component model is consistent with disk truncation during the hard states and reaching the last stable orbit during the intermediate and soft states. We discuss the different values of the last stable radius in the context of possible distance of the source and magnetic field strength. The characteristic frequencies throughout the hard and intermediate states are found to be strongly correlated with the inner radius of the disk. Together with the spectral and fast variability properties, we attempt to trace the evolution of the size of the corona along the outburst. Following the main outburst, the source undergoes a high amplitude reflare wherein it shows a complex behavior with relatively high variability (10 %), but low hardness.

HeH^+ was the first heteronuclear molecule to form in the metal-free Universe after the Big Bang. The molecule gained significant attention following its first circumstellar detection in the young and dense planetary nebula NGC 7027. We target some hydride ions associated with the noble gases (HeH^+, ArH^+, and NeH^+) to investigate their formation in harsh environments like the nova outburst region. We use a photoionization modeling (based on previously published best-fit physical parameters) of the moderately fast ONe type nova, QU Vulpeculae 1984, and the CO type novae, RS Ophiuchi and V1716 Scorpii. Our steady-state modeling reveals a convincing amount of HeH^+, especially in the dense clump of RS Ophiuchi and V1716 Scorpii. The calculated upper limit on the surface brightness of HeH^+ transitions suggests that the James Webb Space Telescope (JWST) could detect some of them, particularly in sources like RS Ophiuchi and V1716 Scorpii, which have similar physical and chemical conditions and evolution. It must be clearly noted that the sources studied are used as templates, and not as targets for observations. The detection of these lines could be useful for determining the physical conditions in similar types of systems and for validating our predictions based on new electron-impact ro-vibrational collisional data at temperatures of up to 20,000 K.

Measuring soil health indicators is an important and challenging task that affects farmers' decisions on timing, placement, and quantity of fertilizers applied in the farms. Most existing methods to measure soil health indicators (SHIs) are in-lab wet chemistry or spectroscopy-based methods, which require significant human input and effort, time-consuming, costly, and are low-throughput in nature. To address this challenge, we develop an artificial intelligence (AI)-driven near real-time unmanned aerial vehicle (UAV)-based multispectral sensing (UMS) solution to estimate total nitrogen (TN) of the soil, an important macro-nutrient or SHI that directly affects the crop health. Accurate prediction of soil TN can significantly increase crop yield through informed decision making on the timing of seed planting, and fertilizer quantity and timing. We train two machine learning models including multi-layer perceptron and support vector machine to predict the soil nitrogen using a suite of data classes including multispectral characteristics of the soil and crops in red, near-infrared, and green spectral bands, computed vegetation indices, and environmental variables including air temperature and relative humidity. To generate the ground-truth data or the training data for the machine learning models, we measure the total nitrogen of the soil samples (collected from a farm) using laser-induced breakdown spectroscopy (LIBS).

Hyperspectral unmixing (HU) is a very useful and increasingly popular preprocessing step for a wide range of hyperspectral applications. However, the HU research has been constrained a lot by three factors: (a) the number of hyperspectral images (especially the ones with ground truths) are very limited; (b) the ground truths of most hyperspectral images are not shared on the web, which may cause lots of unnecessary troubles for researchers to evaluate their algorithms; (c) the codes of most state-of-the-art methods are not shared, which may also delay the testing of new methods. Accordingly, this paper deals with the above issues from the following three perspectives: (1) as a profound contribution, we provide a general labeling method for the HU. With it, we labeled up to 15 hyperspectral images, providing 18 versions of ground truths. To the best of our knowledge, this is the first paper to summarize and share up to 15 hyperspectral images and their 18 versions of ground truths for the HU. Observing that the hyperspectral classification (HyC) has much more standard datasets (whose ground truths are generally publicly shared) than the HU, we propose an interesting method to transform the HyC datasets for the HU research. (2) To further facilitate the evaluation of HU methods under different conditions, we reviewed and implemented the algorithm to generate a complex synthetic hyperspectral image. By tuning the hyper-parameters in the code, we may verify the HU methods from four perspectives. The code would also be shared on the web. (3) To provide a standard comparison, we reviewed up to 10 state-of-the-art HU algorithms, then selected the 5 most benchmark HU algorithms, and compared them on the 15 real hyperspectral datasets. The experiment results are surely reproducible; the implemented codes would be shared on the web.

Evaluations are critical for understanding the capabilities of large language models (LLMs). Fundamentally, evaluations are experiments; but the literature on evaluations has largely ignored the literature from other sciences on experiment analysis and planning. This article shows researchers with some training in statistics how to think about and analyze data from language model evaluations. Conceptualizing evaluation questions as having been drawn from an unseen super-population, we present formulas for analyzing evaluation data, measuring differences between two models, and planning an evaluation experiment. We make a number of specific recommendations for running language model evaluations and reporting experiment results in a way that minimizes statistical noise and maximizes informativeness.

Food safety and quality are paramount concerns worldwide, especially concerning nutritional quality and its impact on human health. Ensuring the accuracy and efficiency of milk quality assessment is vital for maintaining the quality of dairy farm produce. Milk spectral data, Mid-infrared spectra (MIRS) of milk samples, are frequently employed for milk quality evaluations, encompassing various milk quality parameters. However, conventional milk quality analyses have overlooked the scaling nature, known as stochastic similarity in different scales, inherent in milk spectral data. Wavelet transforms are among the tools used in these analyses, although they are primarily used as data pre-processing techniques without fully realizing their potential in extracting valuable insights. The primary purpose of this study is to demonstrate the importance of accounting for scaling properties in assessing milk quality. A set of 12 descriptors is computed to characterize scaling properties in milk spectral data within the wavelet domain. These descriptors are then assessed for their effectiveness in milk quality assessments utilizing 18 different milk quality parameters. They notably demonstrated comparable performance to existing methods while utilizing fewer features when applied to an MIRS dataset. This innovative approach holds substantial promise for advancing the field of milk quality assessment, offering a means to achieve more accurate and efficient evaluations while shedding light on previously unexplored aspects of milk spectral data.

We present Monte Carlo (MC) simulation results from a study of a compact plastic-scintillator detector suitable for imaging fast neutrons in the 1 -- 10 MeV energy range: the miniTimeCube (mTC). Originally designed for antineutrino detection, the mTC consists of 24 MultiChannel Plate (MCP) photodetectors surrounding a 13 cm cube of boron-doped plastic scintillator. Our simulation results show that waveform digitization of 1536 optically sensitive channels surrounding the scintillator should allow for spatiotemporal determination of individual neutron-proton scatters in the detector volume to thicksim100 picoseconds and thicksim5 mm. A Bayesian estimation framework is presented for multiple-scatter reconstruction, and is used to estimate the incoming direction and energy of simulated individual neutrons. Finally, we show how populations of reconstructed neutrons can be used to estimate the direction and energy spectrum of nearby simulated neutron sources.

In science and medicine, model interpretations may be reported as discoveries of natural phenomena or used to guide patient treatments. In such high-stakes tasks, false discoveries may lead investigators astray. These applications would therefore benefit from control over the finite-sample error rate of interpretations. We reframe black box model interpretability as a multiple hypothesis testing problem. The task is to discover "important" features by testing whether the model prediction is significantly different from what would be expected if the features were replaced with uninformative counterfactuals. We propose two testing methods: one that provably controls the false discovery rate but which is not yet feasible for large-scale applications, and an approximate testing method which can be applied to real-world data sets. In simulation, both tests have high power relative to existing interpretability methods. When applied to state-of-the-art vision and language models, the framework selects features that intuitively explain model predictions. The resulting explanations have the additional advantage that they are themselves easy to interpret.

Spectrum of ^7Li and elastic scattering reaction ^4He(^3H, ^3H)^4He are studied using the unified description of the Gamow shell model in the coupled-channel formulation (GSMCC). The reaction channels are constructed using the cluster expansion with the two mass partitions [^4He + ^3H], [^6Li + n].

Catalyst discovery and optimization is key to solving many societal and energy challenges including solar fuels synthesis, long-term energy storage, and renewable fertilizer production. Despite considerable effort by the catalysis community to apply machine learning models to the computational catalyst discovery process, it remains an open challenge to build models that can generalize across both elemental compositions of surfaces and adsorbate identity/configurations, perhaps because datasets have been smaller in catalysis than related fields. To address this we developed the OC20 dataset, consisting of 1,281,040 Density Functional Theory (DFT) relaxations (~264,890,000 single point evaluations) across a wide swath of materials, surfaces, and adsorbates (nitrogen, carbon, and oxygen chemistries). We supplemented this dataset with randomly perturbed structures, short timescale molecular dynamics, and electronic structure analyses. The dataset comprises three central tasks indicative of day-to-day catalyst modeling and comes with pre-defined train/validation/test splits to facilitate direct comparisons with future model development efforts. We applied three state-of-the-art graph neural network models (CGCNN, SchNet, Dimenet++) to each of these tasks as baseline demonstrations for the community to build on. In almost every task, no upper limit on model size was identified, suggesting that even larger models are likely to improve on initial results. The dataset and baseline models are both provided as open resources, as well as a public leader board to encourage community contributions to solve these important tasks.

While machine-learned models are now routinely employed to facilitate astronomical inquiry, model inputs tend to be limited to a primary data source (namely images or time series) and, in the more advanced approaches, some metadata. Yet with the growing use of wide-field, multiplexed observational resources, individual sources of interest often have a broad range of observational modes available. Here we construct an astronomical multimodal dataset and propose AstroM^3, a self-supervised pre-training approach that enables a model to learn from multiple modalities simultaneously. Specifically, we extend the CLIP (Contrastive Language-Image Pretraining) model to a trimodal setting, allowing the integration of time-series photometry data, spectra, and astrophysical metadata. In a fine-tuning supervised setting, our results demonstrate that CLIP pre-training improves classification performance for time-series photometry, where accuracy increases from 84.6% to 91.5%. Furthermore, CLIP boosts classification accuracy by up to 12.6% when the availability of labeled data is limited, showing the effectiveness of leveraging larger corpora of unlabeled data. In addition to fine-tuned classification, we can use the trained model in other downstream tasks that are not explicitly contemplated during the construction of the self-supervised model. In particular we show the efficacy of using the learned embeddings for misclassifications identification, similarity search, and anomaly detection. One surprising highlight is the "rediscovery" of Mira subtypes and two Rotational variable subclasses using manifold learning and dimension reduction algorithm. To our knowledge this is the first construction of an n>2 mode model in astronomy. Extensions to n>3 modes is naturally anticipated with this approach.

This paper revisits datasets and evaluation criteria for Symbolic Regression, a task of expressing given data using mathematical equations, specifically focused on its potential for scientific discovery. Focused on a set of formulas used in the existing datasets based on Feynman Lectures on Physics, we recreate 120 datasets to discuss the performance of symbolic regression for scientific discovery (SRSD). For each of the 120 SRSD datasets, we carefully review the properties of the formula and its variables to design reasonably realistic sampling range of values so that our new SRSD datasets can be used for evaluating the potential of SRSD such as whether or not an SR method can (re)discover physical laws from such datasets. As an evaluation metric, we also propose to use normalized edit distances between a predicted equation and the ground-truth equation trees. While existing metrics are either binary or errors between the target values and an SR model's predicted values for a given input, normalized edit distances evaluate a sort of similarity between the ground-truth and predicted equation trees. We have conducted experiments on our new SRSD datasets using five state-of-the-art SR methods in SRBench and a simple baseline based on a recent Transformer architecture. The results show that we provide a more realistic performance evaluation and open up a new machine learning-based approach for scientific discovery. Our datasets and code repository are publicly available.

In computational social science (CSS), researchers analyze documents to explain social and political phenomena. In most scenarios, CSS researchers first obtain labels for documents and then explain labels using interpretable regression analyses in the second step. One increasingly common way to annotate documents cheaply at scale is through large language models (LLMs). However, like other scalable ways of producing annotations, such surrogate labels are often imperfect and biased. We present a new algorithm for using imperfect annotation surrogates for downstream statistical analyses while guaranteeing statistical properties -- like asymptotic unbiasedness and proper uncertainty quantification -- which are fundamental to CSS research. We show that direct use of surrogate labels in downstream statistical analyses leads to substantial bias and invalid confidence intervals, even with high surrogate accuracy of 80-90%. To address this, we build on debiased machine learning to propose the design-based supervised learning (DSL) estimator. DSL employs a doubly-robust procedure to combine surrogate labels with a smaller number of high-quality, gold-standard labels. Our approach guarantees valid inference for downstream statistical analyses, even when surrogates are arbitrarily biased and without requiring stringent assumptions, by controlling the probability of sampling documents for gold-standard labeling. Both our theoretical analysis and experimental results show that DSL provides valid statistical inference while achieving root mean squared errors comparable to existing alternatives that focus only on prediction without inferential guarantees.

Large Language Models (LLMs) with strong abilities in natural language processing tasks have emerged and have been rapidly applied in various kinds of areas such as science, finance and software engineering. However, the capability of LLMs to advance the field of chemistry remains unclear. In this paper,we establish a comprehensive benchmark containing 8 practical chemistry tasks, including 1) name prediction, 2) property prediction, 3) yield prediction, 4) reaction prediction, 5) retrosynthesis (prediction of reactants from products), 6)text-based molecule design, 7) molecule captioning, and 8) reagent selection. Our analysis draws on widely recognized datasets including BBBP, Tox21, PubChem, USPTO, and ChEBI, facilitating a broad exploration of the capacities of LLMs within the context of practical chemistry. Three GPT models (GPT-4, GPT-3.5,and Davinci-003) are evaluated for each chemistry task in zero-shot and few-shot in-context learning settings with carefully selected demonstration examples and specially crafted prompts. The key results of our investigation are 1) GPT-4 outperforms the other two models among the three evaluated; 2) GPT models exhibit less competitive performance in tasks demanding precise understanding of molecular SMILES representation, such as reaction prediction and retrosynthesis;3) GPT models demonstrate strong capabilities in text-related explanation tasks such as molecule captioning; and 4) GPT models exhibit comparable or better performance to classical machine learning models when applied to chemical problems that can be transformed into classification or ranking tasks, such as property prediction, and yield prediction.

Addressing the critical theme of recycling electronic waste (E-waste), this contribution is dedicated to developing advanced automated data processing pipelines as a basis for decision-making and process control. Aligning with the broader goals of the circular economy and the United Nations (UN) Sustainable Development Goals (SDG), our work leverages non-invasive analysis methods utilizing RGB and hyperspectral imaging data to provide both quantitative and qualitative insights into the E-waste stream composition for optimizing recycling efficiency. In this paper, we introduce 'PCB-Vision'; a pioneering RGB-hyperspectral printed circuit board (PCB) benchmark dataset, comprising 53 RGB images of high spatial resolution paired with their corresponding high spectral resolution hyperspectral data cubes in the visible and near-infrared (VNIR) range. Grounded in open science principles, our dataset provides a comprehensive resource for researchers through high-quality ground truths, focusing on three primary PCB components: integrated circuits (IC), capacitors, and connectors. We provide extensive statistical investigations on the proposed dataset together with the performance of several state-of-the-art (SOTA) models, including U-Net, Attention U-Net, Residual U-Net, LinkNet, and DeepLabv3+. By openly sharing this multi-scene benchmark dataset along with the baseline codes, we hope to foster transparent, traceable, and comparable developments of advanced data processing across various scientific communities, including, but not limited to, computer vision and remote sensing. Emphasizing our commitment to supporting a collaborative and inclusive scientific community, all materials, including code, data, ground truth, and masks, will be accessible at https://github.com/hifexplo/PCBVision.

Understanding the origin(s) of life (OoL) is a fundamental challenge for science in the 21st century. Research on OoL spans many disciplines, including chemistry, physics, biology, planetary sciences, computer science, mathematics and philosophy. The sheer number of different scientific perspectives relevant to the problem has resulted in the coexistence of diverse tools, techniques, data, and software in OoL studies. This has made communication between the disciplines relevant to the OoL extremely difficult because the interpretation of data, analyses, or standards of evidence can vary dramatically. Here, we hope to bridge this wide field of study by providing common ground via the consolidation of tools and techniques rather than positing a unifying view on how life emerges. We review the common tools and techniques that have been used significantly in OoL studies in recent years. In particular, we aim to identify which information is most relevant for comparing and integrating the results of experimental analyses into mathematical and computational models. This review aims to provide a baseline expectation and understanding of technical aspects of origins research, rather than being a primer on any particular topic. As such, it spans broadly -- from analytical chemistry to mathematical models -- and highlights areas of future work that will benefit from a multidisciplinary approach to tackling the mystery of life's origin. Ultimately, we hope to empower a new generation of OoL scientists by reviewing how they can investigate life's origin, rather than dictating how to think about the problem.

The reliability with Machine Learning (ML) techniques in novel materials discovery often depend on the quality of the dataset, in addition to the relevant features used in describing the material. In this regard, the current study presents and validates a newly processed materials dataset that can be utilized for benchmark ML analysis, as it relates to the prediction and classification of deterministic target properties. Originally, the dataset was extracted from the Open Quantum Materials Database (OQMD) and contains a robust 16,323 samples of ABX3 inorganic perovskite structures. The dataset is tabular in form and is preprocessed to include sixty-one generalized input features that broadly describes the physicochemical, stability/geometrical, and Density Functional Theory (DFT) target properties associated with the elemental ionic sites in a three-dimensional ABX3 polyhedral. For validation, four different ML models are employed to predict three distinctive target properties, namely: formation energy, energy band gap, and crystal system. On experimentation, the best accuracy measurements are reported at 0.013 eV/atom MAE, 0.216 eV MAE, and 85% F1, corresponding to the formation energy prediction, band gap prediction and crystal system multi-classification, respectively. Moreover, the realized results are compared with previous literature and as such, affirms the resourcefulness of the current dataset for future benchmark materials analysis via ML techniques. The preprocessed dataset and source codes are openly available to download from github.com/chenebuah/ML_abx3_dataset.

We present constraints on the spacetime variation of the fine-structure constant alpha at redshifts 2.5le z<9.5 using JWST emission-line galaxies. The galaxy sample consists of 621 high-quality spectra with strong and narrow [O III] lambdalambda4959,5007 doublet emission lines from 578 galaxies, including 232 spectra at z>5. The [O III] doublet lines are arguably the best emission lines to probe the variation in alpha. We divide our sample into six subsamples based on redshift and calculate the relative variation Deltaalpha/alpha for the individual subsamples. The calculated Deltaalpha/alpha values are consistent with zero within 1sigma at all redshifts, suggesting no time variation in alpha above a level of (1-2) times10^{-4} (1sigma) in the past 13.2 billion years. When the whole sample is combined, the constraint is improved to be Deltaalpha/alpha = (0.2pm0.7) times10^{-4}. We further test the spatial variation in alpha using four subsamples of galaxies in four different directions on the sky. The measured Deltaalpha/alpha values are consistent with zero at a 1sigma level of sim 2times10^{-4}. While the constraints in this work are not as stringent as those from lower-redshift quasar absorption lines in previous studies, this work uses an independent tracer and provides the first constraints on Deltaalpha/alpha at the highest redshifts. With the growing number of emission-line galaxies from JWST, we expect to achieve stronger constraints in the future.

Despite its importance to experimental design, statistical power (the probability that, given a real effect, an experiment will reject the null hypothesis) has largely been ignored by the NLP community. Underpowered experiments make it more difficult to discern the difference between statistical noise and meaningful model improvements, and increase the chances of exaggerated findings. By meta-analyzing a set of existing NLP papers and datasets, we characterize typical power for a variety of settings and conclude that underpowered experiments are common in the NLP literature. In particular, for several tasks in the popular GLUE benchmark, small test sets mean that most attempted comparisons to state of the art models will not be adequately powered. Similarly, based on reasonable assumptions, we find that the most typical experimental design for human rating studies will be underpowered to detect small model differences, of the sort that are frequently studied. For machine translation, we find that typical test sets of 2000 sentences have approximately 75% power to detect differences of 1 BLEU point. To improve the situation going forward, we give an overview of best practices for power analysis in NLP and release a series of notebooks to assist with future power analyses.

We estimate ([M/H], [alpha/M]) for 48 million giants and dwarfs in low-dust extinction regions from the Gaia DR3 XP spectra by using tree-based machine-learning models trained on APOGEE DR17 and metal-poor star sample from Li et al. The root mean square error of our estimation is 0.0890 dex for [M/H] and 0.0436 dex for [alpha/M], when we evaluate our models on the test data that are not used in training the models. Because the training data is dominated by giants, our estimation is most reliable for giants. The high-[alpha/M] stars and low-[alpha/M] stars selected by our ([M/H], [alpha/M]) show different kinematical properties for giants and low-temperature dwarfs. We further investigate how our machine-learning models extract information on ([M/H], [alpha/M]). Intriguingly, we find that our models seem to extract information on [alpha/M] from Na D lines (589 nm) and Mg I line (516 nm). This result is understandable given the observed correlation between Na and Mg abundances in the literature. The catalog of ([M/H], [alpha/M]) as well as their associated uncertainties are publicly available online.

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological samples. Despite the development of various deep learning methods for identifying amino acid sequences (peptides) responsible for observed spectra, challenges persist in de novo peptide sequencing. Firstly, prior methods struggle to identify amino acids with post-translational modifications (PTMs) due to their lower frequency in training data compared to canonical amino acids, further resulting in decreased peptide-level identification precision. Secondly, diverse types of noise and missing peaks in mass spectra reduce the reliability of training data (peptide-spectrum matches, PSMs). To address these challenges, we propose AdaNovo, a novel framework that calculates conditional mutual information (CMI) between the spectrum and each amino acid/peptide, using CMI for adaptive model training. Extensive experiments demonstrate AdaNovo's state-of-the-art performance on a 9-species benchmark, where the peptides in the training set are almost completely disjoint from the peptides of the test sets. Moreover, AdaNovo excels in identifying amino acids with PTMs and exhibits robustness against data noise. The supplementary materials contain the official code.

The ever-increasing number of materials science articles makes it hard to infer chemistry-structure-property relations from published literature. We used natural language processing (NLP) methods to automatically extract material property data from the abstracts of polymer literature. As a component of our pipeline, we trained MaterialsBERT, a language model, using 2.4 million materials science abstracts, which outperforms other baseline models in three out of five named entity recognition datasets when used as the encoder for text. Using this pipeline, we obtained ~300,000 material property records from ~130,000 abstracts in 60 hours. The extracted data was analyzed for a diverse range of applications such as fuel cells, supercapacitors, and polymer solar cells to recover non-trivial insights. The data extracted through our pipeline is made available through a web platform at https://polymerscholar.org which can be used to locate material property data recorded in abstracts conveniently. This work demonstrates the feasibility of an automatic pipeline that starts from published literature and ends with a complete set of extracted material property information.

Hampering the interpretation of benchmark scores, evaluation data contamination has become a growing concern in the evaluation of LLMs, and an active area of research studies its effects. While evaluation data contamination is easily understood intuitively, it is surprisingly difficult to define precisely which samples should be considered contaminated and, consequently, how it impacts benchmark scores. We propose that these questions should be addressed together and that contamination metrics can be assessed based on whether models benefit from the examples they mark contaminated. We propose a novel analysis method called ConTAM, and show with a large scale survey of existing and novel n-gram based contamination metrics across 13 benchmarks and 7 models from 2 different families that ConTAM can be used to better understand evaluation data contamination and its effects. We find that contamination may have a much larger effect than reported in recent LLM releases and benefits models differently at different scales. We also find that considering only the longest contaminated substring provides a better signal than considering a union of all contaminated substrings, and that doing model and benchmark specific threshold analysis greatly increases the specificity of the results. Lastly, we investigate the impact of hyperparameter choices, finding that, among other things, both using larger values of n and disregarding matches that are infrequent in the pre-training data lead to many false negatives. With ConTAM, we provide a method to empirically ground evaluation data contamination metrics in downstream effects. With our exploration, we shed light on how evaluation data contamination can impact LLMs and provide insight into the considerations important when doing contamination analysis. We end our paper by discussing these in more detail and providing concrete suggestions for future work.

Kilonovae are key to advancing our understanding of r-process nucleosynthesis. To date, only two kilonovae have been spectroscopically observed, AT 2017gfo and AT 2023vfi. Here, we present an analysis of the James Webb Space Telescope (JWST) spectra obtained +29 and +61 days post-merger for AT 2023vfi (the kilonova associated with GRB 230307A). After re-reducing and photometrically flux-calibrating the data, we empirically model the observed X-ray to mid-infrared continua with a power law and a blackbody, to replicate the non-thermal afterglow and apparent thermal continuum gtrsim 2 , mum. We fit Gaussians to the apparent emission features, obtaining line centroids of 20218_{-38}^{+37}, 21874 pm 89 and 44168_{-152}^{+153}\,\AA, and velocity widths spanning 0.057 - 0.110\,c. These line centroid constraints facilitated a detailed forbidden line identification search, from which we shortlist a number of r-process species spanning all three r-process peaks. We rule out Ba II and Ra II as candidates and propose Te I-III, Er I-III and W III as the most promising ions for further investigation, as they plausibly produce multiple emission features from one (W III) or multiple (Te I-III, Er I-III) ion stages. We compare to the spectra of AT 2017gfo, which also exhibit prominent emission at sim 2.1 , mum, and conclude that [Te III] lambda21050 remains the most plausible cause of the observed sim 2.1 , mum emission in both kilonovae. However, the observed line centroids are not consistent between both objects, and they are significantly offset from [Te III] lambda21050. The next strongest [Te III] transition at 29290\,\AA\ is not observed, and we quantify its detectability. Further study is required, with particular emphasis on expanding the available atomic data to enable quantitative non-LTE spectral modelling.

We increase the spectroscopic completeness of the 100 pc white dwarf sample in the SDSS footprint with 840 additional spectra. Our spectroscopy is 86% complete for white dwarfs hotter than T_{rm eff}= 5000 K, where Halpha remains visible and provides reliable constraints on the atmospheric composition. We identify 2108 DA white dwarfs with pure hydrogen atmospheres, and show that ultramassive DA white dwarfs with Mgeq1.1~M_{odot} are an order of magnitude less common below 10,000 K. This is consistent with a fraction of them getting stuck on the crystallization sequence due to ^{22}Ne distillation. In addition, there are no ultramassive DA white dwarfs with Mgeq1.1~M_{odot} and T_{rm eff}leq6000 K in our sample, likely because Debye cooling makes them rapidly fade away. We detect a significant trend in the fraction of He-atmosphere white dwarfs as a function of temperature; the fraction increases from 9% at 20,000 K to 32% at 6000 K. This provides direct evidence of convective mixing in cool DA white dwarfs. Finally, we detect a relatively tight sequence of low-mass DQ white dwarfs in color-magnitude diagrams for the first time. We discuss the implications of this tight DQ sequence, and conclude with a discussion of the future prospects from the upcoming ULTRASAT mission and the large-scale multi-fiber spectroscopic surveys.

Solar photospheric abundances and CI-chondrite compositions are reviewed and updated to obtain representative solar system abundances of the elements and their isotopes. The new photospheric abundances obtained here lead to higher solar metallicity. Full 3D NLTE photospheric analyses are only available for 11 elements. A quality index for analyses is introduced. For several elements, uncertainties remain large. Protosolar mass fractions are H (X = 0.7060), He (Y = 0.2753), and for metals Li to U (Z = 0.0187). The protosolar (C+N)/H agrees within 13% with the ratio for the solar core from the Borexino experiment. Elemental abundances in CI-chondrites were screened by analytical methods, sample sizes, and evaluated using concentration frequency distributions. Aqueously mobile elements (e.g., alkalis, alkaline earths, etc.) often deviate from normal distributions indicating mobilization and/or sequestration into carbonates, phosphates, and sulfates. Revised CI-chondrite abundances of non-volatile elements are similar to earlier estimates. The moderately volatile elements F and Sb are higher than before, as are C, Br and I, whereas the CI-abundances of Hg and N are now significantly lower. The solar system nuclide distribution curves of s-process elements agree within 4% with s-process predictions of Galactic chemical evolution models. P-process nuclide distributions are assessed. No obvious correlation of CI-chondritic to solar elemental abundance ratios with condensation temperatures is observed, nor is there one for ratios of CI-chondrites/solar wind abundances.

LSST and Euclid must address the daunting challenge of analyzing the unprecedented volumes of imaging and spectroscopic data that these next-generation instruments will generate. A promising approach to overcoming this challenge involves rapid, automatic image processing using appropriately trained Deep Learning (DL) algorithms. However, reliable application of DL requires large, accurately labeled samples of training data. Galaxy Zoo Express (GZX) is a recent experiment that simulated using Bayesian inference to dynamically aggregate binary responses provided by citizen scientists via the Zooniverse crowd-sourcing platform in real time. The GZX approach enables collaboration between human and machine classifiers and provides rapidly generated, reliably labeled datasets, thereby enabling online training of accurate machine classifiers. We present selected results from GZX and show how the Bayesian aggregation engine it uses can be extended to efficiently provide object-localization and bounding-box annotations of two-dimensional data with quantified reliability. DL algorithms that are trained using these annotations will facilitate numerous panchromatic data modeling tasks including morphological classification and substructure detection in direct imaging, as well as decontamination and emission line identification for slitless spectroscopy. Effectively combining the speed of modern computational analyses with the human capacity to extrapolate from few examples will be critical if the potential of forthcoming large-scale surveys is to be realized.

In this paper we introduce the concept of what we call "NUDAR" (NeUtrino Direction and Ranging), making the point that measurements of the observed energy and direction vectors can be employed to passively deduce the exact three-dimensional location and thermal power of geophysical and anthropogenic neutrino sources from even a single detector. We present the most precise background estimates to date, all handled in full three dimensions, as functions of depth and geographical location. For the present calculations, we consider a hypothetical 138 kiloton detector which can be transported to an ocean site and deployed to an operational depth. We present a Bayesian estimation framework to incorporate any a priori knowledge of the reactor that we are trying to detect, as well as the estimated uncertainty in the background and the oscillation parameters. Most importantly, we fully employ the knowledge of the reactor spectrum and the distance-dependent effects of neutrino oscillations on such spectra. The latter, in particular, makes possible determination of range from one location, given adequate signal statistics. Further, we explore the rich potential of improving detection with even modest improvements in individual neutrino direction determination. We conclude that a 300 MWth reactor can indeed be geolocated, and its operating power estimated with one or two detectors in the hundred kiloton class at ranges out to a few hundred kilometers. We note that such detectors would have natural and non-interfering utility for scientific studies of geo-neutrinos, neutrino oscillations, and astrophysical neutrinos. This motivates the development of cost effective methods of constructing and deploying such next generation detectors.

We present the MULTIMODAL UNIVERSE, a large-scale multimodal dataset of scientific astronomical data, compiled specifically to facilitate machine learning research. Overall, the MULTIMODAL UNIVERSE contains hundreds of millions of astronomical observations, constituting 100\,TB of multi-channel and hyper-spectral images, spectra, multivariate time series, as well as a wide variety of associated scientific measurements and "metadata". In addition, we include a range of benchmark tasks representative of standard practices for machine learning methods in astrophysics. This massive dataset will enable the development of large multi-modal models specifically targeted towards scientific applications. All codes used to compile the MULTIMODAL UNIVERSE and a description of how to access the data is available at https://github.com/MultimodalUniverse/MultimodalUniverse

This article presents a review about the main CERN n\_TOF contributions to the field of neutron-capture experiments of interest for s-process nucleosynthesis studies over the last 25 years, with special focus on the measurement of radioactive isotopes. A few recent capture experiments on stable isotopes of astrophysical interest are also discussed. Results on s-process branching nuclei are appropriate to illustrate how advances in detection systems and upgrades in the facility have enabled increasingly challenging experiments and, as a consequence, have led to a better understanding and modeling of the s-process mechanism of nucleosynthesis. New endeavors combining radioactive-ion beams from ISOLDE for the production of radioisotopically pure samples for activation experiments at the new NEAR facility at n\_TOF are briefly discussed. On the basis of these new exciting results, also current limitations of state-of-the-art TOF and activation techniques will be depicted, thereby showing the pressing need for further upgrades and enhancements on both facilities and detection systems. A brief account of the potential technique based on inverse kinematics for direct neutron-capture measurements is also presented.

Red supergiants may lose significant mass through steady winds and episodic eruptions in the final 100-1000 years before the core collapses, shaping their circumstellar environment. Interaction between supernova (SN) ejecta and distant circumstellar material (CSM) can generate shocks, which can energize the ejecta and serve as a key power source during the nebular phase of the SN. In the present work, we investigate the nebular spectrum of SN 2023ixf, observed one year post-explosion (at +363 d) with the recently commissioned WEAVE instrument on the 4.2m William Herschel Telescope. This marks the first supernova spectrum captured with WEAVE. In this spectrum, Halpha exhibits a peculiar evolution, flanked by blueward and redward broad components centred at simpm 5650,km,s^{-1} from the rest velocity of Halpha, which are seen for only a few SNe to date. These features indicate energy deposition from shocks generated by the interaction of ejecta with a CSM expelled nearly 350 - 640 years pre-explosion. Comparisons of the +363 d spectrum with model spectra from the literature, that include varying shock powers, suggest a shock power of at least sim 5 times 10 ^{40},erg,s^{-1} at this epoch. Additionally, analysis of the [O I] doublet, along with other prominent emission lines, provides evidence for clumpiness, dust formation, and asymmetry within the ejecta and/or the surrounding CSM. These emission lines also helped to constrain the oxygen mass (approx0.19^{scriptscriptstyle +0.08}_{scriptscriptstyle -0.04} M_odot), He-core mass (<3 M_odot) and the zero-age main sequence mass (lesssim 12 M_odot) of the progenitor of SN 2023ixf. The comparison with other Type II SNe highlights SN 2023ixf's unique shock interaction signatures and evidence of dust formation, setting it apart in terms of evolution and dynamics.

Literature research, vital for scientific work, faces the challenge of the surging torrent of information in the vast ocean of literature exceeding researchers' processing capabilities. To address this issue, we present an automated review generation method based on Large Language Models (LLMs), aimed at overcoming efficiency bottlenecks in literature processing and reducing cognitive load. Our statistically validated evaluation framework demonstrates that the generated reviews match or exceed manual quality, offering broad applicability across research fields due to minimal domain knowledge requirements. In a case study on propane dehydrogenation (PDH) catalysts, our method swiftly analyzed 343 articles, averaging seconds per article per LLM account, producing comprehensive reviews spanning 35 topics. Extended analysis of 1041 articles provided deep insights into catalysts' composition, structure, and performance. Recognizing LLMs' hallucinations, we implemented a multi-layered quality control strategy, effectively mitigating risks and ensuring reliability, as quantitatively demonstrated through manual verification. Expert verification confirms the accuracy and citation integrity of generated reviews, demonstrating LLM hallucination risks reduced to below 0.5\% with over 95\% confidence. Released Windows application enables one-click review generation, aiding researchers in tracking advancements and recommending literature. This approach showcases LLMs' role in enhancing scientific research productivity and sets the stage for further exploration.

The radial gradient of gas-phase metallicity is a powerful probe of the chemical and structural evolution of star-forming galaxies, closely tied to disk formation and gas kinematics in the early universe. We present spatially resolved chemical and dynamical properties for a sample of 25 galaxies at 0.5 lesssim z lesssim 1.7 from the \msasd survey. These innovative observations provide 3D spectroscopy of galaxies at a spatial resolution approaching JWST's diffraction limit and a high spectral resolution of Rsimeq2700. The metallicity gradients measured in our galaxy sample range from -0.03 to 0.02 dex~kpc^{-1}. Most galaxies exhibit negative or flat radial gradients, indicating lower metallicity in the outskirts or uniform metallicity throughout the entire galaxy. We confirm a tight relationship between stellar mass and metallicity gradient at zsim1 with small intrinsic scatter of 0.02 dex~kpc^{-1}. Our results indicate that metallicity gradients become increasingly negative as stellar mass increases, likely because the more massive galaxies tend to be more ``disky". This relationship is consistent with the predictions from cosmological hydrodynamic zoom-in simulations with strong stellar feedback. This work presents the effort to harness the multiplexing capability of JWST NIRSpec/MSA in slit-stepping mode to map the chemical and kinematic profiles of high-redshift galaxies in large samples and at high spatial and spectral resolution.

As host to two accreting planets, PDS 70 provides a unique opportunity to probe the chemical complexity of atmosphere-forming material. We present ALMA Band 6 observations of the PDS~70 disk and report the first chemical inventory of the system. With a spatial resolution of 0.4''-0.5'' (sim50 au), 12 species are detected, including CO isotopologues and formaldehyde, small hydrocarbons, HCN and HCO+ isotopologues, and S-bearing molecules. SO and CH3OH are not detected. All lines show a large cavity at the center of the disk, indicative of the deep gap carved by the massive planets. The radial profiles of the line emission are compared to the (sub-)mm continuum and infrared scattered light intensity profiles. Different molecular transitions peak at different radii, revealing the complex interplay between density, temperature and chemistry in setting molecular abundances. Column densities and optical depth profiles are derived for all detected molecules, and upper limits obtained for the non detections. Excitation temperature is obtained for H2CO. Deuteration and nitrogen fractionation profiles from the hydro-cyanide lines show radially increasing fractionation levels. Comparison of the disk chemical inventory to grids of chemical models from the literature strongly suggests a disk molecular layer hosting a carbon to oxygen ratio C/O>1, thus providing for the first time compelling evidence of planets actively accreting high C/O ratio gas at present time.

This paper will discuss the microphysical simulation of interactions in liquid xenon, the active detector medium in many leading rare-event searches for new physics, and describe experimental observables useful for understanding detector performance. The scintillation and ionization yield distributions for signal and background will be presented using the Noble Element Simulation Technique (NEST), which is a toolkit based on experimental data and simple, empirical formulae, which mimic previous microphysics modeling, but are guided by data. The NEST models for light and charge production as a function of the particle type, energy, and electric field will be reviewed, as well as models for energy resolution and final pulse areas. NEST will be compared to other models or sets of models, and vetted against real data, with several specific examples pulled from XENON, ZEPLIN, LUX, LZ, PandaX, and table-top experiments used for calibrations.

Earth system models suffer from various structural and parametric errors in their representation of nonlinear, multi-scale processes, leading to uncertainties in their long-term projections. The effects of many of these errors (particularly those due to fast physics) can be quantified in short-term simulations, e.g., as differences between the predicted and observed states (analysis increments). With the increase in the availability of high-quality observations and simulations, learning nudging from these increments to correct model errors has become an active research area. However, most studies focus on using neural networks, which while powerful, are hard to interpret, are data-hungry, and poorly generalize out-of-distribution. Here, we show the capabilities of Model Error Discovery with Interpretability and Data Assimilation (MEDIDA), a general, data-efficient framework that uses sparsity-promoting equation-discovery techniques to learn model errors from analysis increments. Using two-layer quasi-geostrophic turbulence as the test case, MEDIDA is shown to successfully discover various linear and nonlinear structural/parametric errors when full observations are available. Discovery from spatially sparse observations is found to require highly accurate interpolation schemes. While NNs have shown success as interpolators in recent studies, here, they are found inadequate due to their inability to accurately represent small scales, a phenomenon known as spectral bias. We show that a general remedy, adding a random Fourier feature layer to the NN, resolves this issue enabling MEDIDA to successfully discover model errors from sparse observations. These promising results suggest that with further development, MEDIDA could be scaled up to models of the Earth system and real observations.

This work proposes a Residual Recurrent Neural Network (RRNet) for synthetically extracting spectral information, and estimating stellar atmospheric parameters together with 15 chemical element abundances for medium-resolution spectra from Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST). The RRNet consists of two fundamental modules: a residual module and a recurrent module. The residual module extracts spectral features based on the longitudinally driving power from parameters, while the recurrent module recovers spectral information and restrains the negative influences from noises based on Cross-band Belief Enhancement. RRNet is trained by the spectra from common stars between LAMOST DR7 and APOGEE-Payne catalog. The 17 stellar parameters and their uncertainties for 2.37 million medium-resolution spectra from LAMOST DR7 are predicted. For spectra with S/N >= 10, the precision of estimations Teff and log g are 88 K and 0.13 dex respectively, elements C, Mg, Al, Si, Ca, Fe, Ni are 0.05 dex to 0.08 dex, and N, O, S, K, Ti, Cr, Mn are 0.09 dex to 0.14 dex, while that of Cu is 0.19 dex. Compared with StarNet and SPCANet, RRNet shows higher accuracy and robustness. In comparison to Apache Point Observatory Galactic Evolution Experiment and Galactic Archaeology with HERMES surveys, RRNet manifests good consistency within a reasonable range of bias. Finally, this work releases a catalog for 2.37 million medium-resolution spectra from the LAMOST DR7, the source code, the trained model and the experimental data respectively for astronomical science exploration and data processing algorithm research reference.

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

This paper challenges the recent paradigm in atomic property prediction that links progress to growing dataset sizes and computational resources. We show that pretraining on a carefully selected, task-relevant dataset can match or even surpass large-scale pretraining, while using as little as 1/24th of the computational cost. We introduce the Chemical Similarity Index (CSI), a novel metric inspired by computer vision's Fr\'echet Inception Distance, for molecular graphs which quantifies the alignment between upstream pretraining datasets and downstream tasks. By selecting the most relevant dataset with minimal CSI distance, we show that models pretrained on a smaller, focused dataset consistently outperform those pretrained on massive, mixed datasets such as JMP, even when those larger datasets include the relevant dataset. Counterintuitively, we also find that indiscriminately adding more data can degrade model performance when the additional data poorly aligns with the task at hand. Our findings highlight that quality often outperforms quantity in pretraining for atomic property prediction.

Recent research has repeatedly shown that machine learning techniques can be applied to either whole files or file fragments to classify them for analysis. We build upon these techniques to show that for samples of un-labeled compiled computer object code, one can apply the same type of analysis to classify important aspects of the code, such as its target architecture and endianess. We show that using simple byte-value histograms we retain enough information about the opcodes within a sample to classify the target architecture with high accuracy, and then discuss heuristic-based features that exploit information within the operands to determine endianess. We introduce a dataset with over 16000 code samples from 20 architectures and experimentally show that by using our features, classifiers can achieve very high accuracy with relatively small sample sizes.

The measured neutron flux from the Moons south polar region shows evidence of locally enhanced hydrogen concentrations, likely in the form of water ice, within most permanently shadowed regions (PSR), poleward of 77 deg S latitude. Results are consistent with the original findings of Watson et al, 1961, which found that the PSRs cryogenic surfaces create exclusive conditions for the sequestration of water ice, due to their extremely low sublimation rates. Widespread PSR hydrogenation is demonstrated in several studies by showing that the contrasting PSR area distribution is being instrumentally blurred. The PSRs expected hydrogen observations are correlated by their area fraction of the fixed 30 km diameter footprint area of the Collimated Sensor for Epithermal Neutrons (CSETN), which is part of the Lunar Exploration Neutron Detector (LEND) onboard the Lunar Reconnaissance Orbiter (LRO). The correlation indicates that the PSRs are similarly hydrogenated, with an expected concentration = 0.27 wt%, relative to that of the anhydrous reference terrain (lower bounds). Hydrogen concentrations are demonstrated to be correlated to maximum temperature distributions within the basins of Haworth, Shoemaker and Faustini PSRs. Cabeus-1 PSR shows an anomalously enhanced hydrogen concentration indicating a second process contributes to its hydrogen budget. Results are consistent with ongoing processes that introduce volatiles to the surface including outgassing, solar wind production with regolith silicates, and mixing from small scale meteor impacts and diurnal temperature variation. We validate the bandpass filter used to subtract CSETNs detection of uncollimated neutrons with profiles of several PSRs neutron suppression before and after processing. Keywords: Moon, Epithermal Neutron, Hydrogen, Water, Ice, Volatiles, LRO, LEND, Diviner, LOLA

We present an overview of a new integral field spectroscopic survey called MaNGA (Mapping Nearby Galaxies at Apache Point Observatory), one of three core programs in the fourth-generation Sloan Digital Sky Survey (SDSS-IV) that began on 2014 July 1. MaNGA will investigate the internal kinematic structure and composition of gas and stars in an unprecedented sample of 10,000 nearby galaxies. We summarize essential characteristics of the instrument and survey design in the context of MaNGA's key science goals and present prototype observations to demonstrate MaNGA's scientific potential. MaNGA employs dithered observations with 17 fiber-bundle integral field units that vary in diameter from 12" (19 fibers) to 32" (127 fibers). Two dual-channel spectrographs provide simultaneous wavelength coverage over 3600-10300 A at R~2000. With a typical integration time of 3 hr, MaNGA reaches a target r-band signal-to-noise ratio of 4-8 (per A, per 2" fiber) at 23 AB mag per sq. arcsec, which is typical for the outskirts of MaNGA galaxies. Targets are selected with stellar mass greater than 1e9 Msun using SDSS-I redshifts and i-band luminosity to achieve uniform radial coverage in terms of the effective radius, an approximately flat distribution in stellar mass, and a sample spanning a wide range of environments. Analysis of our prototype observations demonstrates MaNGA's ability to probe gas ionization, shed light on recent star formation and quenching, enable dynamical modeling, decompose constituent components, and map the composition of stellar populations. MaNGA's spatially resolved spectra will enable an unprecedented study of the astrophysics of nearby galaxies in the coming 6 yr.

The measurements of the temperature and polarisation anisotropies of the Cosmic Microwave Background (CMB) by the ESA Planck mission have strongly supported the current concordance model of cosmology. However, the latest cosmological data release from ESA Planck mission still has a powerful potential to test new data science algorithms and inference techniques. In this paper, we use advanced Machine Learning (ML) algorithms, such as Neural Networks (NNs), to discern among different underlying cosmological models at the angular power spectra level, using both temperature and polarisation Planck 18 data. We test two different models beyond LambdaCDM: a modified gravity model: the Hu-Sawicki model, and an alternative inflationary model: a feature-template in the primordial power spectrum. Furthermore, we also implemented an interpretability method based on SHAP values to evaluate the learning process and identify the most relevant elements that drive our architecture to certain outcomes. We find that our NN is able to distinguish between different angular power spectra successfully for both alternative models and LambdaCDM. We conclude by explaining how archival scientific data has still a strong potential to test novel data science algorithms that are interesting for the next generation of cosmological experiments.

Materials synthesis is vital for innovations such as energy storage, catalysis, electronics, and biomedical devices. Yet, the process relies heavily on empirical, trial-and-error methods guided by expert intuition. Our work aims to support the materials science community by providing a practical, data-driven resource. We have curated a comprehensive dataset of 17K expert-verified synthesis recipes from open-access literature, which forms the basis of our newly developed benchmark, AlchemyBench. AlchemyBench offers an end-to-end framework that supports research in large language models applied to synthesis prediction. It encompasses key tasks, including raw materials and equipment prediction, synthesis procedure generation, and characterization outcome forecasting. We propose an LLM-as-a-Judge framework that leverages large language models for automated evaluation, demonstrating strong statistical agreement with expert assessments. Overall, our contributions offer a supportive foundation for exploring the capabilities of LLMs in predicting and guiding materials synthesis, ultimately paving the way for more efficient experimental design and accelerated innovation in materials science.

We describe HypotheSAEs, a general method to hypothesize interpretable relationships between text data (e.g., headlines) and a target variable (e.g., clicks). HypotheSAEs has three steps: (1) train a sparse autoencoder on text embeddings to produce interpretable features describing the data distribution, (2) select features that predict the target variable, and (3) generate a natural language interpretation of each feature (e.g., "mentions being surprised or shocked") using an LLM. Each interpretation serves as a hypothesis about what predicts the target variable. Compared to baselines, our method better identifies reference hypotheses on synthetic datasets (at least +0.06 in F1) and produces more predictive hypotheses on real datasets (~twice as many significant findings), despite requiring 1-2 orders of magnitude less compute than recent LLM-based methods. HypotheSAEs also produces novel discoveries on two well-studied tasks: explaining partisan differences in Congressional speeches and identifying drivers of engagement with online headlines.

Combined electric power system and High-Altitude Electromagnetic Pulse (HEMP) models are being developed to determine the effect of a HEMP on the US power grid. The work relies primarily on deterministic methods; however, it is computationally untenable to evaluate the E1 HEMP response of large numbers of grid components distributed across a large interconnection. Further, the deterministic assessment of these components' failures are largely unachievable. E1 HEMP laboratory testing of the components is accomplished, but is expensive, leaving few data points to construct failure models of grid components exposed to E1 HEMP. The use of Bayesian priors, developed using the subject matter expertise, combined with the minimal test data in a Bayesian inference process, provides the basis for the development of more robust and cost-effective statistical component failure models. These can be used with minimal computational burden in a simulation environment such as sampling of Cumulative Distribution Functions (CDFs).

In recent years, Large Language Models (LLMs) have achieved significant success in natural language processing (NLP) and various interdisciplinary areas. However, applying LLMs to chemistry is a complex task that requires specialized domain knowledge. This paper provides a thorough exploration of the nuanced methodologies employed in integrating LLMs into the field of chemistry, delving into the complexities and innovations at this interdisciplinary juncture. Specifically, our analysis begins with examining how molecular information is fed into LLMs through various representation and tokenization methods. We then categorize chemical LLMs into three distinct groups based on the domain and modality of their input data, and discuss approaches for integrating these inputs for LLMs. Furthermore, this paper delves into the pretraining objectives with adaptations to chemical LLMs. After that, we explore the diverse applications of LLMs in chemistry, including novel paradigms for their application in chemistry tasks. Finally, we identify promising research directions, including further integration with chemical knowledge, advancements in continual learning, and improvements in model interpretability, paving the way for groundbreaking developments in the field.

The field of exocomets has been built around the unmatched number of detections made in the circumstellar disc of the archetypal star Beta Pictoris. An exocomet detection in spectroscopy is identified by variable atomic absorption features in a stellar spectrum, associated with transiting gas in and trailing an exocomet coma. This paper presents the largest spectroscopic search for exocomet transits to date, which overcomes the limitations of biased samples of stars with debris discs, and instead looks through the approx7500 stars in the HARPS archive for signs of exocomets in the CaII doublet (H:396.847nm and K:393.366nm). The search resulted in 155 candidate stars, which after filtering for false positives (e.g. binaries, stellar activity, etc.), were cut down to 22 stars. These 22 stars are classified into Tier1, 2, and 3 exocomet candidates, reflecting the confidence level of their exocomet detection. Our two best candidates (Tier1: Beta Pictoris, HD172555) and four lower confidence candidates (Tier2: Gl1, HIP5158, HD94771, HR1996) are discussed, yielding a detection rate of 0.03% (Tier1 only) and 0.1% (Tier1 & 2) in the HARPS sample. Both Tier1 stars are known exocomet host stars. These two young A-type stars correspond to 0.4% of all A-types in the sample, suggesting that detecting signs of exocomet transits using CaII is more likely around young A-type stars. Reanalysing a past HARPS study, we found no evidence to support the previously claimed four exocomet detections, indicating either that those detections are not robust or that we are only sensitive to the strongest signals.

About 90% of the computing resources available to the LHCb experiment has been spent to produce simulated data samples for Run 2 of the Large Hadron Collider at CERN. The upgraded LHCb detector will be able to collect larger data samples, requiring many more simulated events to analyze the data to be collected in Run 3. Simulation is a key necessity of analysis to interpret signal, reject background and measure efficiencies. The needed simulation will far exceed the pledged resources, requiring an evolution in technologies and techniques to produce these simulated data samples. In this contribution, we discuss Lamarr, a Gaudi-based framework to speed-up the simulation production parameterizing both the detector response and the reconstruction algorithms of the LHCb experiment. Deep Generative Models powered by several algorithms and strategies are employed to effectively parameterize the high-level response of the single components of the LHCb detector, encoding within neural networks the experimental errors and uncertainties introduced in the detection and reconstruction phases. Where possible, models are trained directly on real data, statistically subtracting any background components by applying appropriate reweighing procedures. Embedding Lamarr in the general LHCb Gauss Simulation framework allows to combine its execution with any of the available generators in a seamless way. The resulting software package enables a simulation process independent of the detailed simulation used to date.

We present photometric properties and distance measurements of 252 high redshift Type Ia supernovae (0.15 < z < 1.1) discovered during the first three years of the Supernova Legacy Survey (SNLS). These events were detected and their multi-colour light curves measured using the MegaPrime/MegaCam instrument at the Canada-France-Hawaii Telescope (CFHT), by repeatedly imaging four one-square degree fields in four bands. Follow-up spectroscopy was performed at the VLT, Gemini and Keck telescopes to confirm the nature of the supernovae and to measure their redshifts. Systematic uncertainties arising from light curve modeling are studied, making use of two techniques to derive the peak magnitude, shape and colour of the supernovae, and taking advantage of a precise calibration of the SNLS fields. A flat LambdaCDM cosmological fit to 231 SNLS high redshift Type Ia supernovae alone gives Omega_M = 0.211 +/- 0.034(stat) +/- 0.069(sys). The dominant systematic uncertainty comes from uncertainties in the photometric calibration. Systematic uncertainties from light curve fitters come next with a total contribution of +/- 0.026 on Omega_M. No clear evidence is found for a possible evolution of the slope (beta) of the colour-luminosity relation with redshift.

The Apache Point Observatory Galactic Evolution Experiment (APOGEE) has built the largest moderately high-resolution (R=22, 500) spectroscopic map of the stars across the Milky Way, and including dust-obscured areas. The APOGEE Stellar Parameter and Chemical Abundances Pipeline (ASPCAP) is the software developed for the automated analysis of these spectra. ASPCAP determines atmospheric parameters and chemical abundances from observed spectra by comparing observed spectra to libraries of theoretical spectra, using chi-2 minimization in a multidimensional parameter space. The package consists of a fortran90 code that does the actual minimization, and a wrapper IDL code for book-keeping and data handling. This paper explains in detail the ASPCAP components and functionality, and presents results from a number of tests designed to check its performance. ASPCAP provides stellar effective temperatures, surface gravities, and metallicities precise to 2%, 0.1 dex, and 0.05 dex, respectively, for most APOGEE stars, which are predominantly giants. It also provides abundances for up to 15 chemical elements with various levels of precision, typically under 0.1 dex. The final data release (DR12) of the Sloan Digital Sky Survey III contains an APOGEE database of more than 150,000 stars. ASPCAP development continues in the SDSS-IV APOGEE-2 survey.

Stars on the AGB can exhibit acoustic pulsation modes of different radial orders, along with non-radial modes. These pulsations are essential to the mass-loss process and influence the evolutionary pathways of AGB stars. P-L relations serve as a valuable diagnostic for understanding stellar evolution along the AGB. 3D RHD simulations provide a powerful tool for investigating pulsation phenomena driven by convective processes and their non-linear coupling with stellar oscillations. We investigate multi-mode pulsations in AGB stars using advanced 3D 'star-in-a-box' simulations with the CO5BOLD code. Signatures of these multi-mode pulsations were weak in our previous 3D models. Our focus is on identifying and characterising the various pulsation modes, examining their persistence and transitions, and comparing the results with 1D model predictions and observational data where applicable. We produced a new model grid comprising AGB stars with current masses of 0.7, 0.8, and 1,M_{odot}. Fourier analysis was applied to dynamic, time-dependent quantities to extract dominant pulsation modes and their corresponding periods. Additionally, wavelet transforms were employed to identify mode-switching behaviour over time. The models successfully reproduce the P-L sequences found in AGB stars. Mode-switching phenomena are found in both the models and wavelet analyses of observational data, allowing us to infer similarities in the underlying pulsation dynamics. These 3D simulations highlight the natural emergence of multi-mode pulsations, including both radial and non-radial modes, driven by the self-consistent interplay of convection and oscillations. Our findings underscore the value of 3D RHD models in capturing the non-linear behaviour of AGB pulsations, providing insights into mode switching, envelope structures, and potential links to episodic mass-loss events.

We present a comprehensive evaluation of proprietary and open-weights large language models using the first astronomy-specific benchmarking dataset. This dataset comprises 4,425 multiple-choice questions curated from the Annual Review of Astronomy and Astrophysics, covering a broad range of astrophysical topics. Our analysis examines model performance across various astronomical subfields and assesses response calibration, crucial for potential deployment in research environments. Claude-3.5-Sonnet outperforms competitors by up to 4.6 percentage points, achieving 85.0% accuracy. For proprietary models, we observed a universal reduction in cost every 3-to-12 months to achieve similar score in this particular astronomy benchmark. Open-source models have rapidly improved, with LLaMA-3-70b (80.6%) and Qwen-2-72b (77.7%) now competing with some of the best proprietary models. We identify performance variations across topics, with non-English-focused models generally struggling more in exoplanet-related fields, stellar astrophysics, and instrumentation related questions. These challenges likely stem from less abundant training data, limited historical context, and rapid recent developments in these areas. This pattern is observed across both open-weights and proprietary models, with regional dependencies evident, highlighting the impact of training data diversity on model performance in specialized scientific domains. Top-performing models demonstrate well-calibrated confidence, with correlations above 0.9 between confidence and correctness, though they tend to be slightly underconfident. The development for fast, low-cost inference of open-weights models presents new opportunities for affordable deployment in astronomy. The rapid progress observed suggests that LLM-driven research in astronomy may become feasible in the near future.

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Many deep learning methods have been developed for de novo peptide sequencing task, i.e., predicting the peptide sequence for the observed mass spectrum. However, two key challenges seriously hinder the further advancement of this important task. Firstly, since there is no consensus for the evaluation datasets, the empirical results in different research papers are often not comparable, leading to unfair comparison. Secondly, the current methods are usually limited to amino acid-level or peptide-level precision and recall metrics. In this work, we present the first unified benchmark NovoBench for de novo peptide sequencing, which comprises diverse mass spectrum data, integrated models, and comprehensive evaluation metrics. Recent impressive methods, including DeepNovo, PointNovo, Casanovo, InstaNovo, AdaNovo and pi-HelixNovo are integrated into our framework. In addition to amino acid-level and peptide-level precision and recall, we evaluate the models' performance in terms of identifying post-tranlational modifications (PTMs), efficiency and robustness to peptide length, noise peaks and missing fragment ratio, which are important influencing factors while seldom be considered. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development.

X-ray observing facilities, such as the Chandra X-ray Observatory and the eROSITA, have detected millions of astronomical sources associated with high-energy phenomena. The arrival of photons as a function of time follows a Poisson process and can vary by orders-of-magnitude, presenting obstacles for common tasks such as source classification, physical property derivation, and anomaly detection. Previous work has either failed to directly capture the Poisson nature of the data or only focuses on Poisson rate function reconstruction. In this work, we present Poisson Process AutoDecoder (PPAD). PPAD is a neural field decoder that maps fixed-length latent features to continuous Poisson rate functions across energy band and time via unsupervised learning. PPAD reconstructs the rate function and yields a representation at the same time. We demonstrate the efficacy of PPAD via reconstruction, regression, classification and anomaly detection experiments using the Chandra Source Catalog.

Gaussian analysis of new, high-angular-resolution interstellar 21-cm neutral hydrogen emission profile structure more clearly reveals the presence of the previously reported signature of the critical ionization velocity ({\it CIV}) of Helium (34 km s^{-1}). The present analysis includes 1496 component line widths for 178 neutral hydrogen profiles in two areas of sky at galactic latitudes around -50^circ, well away from the galactic plane. The new data considered here allow the interstellar abundance of Helium to be calculated, and the derived value of 0.095 pm 0.020 compares extremely well with the value of 0.085 for the cosmic abundance based on solar data. Although the precise mechanisms that give rise to the {\it CIV} effect in interstellar space are not yet understood, our results may provide additional motivation for further theoretical study of how the mechanism operates.

It is known that human speech and certain animal vocalizations can convey meaningful content because we can decipher the content that a given utterance does convey. This paper explores an alternative approach to determining whether a signal is meaningful, one that analyzes only the signal itself and is independent of what the conveyed meaning might be. We devise a method that takes a waveform as input and outputs a score indicating its degree of `meaningfulness`. We cluster contiguous portions of the input to minimize the total description length, and then take the length of the code of the assigned cluster labels as meaningfulness score. We evaluate our method empirically, against several baselines, and show that it is the only one to give a high score to human speech in various languages and with various speakers, a moderate score to animal vocalizations from birds and orcas, and a low score to ambient noise from various sources.

Methods of computational quantum chemistry provide accurate approximations of molecular properties crucial for computer-aided drug discovery and other areas of chemical science. However, high computational complexity limits the scalability of their applications. Neural network potentials (NNPs) are a promising alternative to quantum chemistry methods, but they require large and diverse datasets for training. This work presents a new dataset and benchmark called nabla^2DFT that is based on the nablaDFT. It contains twice as much molecular structures, three times more conformations, new data types and tasks, and state-of-the-art models. The dataset includes energies, forces, 17 molecular properties, Hamiltonian and overlap matrices, and a wavefunction object. All calculations were performed at the DFT level (omegaB97X-D/def2-SVP) for each conformation. Moreover, nabla^2DFT is the first dataset that contains relaxation trajectories for a substantial number of drug-like molecules. We also introduce a novel benchmark for evaluating NNPs in molecular property prediction, Hamiltonian prediction, and conformational optimization tasks. Finally, we propose an extendable framework for training NNPs and implement 10 models within it.

Source separation involves the ill-posed problem of retrieving a set of source signals that have been observed through a mixing operator. Solving this problem requires prior knowledge, which is commonly incorporated by imposing regularity conditions on the source signals, or implicitly learned through supervised or unsupervised methods from existing data. While data-driven methods have shown great promise in source separation, they often require large amounts of data, which rarely exists in planetary space missions. To address this challenge, we propose an unsupervised source separation scheme for domains with limited data access that involves solving an optimization problem in the wavelet scattering covariance representation spacex2014an interpretable, low-dimensional representation of stationary processes. We present a real-data example in which we remove transient, thermally-induced microtiltsx2014known as glitchesx2014from data recorded by a seismometer during NASA's InSight mission on Mars. Thanks to the wavelet scattering covariances' ability to capture non-Gaussian properties of stochastic processes, we are able to separate glitches using only a few glitch-free data snippets.

We present a spectroscopic analysis of two star-forming galaxies at z~5 observed with JWST/NIRSpec as part of the Early eXtragalactic Continuum and Emission Line Science (EXCELS) survey. The detection of the C III]lambdalambda1906,09, [O II]lambdalambda3726,29, [O III]lambdalambda4363,5007, and [N II]lambda6584 nebular emission lines enables investigation of the C/O, N/O, and C/N abundance ratios using the temperature-sensitive method. The two galaxies have stellar masses of log(M_{star}/M_{odot} ) = 8.13pm0.09 and log(M_{star}/M_{odot} )=8.52pm0.13 and corresponding metallicities of Z~0.2Z_{odot} and Z~0.3Z_{odot}. These metallicities are somewhat higher than is typical for other z>5 galaxies with similar stellar mass and are in fact comparable to high-redshift analogue galaxies at z~0. Both galaxies display evidence for N/O enhancement with respect to the z~0 sample, with log(N/O)=-1.07pm0.17 and log(N/O)=-0.86pm0.15 respectively. In contrast, we find low C abundances, with log(C/O)=-0.82pm0.22 and log(C/O)=-1.02pm0.22, consistent with the predicted yields of core-collapse supernovae. Following the trend observed in other high-redshift sources, we find that the C/N ratios are lower at fixed O/H compared to the majority of local galaxies. In contrast to the top-heavy IMF invoked in some studies to explain low C/N ratios in metal-poor galaxies, we find, via comparison to chemical evolution models, that a standard or bottom-heavy IMF better explains the observed abundance ratios in more enriched systems due to an increase in N-enrichment from intermediate mass (4-7M_{odot}) stars. Our results demonstrate that robust measurements of CNO abundances with JWST can reveal unique enrichment pathways in galaxies as a function of both metallicity and redshift.

The search for evidence of past life on Mars presents a tremendous challenge that requires the usage of very advanced robotic technologies to overcome it. Current digital microscopic imagers and spectrometers used for astrobiological examination suffer from limitations such as insufficient resolution, narrow detection range, and lack of portability. To overcome these challenges, this research study presents modifications to the Phoenix rover to expand its capability for detecting biosignatures on Mars. This paper examines the modifications implemented on the Phoenix rover to enhance its capability to detect a broader spectrum of biosignatures. One of the notable improvements comprises the integration of advanced digital microscopic imagers and spectrometers, enabling high-resolution examination of soil samples. Additionally, the mechanical components of the device have been reinforced to enhance maneuverability and optimize subsurface sampling capabilities. Empirical investigations have demonstrated that Phoenix has the capability to navigate diverse geological environments and procure samples for the purpose of biomolecular analysis. The biomolecular instrumentation and hybrid analytical methods showcased in this study demonstrate considerable potential for future astrobiology missions on Mars. The potential for enhancing the system lies in the possibility of broadening the range of detectable biomarkers and biosignatures.

A great deal of effort has been devoted to reducing the risk of spurious scientific discoveries, from the use of sophisticated validation techniques, to deep statistical methods for controlling the false discovery rate in multiple hypothesis testing. However, there is a fundamental disconnect between the theoretical results and the practice of data analysis: the theory of statistical inference assumes a fixed collection of hypotheses to be tested, or learning algorithms to be applied, selected non-adaptively before the data are gathered, whereas in practice data is shared and reused with hypotheses and new analyses being generated on the basis of data exploration and the outcomes of previous analyses. In this work we initiate a principled study of how to guarantee the validity of statistical inference in adaptive data analysis. As an instance of this problem, we propose and investigate the question of estimating the expectations of m adaptively chosen functions on an unknown distribution given n random samples. We show that, surprisingly, there is a way to estimate an exponential in n number of expectations accurately even if the functions are chosen adaptively. This gives an exponential improvement over standard empirical estimators that are limited to a linear number of estimates. Our result follows from a general technique that counter-intuitively involves actively perturbing and coordinating the estimates, using techniques developed for privacy preservation. We give additional applications of this technique to our question.

Harsh vocal effects such as screams or growls are far more common in heavy metal vocals than the traditionally sung vocal. This paper explores the problem of detection and classification of extreme vocal techniques in heavy metal music, specifically the identification of different scream techniques. We investigate the suitability of various feature representations, including cepstral, spectral, and temporal features as input representations for classification. The main contributions of this work are (i) a manually annotated dataset comprised of over 280 minutes of heavy metal songs of various genres with a statistical analysis of occurrences of different extreme vocal techniques in heavy metal music, and (ii) a systematic study of different input feature representations for the classification of heavy metal vocals

Detailed detector simulation is the major consumer of CPU resources at LHCb, having used more than 90% of the total computing budget during Run 2 of the Large Hadron Collider at CERN. As data is collected by the upgraded LHCb detector during Run 3 of the LHC, larger requests for simulated data samples are necessary, and will far exceed the pledged resources of the experiment, even with existing fast simulation options. An evolution of technologies and techniques to produce simulated samples is mandatory to meet the upcoming needs of analysis to interpret signal versus background and measure efficiencies. In this context, we propose Lamarr, a Gaudi-based framework designed to offer the fastest solution for the simulation of the LHCb detector. Lamarr consists of a pipeline of modules parameterizing both the detector response and the reconstruction algorithms of the LHCb experiment. Most of the parameterizations are made of Deep Generative Models and Gradient Boosted Decision Trees trained on simulated samples or alternatively, where possible, on real data. Embedding Lamarr in the general LHCb Gauss Simulation framework allows combining its execution with any of the available generators in a seamless way. Lamarr has been validated by comparing key reconstructed quantities with Detailed Simulation. Good agreement of the simulated distributions is obtained with two-order-of-magnitude speed-up of the simulation phase.

The Apache Point Observatory Galactic Evolution Experiment (APOGEE), one of the programs in the Sloan Digital Sky Survey III (SDSS-III), has now completed its systematic, homogeneous spectroscopic survey sampling all major populations of the Milky Way. After a three year observing campaign on the Sloan 2.5-m Telescope, APOGEE has collected a half million high resolution (R~22,500), high S/N (>100), infrared (1.51-1.70 microns) spectra for 146,000 stars, with time series information via repeat visits to most of these stars. This paper describes the motivations for the survey and its overall design---hardware, field placement, target selection, operations---and gives an overview of these aspects as well as the data reduction, analysis and products. An index is also given to the complement of technical papers that describe various critical survey components in detail. Finally, we discuss the achieved survey performance and illustrate the variety of potential uses of the data products by way of a number of science demonstrations, which span from time series analysis of stellar spectral variations and radial velocity variations from stellar companions, to spatial maps of kinematics, metallicity and abundance patterns across the Galaxy and as a function of age, to new views of the interstellar medium, the chemistry of star clusters, and the discovery of rare stellar species. As part of SDSS-III Data Release 12, all of the APOGEE data products are now publicly available.

An ultra high energy electromagnetic cascade, a purely leptonic process and initiated by either photons or e^pm, can be a source of high energy neutrinos. We present a public python3 code, MUNHECA, to compute the neutrino spectrum by taking into account various QED processes, with the cascade developing either along the propagation in the cosmic microwave background in the high-redshift universe or in a predefined photon background surrounding the astrophysical source. The user can adjust various settings of MUNHECA, including the spectrum of injected high energy photons, the background photon field and the QED processes governing the cascade evolution. We improve the modeling of several processes, provide examples of the execution of MUNHECA and compare it with some earlier and more simplified estimates of the neutrino spectrum from electromagnetic cascades.

We present an extragalactic HI 21-cm absorption lines catalog from a blind search at z leqslant 0.35, using drift-scan data collected in 1325.6 hours by the ongoing Commensal Radio Astronomy FasT Survey (CRAFTS) and FAST All Sky HI Survey (FASHI), which spans a sky area of 6072.0 deg^{2} and covers 84533 radio sources with a flux density greater than 12 mJy. 14 previously identified HI absorbers and 20 newly discovered HI absorbers were detected, comprising 15 associated systems, 10 intervening systems, and 9 systems with undetermined classifications. Through spectral stacking, the mean peak optical path, mean velocity-integrated optical path, mean FWHM and mean HI column density are measured to be 0.47 and 0.30; 27.19 and 4.36 km s^{-1}; 42.61 and 9.33 km s^{-1}; 0.49 and 0.08 T_{s} times 10^{20}cm^{-2}K^{-1}, for the associated and intervening samples, respectively. Statistical analysis also reveals that associated systems tend to be hosted by red (g-r>0.7) galaxies at lower redshifts, whereas galaxies hosting intervening HI absorption are typically found at higher redshifts and are of a bluer (g-rleqslant0.7) type. A noticeable difference is observed in the positions of foregrounds, backgrounds of intervening systems, and high-redshift and low-redshift associated systems on the WISE color-color diagram. All identified foreground sources in our sample have W1-W2 magnitudes below 0.8, suggesting no Active Galactic Nuclei (AGN). In contrast, backgrounds of intervening systems tend to have W1-W2 magnitudes above 0.8, indicating AGN presence. For associated absorption, most low-redshift (zleqslant0.5) systems show W1-W2 values below 0.8, while higher-redshift associated absorption (z>0.5) displays a broader range of W1-W2 values.

Exotic hadrons are a new class of hadronic states whose properties do not allow them to be classified as conventional quark-antiquark mesons or three quark baryons. Finding new and understanding established exotic states is the most important topic in today's hadron spectroscopy and a promising avenue to advance our knowledge on Quantum Chromodynamics in the non-perturbative regime. While several high-quality reviews on the topic exist, they are all at an advanced level. The present article aims to address new-comers to the field with a simple introduction to exotic hadrons with an emphasis on the experimental studies.

We present the third data release of the European Space Agency's Gaia mission, GDR3. The GDR3 catalogue is the outcome of the processing of raw data collected with the Gaia instruments during the first 34 months of the mission by the Gaia Data Processing and Analysis Consortium. The GDR3 catalogue contains the same source list, celestial positions, proper motions, parallaxes, and broad band photometry in the G, G_{BP}, and G_{RP} pass-bands already present in the Early Third Data Release. GDR3 introduces an impressive wealth of new data products. More than 33 million objects in the ranges G_{rvs} < 14 and 3100 <T_{eff} <14500 , have new determinations of their mean radial velocities based on data collected by Gaia. We provide G_{rvs} magnitudes for most sources with radial velocities, and a line broadening parameter is listed for a subset of these. Mean Gaia spectra are made available to the community. The GDR3 catalogue includes about 1 million mean spectra from the radial velocity spectrometer, and about 220 million low-resolution blue and red prism photometer BPRP mean spectra. The results of the analysis of epoch photometry are provided for some 10 million sources across 24 variability types. GDR3 includes astrophysical parameters and source class probabilities for about 470 million and 1500 million sources, respectively, including stars, galaxies, and quasars. Orbital elements and trend parameters are provided for some 800,000 astrometric, spectroscopic and eclipsing binaries. More than 150,000 Solar System objects, including new discoveries, with preliminary orbital solutions and individual epoch observations are part of this release. Reflectance spectra derived from the epoch BPRP spectral data are published for about 60\,000 asteroids. Finally, an additional data set is provided, namely the Gaia Andromeda Photometric Survey (abridged)

Keeping track of all relevant recent publications and experimental results for a research area is a challenging task. Prior work has demonstrated the efficacy of information extraction models in various scientific areas. Recently, several datasets have been released for the yet understudied materials science domain. However, these datasets focus on sub-problems such as parsing synthesis procedures or on sub-domains, e.g., solid oxide fuel cells. In this resource paper, we present MuLMS, a new dataset of 50 open-access articles, spanning seven sub-domains of materials science. The corpus has been annotated by domain experts with several layers ranging from named entities over relations to frame structures. We present competitive neural models for all tasks and demonstrate that multi-task training with existing related resources leads to benefits.

Prior works on detoxification are scattered in the sense that they do not cover all aspects of detoxification needed in a real-world scenario. Notably, prior works restrict the task of developing detoxification models to only a seen subset of platforms, leaving the question of how the models would perform on unseen platforms unexplored. Additionally, these works do not address non-detoxifiability, a phenomenon whereby the toxic text cannot be detoxified without altering the meaning. We propose GreenLLaMA, the first comprehensive end-to-end detoxification framework, which attempts to alleviate the aforementioned limitations. We first introduce a cross-platform pseudo-parallel corpus applying multi-step data processing and generation strategies leveraging ChatGPT. We then train a suite of detoxification models with our cross-platform corpus. We show that our detoxification models outperform the SoTA model trained with human-annotated parallel corpus. We further introduce explanation to promote transparency and trustworthiness. GreenLLaMA additionally offers a unique paraphrase detector especially dedicated for the detoxification task to tackle the non-detoxifiable cases. Through experimental analysis, we demonstrate the effectiveness of our cross-platform corpus and the robustness of GreenLLaMA against adversarial toxicity.

Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs are mainly good at leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method that implicitly projects all original atoms into a few Neural Atoms, which abstracts the collective information of atomic groups within a molecule. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms' representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection with the traditional LRI calculation method, Ewald Summation. We conduct extensive experiments on three long-range graph benchmarks, covering both graph-level and link-level tasks on molecular graphs. We empirically justify that our method can be equipped with an arbitrary GNN and help to capture LRI.

CONTEXT The R programming language has a huge and active community, especially in the area of statistical computing. Its interpreted nature allows for several interesting constructs, like the manipulation of functions at run-time, that hinder the static analysis of R programs. At the same time, there is a lack of existing research regarding how these features, or even the R language as a whole are used in practice. OBJECTIVE In this paper, we conduct a large-scale, static analysis of more than 50 million lines of real-world R programs and packages to identify their characteristics and the features that are actually used. Moreover, we compare the similarities and differences between the scripts of R users and the implementations of package authors. We provide insights for static analysis tools like the lintr package as well as potential interpreter optimizations and uncover areas for future research. METHOD We analyze 4230 R scripts submitted alongside publications and the sources of 19450 CRAN packages for over 350000 R files, collecting and summarizing quantitative information for features of interest. RESULTS We find a high frequency of name-based indexing operations, assignments, and loops, but a low frequency for most of R's reflective functions. Furthermore, we find neither testing functions nor many calls to R's foreign function interface (FFI) in the publication submissions. CONCLUSION R scripts and package sources differ, for example, in their size, the way they include other packages, and their usage of R's reflective capabilities. We provide features that are used frequently and should be prioritized by static analysis tools, like operator assignments, function calls, and certain reflective functions like load.

The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the molecule structures. However, automatically parsing the exact chemical structure is a formidable challenge, due to the amount of detailed information, the diversity of drawing styles, and the need for training data. In this work, we introduce MolGrapher to recognize chemical structures visually. First, a deep keypoint detector detects the atoms. Second, we treat all candidate atoms and bonds as nodes and put them in a graph. This construct allows a natural graph representation of the molecule. Last, we classify atom and bond nodes in the graph with a Graph Neural Network. To address the lack of real training data, we propose a synthetic data generation pipeline producing diverse and realistic results. In addition, we introduce a large-scale benchmark of annotated real molecule images, USPTO-30K, to spur research on this critical topic. Extensive experiments on five datasets show that our approach significantly outperforms classical and learning-based methods in most settings. Code, models, and datasets are available.

Data-driven scientific discovery requires the iterative integration of scientific domain knowledge, statistical expertise, and an understanding of data semantics to make nuanced analytical decisions, e.g., about which variables, transformations, and statistical models to consider. LM-based agents equipped with planning, memory, and code execution capabilities have the potential to support data-driven science. However, evaluating agents on such open-ended tasks is challenging due to multiple valid approaches, partially correct steps, and different ways to express the same decisions. To address these challenges, we present BLADE, a benchmark to automatically evaluate agents' multifaceted approaches to open-ended research questions. BLADE consists of 12 datasets and research questions drawn from existing scientific literature, with ground truth collected from independent analyses by expert data scientists and researchers. To automatically evaluate agent responses, we developed corresponding computational methods to match different representations of analyses to this ground truth. Though language models possess considerable world knowledge, our evaluation shows that they are often limited to basic analyses. However, agents capable of interacting with the underlying data demonstrate improved, but still non-optimal, diversity in their analytical decision making. Our work enables the evaluation of agents for data-driven science and provides researchers deeper insights into agents' analysis approaches.

We present subarcsecond-resolution ALMA mosaics of the Orion Bar PDR in [CI] 609 um, C2H (4-3), and C18O (3-2) emission lines, complemented by JWST images of H2 and aromatic infrared band (AIB) emission. The rim of the Bar shows very corrugated structures made of small-scale H2 dissociation fronts (DFs). The [CI] 609 um emission peaks very close (~0.002 pc) to the main H2-emitting DFs, suggesting the presence of gas density gradients. These DFs are also bright and remarkably similar in C2H emission, which traces 'hydrocarbon radical peaks' characterized by very high C2H abundances, reaching up to several x10^-7. The high abundance of C2H and of related hydrocarbon radicals, such as CH3, CH2, and CH, can be attributed to gas-phase reactions driven by elevated temperatures, the presence of C+ and C, and the reactivity of FUV-pumped H2. The hydrocarbon radical peaks roughly coincide with maxima of the 3.4/3.3 um AIB intensity ratio, a proxy for the aliphatic-to-aromatic content of PAHs. This implies that the conditions triggering the formation of simple hydrocarbons also favor the formation (and survival) of PAHs with aliphatic side groups, potentially via the contribution of bottom-up processes in which abundant hydrocarbon radicals react in situ with PAHs. Ahead of the DFs, in the atomic PDR zone (where [H]>>[H2]), the AIB emission is brightest, but small PAHs and carbonaceous grains undergo photo-processing due to the stronger FUV field. Our detection of trace amounts of C2H in this zone may result from the photoerosion of these species. This study provides a spatially resolved view of the chemical stratification of key carbon carriers in a PDR. Overall, both bottom-up and top-down processes appear to link simple hydrocarbon molecules with PAHs in molecular clouds; however, the exact chemical pathways and their relative contributions remain to be quantified.

Clinical diagnosis is critical in medical practice, typically requiring a continuous and evolving process that includes primary diagnosis, differential diagnosis, and final diagnosis. However, most existing clinical diagnostic tasks are single-step processes, which does not align with the complex multi-step diagnostic procedures found in real-world clinical settings. In this paper, we propose a multi-step diagnostic task and annotate a clinical diagnostic dataset (MSDiagnosis). This dataset includes primary diagnosis, differential diagnosis, and final diagnosis questions. Additionally, we propose a novel and effective framework. This framework combines forward inference, backward inference, reflection, and refinement, enabling the LLM to self-evaluate and adjust its diagnostic results. To assess the effectiveness of our proposed method, we design and conduct extensive experiments. The experimental results demonstrate the effectiveness of the proposed method. We also provide a comprehensive experimental analysis and suggest future research directions for this task.

Amid mounting concern about the reliability and credibility of machine learning research, we present a principled framework for making robust and generalizable claims: the multiverse analysis. Our framework builds upon the multiverse analysis (Steegen et al., 2016) introduced in response to psychology's own reproducibility crisis. To efficiently explore high-dimensional and often continuous ML search spaces, we model the multiverse with a Gaussian Process surrogate and apply Bayesian experimental design. Our framework is designed to facilitate drawing robust scientific conclusions about model performance, and thus our approach focuses on exploration rather than conventional optimization. In the first of two case studies, we investigate disputed claims about the relative merit of adaptive optimizers. Second, we synthesize conflicting research on the effect of learning rate on the large batch training generalization gap. For the machine learning community, the multiverse analysis is a simple and effective technique for identifying robust claims, for increasing transparency, and a step toward improved reproducibility.

Identifying the chemical structure from a graphical representation, or image, of a molecule is a challenging pattern recognition task that would greatly benefit drug development. Yet, existing methods for chemical structure recognition do not typically generalize well, and show diminished effectiveness when confronted with domains where data is sparse, or costly to generate, such as hand-drawn molecule images. To address this limitation, we propose a new chemical structure recognition tool that delivers state-of-the-art performance and can adapt to new domains with a limited number of data samples and supervision. Unlike previous approaches, our method provides atom-level localization, and can therefore segment the image into the different atoms and bonds. Our model is the first model to perform OCSR with atom-level entity detection with only SMILES supervision. Through rigorous and extensive benchmarking, we demonstrate the preeminence of our chemical structure recognition approach in terms of data efficiency, accuracy, and atom-level entity prediction.

We consider the problem of performing Bayesian inference in probabilistic models where observations are accompanied by uncertainty, referred to as "uncertain evidence." We explore how to interpret uncertain evidence, and by extension the importance of proper interpretation as it pertains to inference about latent variables. We consider a recently-proposed method "distributional evidence" as well as revisit two older methods: Jeffrey's rule and virtual evidence. We devise guidelines on how to account for uncertain evidence and we provide new insights, particularly regarding consistency. To showcase the impact of different interpretations of the same uncertain evidence, we carry out experiments in which one interpretation is defined as "correct." We then compare inference results from each different interpretation illustrating the importance of careful consideration of uncertain evidence.

Property prediction accuracy has long been a key parameter of machine learning in materials informatics. Accordingly, advanced models showing state-of-the-art performance turn into highly parameterized black boxes missing interpretability. Here, we present an elegant way to make their reasoning transparent. Human-readable text-based descriptions automatically generated within a suite of open-source tools are proposed as materials representation. Transformer language models pretrained on 2 million peer-reviewed articles take as input well-known terms, e.g., chemical composition, crystal symmetry, and site geometry. Our approach outperforms crystal graph networks by classifying four out of five analyzed properties if one considers all available reference data. Moreover, fine-tuned text-based models show high accuracy in the ultra-small data limit. Explanations of their internal machinery are produced using local interpretability techniques and are faithful and consistent with domain expert rationales. This language-centric framework makes accurate property predictions accessible to people without artificial-intelligence expertise.

The last decade has witnessed a rapid growth of the field of exoplanet discovery and characterisation. However, several big challenges remain, many of which could be addressed using machine learning methodology. For instance, the most prolific method for detecting exoplanets and inferring several of their characteristics, transit photometry, is very sensitive to the presence of stellar spots. The current practice in the literature is to identify the effects of spots visually and correct for them manually or discard the affected data. This paper explores a first step towards fully automating the efficient and precise derivation of transit depths from transit light curves in the presence of stellar spots. The methods and results we present were obtained in the context of the 1st Machine Learning Challenge organized for the European Space Agency's upcoming Ariel mission. We first present the problem, the simulated Ariel-like data and outline the Challenge while identifying best practices for organizing similar challenges in the future. Finally, we present the solutions obtained by the top-5 winning teams, provide their code and discuss their implications. Successful solutions either construct highly non-linear (w.r.t. the raw data) models with minimal preprocessing -deep neural networks and ensemble methods- or amount to obtaining meaningful statistics from the light curves, constructing linear models on which yields comparably good predictive performance.

In this paper, we present a novel approach to knowledge extraction and retrieval using Natural Language Processing (NLP) techniques for material science. Our goal is to automatically mine structured knowledge from millions of research articles in the field of polycrystalline materials and make it easily accessible to the broader community. The proposed method leverages NLP techniques such as entity recognition and document classification to extract relevant information and build an extensive knowledge base, from a collection of 9.5 Million publications. The resulting knowledge base is integrated into a search engine, which enables users to search for information about specific materials, properties, and experiments with greater precision than traditional search engines like Google. We hope our results can enable material scientists quickly locate desired experimental procedures, compare their differences, and even inspire them to design new experiments. Our website will be available at Github https://github.com/Xianjun-Yang/PcMSP.git soon.

We introduce a new molecular dataset, named Alchemy, for developing machine learning models useful in chemistry and material science. As of June 20th 2019, the dataset comprises of 12 quantum mechanical properties of 119,487 organic molecules with up to 14 heavy atoms, sampled from the GDB MedChem database. The Alchemy dataset expands the volume and diversity of existing molecular datasets. Our extensive benchmarks of the state-of-the-art graph neural network models on Alchemy clearly manifest the usefulness of new data in validating and developing machine learning models for chemistry and material science. We further launch a contest to attract attentions from researchers in the related fields. More details can be found on the contest website https://alchemy.tencent.com. At the time of benchamrking experiment, we have generated 119,487 molecules in our Alchemy dataset. More molecular samples are generated since then. Hence, we provide a list of molecules used in the reported benchmarks.

Strongly lensed variable quasars can serve as precise cosmological probes, provided that time delays between the image fluxes can be accurately measured. A number of methods have been proposed to address this problem. In this paper, we explore in detail a new approach based on kernel regression estimates, which is able to estimate a single time delay given several datasets for the same quasar. We develop realistic artificial data sets in order to carry out controlled experiments to test of performance of this new approach. We also test our method on real data from strongly lensed quasar Q0957+561 and compare our estimates against existing results.

Understanding the world and explaining it with scientific theories is a central aspiration of artificial intelligence research. Proposing theories, designing experiments to test them, and then revising them based on data are fundamental to scientific discovery. Despite the significant promise of LLM-based scientific agents, no benchmarks systematically test LLM's ability to propose scientific models, collect experimental data, and revise them in light of new data. We introduce BoxingGym, a benchmark with 10 environments for systematically evaluating both experimental design (e.g. collecting data to test a scientific theory) and model discovery (e.g. proposing and revising scientific theories). To enable tractable and quantitative evaluation, we implement each environment as a generative probabilistic model with which a scientific agent can run interactive experiments. These probabilistic models are drawn from various real-world scientific domains ranging from psychology to ecology. To quantitatively evaluate a scientific agent's ability to collect informative experimental data, we compute the expected information gain (EIG), an information-theoretic quantity which measures how much an experiment reduces uncertainty about the parameters of a generative model. A good scientific theory is a concise and predictive explanation. Therefore, to quantitatively evaluate model discovery, we ask a scientific agent to explain their model and then assess whether this explanation enables another scientific agent to make reliable predictions about this environment. In addition to this explanation-based evaluation, we compute standard model evaluation metrics such as prediction errors. We find that current LLMs, such as GPT-4o, struggle with both experimental design and model discovery. We find that augmenting the LLM-based agent with an explicit statistical model does not reliably improve these results.

We report an optical method of generating arbitrary polarization states by manipulating the thicknesses of a pair of uniaxial birefringent plates, the optical axes of which are set at a crossing angle of {\pi}/4. The method has the remarkable feature of being able to generate a distribution of arbitrary polarization states in a group of highly discrete spectra without spatially separating the individual spectral components. The target polarization-state distribution is obtained as an optimal solution through an exploration. Within a realistic exploration range, a sufficient number of near-optimal solutions are found. This property is also reproduced well by a concise model based on a distribution of exploration points on a Poincar\'e sphere, showing that the number of near-optimal solutions behaves according to a power law with respect to the number of spectral components of concern. As a typical example of an application, by applying this method to a set of phase-locked highly discrete spectra, we numerically demonstrate the continuous generation of a vector-like optical electric field waveform, the helicity of which is alternated within a single optical cycle in the time domain.

A core sample of 59 unobscured type 1 AGNs with simultaneous XMM-Newton X-ray and UV observations is compiled from archive to probe the nature of soft X-ray excess (SE). In the first paper of this series, our focus centers on scrutinizing the spectral profile of the soft excess. Of the sources, approx 71% (42/59) exhibit powerlaw-like (po-like) soft excess, while approx 29% (17/59) exhibit blackbody-like (bb-like) soft excess. We show a cut-off powerlaw could uniformly characterize both types of soft excesses, with median Ecut of 1.40 keV for po-like and 0.14 keV for bb-like. For the first time, we report a robust and quantitative correlation between the SE profile and SE strength (the ratio of SE luminosity to that of the primary powerlaw continuum in 0.5 - 2.0 keV), indicating that stronger soft excess is more likely to be po-like, or effectively has a higher Ecut. This correlation cannot be explained by ionized disk reflection alone, which produces mostly bb-like soft excess (Ecut sim 0.1 keV) as revealed by relxilllp simulation. Remarkably, we show with simulations that a toy hybrid scenario, where both ionized disk reflection (relxilllp, with all reflection parameters fixed at default values except for ionization of the disk) and warm corona (compTT, with temperature fixed at 1 keV) contribute to the observed soft excess, can successfully reproduce the observed correlation. This highlights the ubiquitous hybrid nature of the soft X-ray excess in AGNs, and underscores the importance of considering both components while fitting the spectra of soft excess.

As machine learning and algorithmic decision making systems are increasingly being leveraged in high-stakes human-in-the-loop settings, there is a pressing need to understand the rationale of their predictions. Researchers have responded to this need with explainable AI (XAI), but often proclaim interpretability axiomatically without evaluation. When these systems are evaluated, they are often tested through offline simulations with proxy metrics of interpretability (such as model complexity). We empirically evaluate the veracity of three common interpretability assumptions through a large scale human-subjects experiment with a simple "placebo explanation" control. We find that feature attribution explanations provide marginal utility in our task for a human decision maker and in certain cases result in worse decisions due to cognitive and contextual confounders. This result challenges the assumed universal benefit of applying these methods and we hope this work will underscore the importance of human evaluation in XAI research. Supplemental materials -- including anonymized data from the experiment, code to replicate the study, an interactive demo of the experiment, and the models used in the analysis -- can be found at: https://doi.pizza/challenging-xai.

TOI-836 is a ~2-3 Gyr K dwarf with an inner super Earth (R=1.7 R_oplus, P=3.8 d) and an outer mini Neptune (R=2.6 R_oplus, P=8.6 d). JWST/NIRSpec 2.8--5.2 mum transmission spectra are flat for both planets. We present Keck/NIRSPEC observations of escaping helium for super-Earth b, which shows no excess absorption in the 1083 nm triplet to deep limits (<0.2%), and mini-Neptune c, which shows strong (0.7%) excess absorption in both visits. These results demonstrate that planet c retains at least some primordial atmosphere, while planet b is consistent with having lost its entire primordial envelope. Self-consistent 1D radiative-hydrodynamic models of planet c reveal that the helium excess absorption signal is highly sensitive to metallicity: its equivalent width collapses by a factor of 13 as metallicity increases from 10x to 100x solar, and by a further factor of 12 as it increases to 200x solar. The observed equivalent width is 88\% the model prediction for 100x metallicity, suggesting an atmospheric metallicity similar to K2-18b and TOI-270d, the first two mini-Neptunes with detected absorption features in JWST transmission spectra. We highlight the helium triplet as a potentially powerful probe of atmospheric composition, with complementary strengths and weaknesses to atmospheric retrievals. The main strength is its extreme sensitivity to metallicity in the scientifically significant range of 10--200x solar, and the main weakness is the enormous model uncertainties in outflow suppression and confinement mechanisms, such as magnetic fields and stellar winds, which can suppress the signal by at least a factor of ~several.

Molecule-text modeling, which aims to facilitate molecule-relevant tasks with a textual interface and textual knowledge, is an emerging research direction. Beyond single molecules, studying reaction-text modeling holds promise for helping the synthesis of new materials and drugs. However, previous works mostly neglect reaction-text modeling: they primarily focus on modeling individual molecule-text pairs or learning chemical reactions without texts in context. Additionally, one key task of reaction-text modeling -- experimental procedure prediction -- is less explored due to the absence of an open-source dataset. The task is to predict step-by-step actions of conducting chemical experiments and is crucial to automating chemical synthesis. To resolve the challenges above, we propose a new pretraining method, ReactXT, for reaction-text modeling, and a new dataset, OpenExp, for experimental procedure prediction. Specifically, ReactXT features three types of input contexts to incrementally pretrain LMs. Each of the three input contexts corresponds to a pretraining task to improve the text-based understanding of either reactions or single molecules. ReactXT demonstrates consistent improvements in experimental procedure prediction and molecule captioning and offers competitive results in retrosynthesis. Our code is available at https://github.com/syr-cn/ReactXT.

To effectively optimize and personalize treatments, it is necessary to investigate the heterogeneity of treatment effects. With the wide range of users being treated over many online controlled experiments, the typical approach of manually investigating each dimension of heterogeneity becomes overly cumbersome and prone to subjective human biases. We need an efficient way to search through thousands of experiments with hundreds of target covariates and hundreds of breakdown dimensions. In this paper, we propose a systematic paradigm for detecting, surfacing and characterizing heterogeneous treatment effects. First, we detect if treatment effect variation is present in an experiment, prior to specifying any breakdowns. Second, we surface the most relevant dimensions for heterogeneity. Finally, we characterize the heterogeneity beyond just the conditional average treatment effects (CATE) by studying the conditional distributions of the estimated individual treatment effects. We show the effectiveness of our methods using simulated data and empirical studies.

We present SciRIFF (Scientific Resource for Instruction-Following and Finetuning), a dataset of 137K instruction-following demonstrations for 54 tasks covering five essential scientific literature understanding capabilities: information extraction, summarization, question answering, claim verification, and classification. SciRIFF demonstrations are notable for their long input contexts, detailed task specifications, and complex structured outputs. While instruction-following resources are available in specific domains such as clinical medicine and chemistry, SciRIFF is the first dataset focused on extracting and synthesizing information from research literature across a wide range of scientific fields. To demonstrate the utility of SciRIFF, we develop a sample-efficient strategy to adapt a general instruction-following model for science by performing additional finetuning on a mix of general-domain and SciRIFF demonstrations. In evaluations on nine held-out scientific tasks, our model -- called SciTulu -- improves over a strong LLM baseline by 28.1% and 6.5% at the 7B and 70B scales respectively, while maintaining general instruction-following performance within 2% of the baseline. We are optimistic that SciRIFF will facilitate the development and evaluation of LLMs to help researchers navigate the ever-growing body of scientific literature. We release our dataset, model checkpoints, and data processing and evaluation code to enable further research.

The Ultra-Violet Optical Telescope on the Swift spacecraft has observed hundreds of supernovae, covering all major types and most subtypes. Here we introduce the Swift Optical/Ultraviolet Supernova Archive (SOUSA), which will contain all of the supernova images and photometry. We describe the observation and reduction procedures and how they impact the final data. We show photometry from well-observed examples of most supernova classes, whose absolute magnitudes and colors may be used to infer supernova types in the absence of a spectrum. A full understanding of the variety within classes and a robust photometric separation of the groups requires a larger sample, which will be provided by the final archive. The data from the existing Swift supernovae are also useful for planning future observations with Swift as well as future UV observatories.

In the development of science, accurate and reproducible documentation of the experimental process is crucial. Automatic recognition of the actions in experiments from videos would help experimenters by complementing the recording of experiments. Towards this goal, we propose FineBio, a new fine-grained video dataset of people performing biological experiments. The dataset consists of multi-view videos of 32 participants performing mock biological experiments with a total duration of 14.5 hours. One experiment forms a hierarchical structure, where a protocol consists of several steps, each further decomposed into a set of atomic operations. The uniqueness of biological experiments is that while they require strict adherence to steps described in each protocol, there is freedom in the order of atomic operations. We provide hierarchical annotation on protocols, steps, atomic operations, object locations, and their manipulation states, providing new challenges for structured activity understanding and hand-object interaction recognition. To find out challenges on activity understanding in biological experiments, we introduce baseline models and results on four different tasks, including (i) step segmentation, (ii) atomic operation detection (iii) object detection, and (iv) manipulated/affected object detection. Dataset and code are available from https://github.com/aistairc/FineBio.

We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based platforms able to sequence non-native peptides. Current protein sequencing techniques face limitations in accurately identifying all amino acids, hindering comprehensive proteome analysis. Our method simulates partial sequencing data by selectively masking amino acids that are experimentally difficult to identify in protein sequences from the UniRef database. This targeted masking mimics real-world sequencing limitations. We then modify and finetune a ProtBert derived transformer-based model, for a new downstream task predicting these masked residues, providing an approximation of the complete sequence. Evaluating on three bacterial Escherichia species, we achieve per-amino-acid accuracy up to 90.5% when only four amino acids ([KCYM]) are known. Structural assessment using AlphaFold and TM-score validates the biological relevance of our predictions. The model also demonstrates potential for evolutionary analysis through cross-species performance. This integration of simulated experimental constraints with computational predictions offers a promising avenue for enhancing protein sequence analysis, potentially accelerating advancements in proteomics and structural biology by providing a probabilistic reconstruction of the complete protein sequence from limited experimental data.

We present a generic framework for creating differentially private versions of any hypothesis test in a black-box way. We analyze the resulting tests analytically and experimentally. Most crucially, we show good practical performance for small data sets, showing that at epsilon = 1 we only need 5-6 times as much data as in the fully public setting. We compare our work to the one existing framework of this type, as well as to several individually-designed private hypothesis tests. Our framework is higher power than other generic solutions and at least competitive with (and often better than) individually-designed tests.

How might one test the hypothesis that networks were sampled from the same distribution? Here, we compare two statistical tests that use subgraph counts to address this question. The first uses the empirical subgraph densities themselves as estimates of those of the underlying distribution. The second test uses a new approach that converts these subgraph densities into estimates of the graph cumulants of the distribution (without any increase in computational complexity). We demonstrate -- via theory, simulation, and application to real data -- the superior statistical power of using graph cumulants. In summary, when analyzing data using subgraph/motif densities, we suggest using the corresponding graph cumulants instead.

This paper addresses a regression problem in which output label values are the results of sensing the magnitude of a phenomenon. A low value of such labels can mean either that the actual magnitude of the phenomenon was low or that the sensor made an incomplete observation. This leads to a bias toward lower values in labels and the resultant learning because labels may have lower values due to incomplete observations, even if the actual magnitude of the phenomenon was high. Moreover, because an incomplete observation does not provide any tags indicating incompleteness, we cannot eliminate or impute them. To address this issue, we propose a learning algorithm that explicitly models incomplete observations corrupted with an asymmetric noise that always has a negative value. We show that our algorithm is unbiased as if it were learned from uncorrupted data that does not involve incomplete observations. We demonstrate the advantages of our algorithm through numerical experiments.

High-throughput screening techniques are commonly used to obtain large quantities of data in many fields of biology. It is well known that artifacts arising from variability in the technical execution of different experimental batches within such screens confound these observations and can lead to invalid biological conclusions. It is therefore necessary to account for these batch effects when analyzing outcomes. In this paper we describe RxRx1, a biological dataset designed specifically for the systematic study of batch effect correction methods. The dataset consists of 125,510 high-resolution fluorescence microscopy images of human cells under 1,138 genetic perturbations in 51 experimental batches across 4 cell types. Visual inspection of the images alone clearly demonstrates significant batch effects. We propose a classification task designed to evaluate the effectiveness of experimental batch correction methods on these images and examine the performance of a number of correction methods on this task. Our goal in releasing RxRx1 is to encourage the development of effective experimental batch correction methods that generalize well to unseen experimental batches. The dataset can be downloaded at https://rxrx.ai.

B[e] stars are massive B type emission line stars in different evolutionary stages ranging from pre-main sequence to post-main sequence. Due to their mass loss and ejection events these objects deposit huge amounts of mass and energy into their environment and enrich it with chemically processed material, contributing significantly to the chemical and dynamical evolution of their host galaxies. However, the large-scale environments of these enigmatic objects have not attracted much attention. The first and so far only catalog reporting the detection of extended shells around a sample of B[e] stars was an Ha imaging survey carried out in the year 2001, and was limited to bright targets in the northern hemisphere. We have recently started a follow-up of those targets to detect possible evolution of their nebulae in the plane of the sky over a baseline of two decades. Furthermore, we extend our survey to southern targets and fainter northern ones to complement and complete our knowledge on large-scale ejecta surrounding B[e] stars. Besides imaging in Ha and selected nebular lines, we utilize long-slit and 3D spectral observations across the nebulae to derive their physical properties. We discovered pronounced nebula structures around 15 more objects, resulting in a total of 27 B[e] stars with a large-scale nebula. Here we present our (preliminary) results for three selected objects: the two massive supergiants MWC137 and MWC 314, and the unclassified B[e] star MWC 819.

Protein modeling is an increasingly popular area of machine learning research. Semi-supervised learning has emerged as an important paradigm in protein modeling due to the high cost of acquiring supervised protein labels, but the current literature is fragmented when it comes to datasets and standardized evaluation techniques. To facilitate progress in this field, we introduce the Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. We curate tasks into specific training, validation, and test splits to ensure that each task tests biologically relevant generalization that transfers to real-life scenarios. We benchmark a range of approaches to semi-supervised protein representation learning, which span recent work as well as canonical sequence learning techniques. We find that self-supervised pretraining is helpful for almost all models on all tasks, more than doubling performance in some cases. Despite this increase, in several cases features learned by self-supervised pretraining still lag behind features extracted by state-of-the-art non-neural techniques. This gap in performance suggests a huge opportunity for innovative architecture design and improved modeling paradigms that better capture the signal in biological sequences. TAPE will help the machine learning community focus effort on scientifically relevant problems. Toward this end, all data and code used to run these experiments are available at https://github.com/songlab-cal/tape.

Scientific discovery contributes largely to human society's prosperity, and recent progress shows that LLMs could potentially catalyze this process. However, it is still unclear whether LLMs can discover novel and valid hypotheses in chemistry. In this work, we investigate this central research question: Can LLMs automatically discover novel and valid chemistry research hypotheses given only a chemistry research background (consisting of a research question and/or a background survey), without limitation on the domain of the research question? After extensive discussions with chemistry experts, we propose an assumption that a majority of chemistry hypotheses can be resulted from a research background and several inspirations. With this key insight, we break the central question into three smaller fundamental questions. In brief, they are: (1) given a background question, whether LLMs can retrieve good inspirations; (2) with background and inspirations, whether LLMs can lead to hypothesis; and (3) whether LLMs can identify good hypotheses to rank them higher. To investigate these questions, we construct a benchmark consisting of 51 chemistry papers published in Nature, Science, or a similar level in 2024 (all papers are only available online since 2024). Every paper is divided by chemistry PhD students into three components: background, inspirations, and hypothesis. The goal is to rediscover the hypothesis, given only the background and a large randomly selected chemistry literature corpus consisting the ground truth inspiration papers, with LLMs trained with data up to 2023. We also develop an LLM-based multi-agent framework that leverages the assumption, consisting of three stages reflecting the three smaller questions. The proposed method can rediscover many hypotheses with very high similarity with the ground truth ones, covering the main innovations.

Depression is a common mental disorder. Automatic depression detection tools using speech, enabled by machine learning, help early screening of depression. This paper addresses two limitations that may hinder the clinical implementations of such tools: noise resulting from segment-level labelling and a lack of model interpretability. We propose a bi-modal speech-level transformer to avoid segment-level labelling and introduce a hierarchical interpretation approach to provide both speech-level and sentence-level interpretations, based on gradient-weighted attention maps derived from all attention layers to track interactions between input features. We show that the proposed model outperforms a model that learns at a segment level (p=0.854, r=0.947, F1=0.947 compared to p=0.732, r=0.808, F1=0.768). For model interpretation, using one true positive sample, we show which sentences within a given speech are most relevant to depression detection; and which text tokens and Mel-spectrogram regions within these sentences are most relevant to depression detection. These interpretations allow clinicians to verify the validity of predictions made by depression detection tools, promoting their clinical implementations.

In supervised learning, acquiring labeled training data for a predictive model can be very costly, but acquiring a large amount of unlabeled data is often quite easy. Active learning is a method of obtaining predictive models with high precision at a limited cost through the adaptive selection of samples for labeling. This paper explains the basic problem settings of active learning and recent research trends. In particular, research on learning acquisition functions to select samples from the data for labeling, theoretical work on active learning algorithms, and stopping criteria for sequential data acquisition are highlighted. Application examples for material development and measurement are introduced.

Foundation models have been transformational in machine learning fields such as natural language processing and computer vision. Similar success in atomic property prediction has been limited due to the challenges of training effective models across multiple chemical domains. To address this, we introduce Joint Multi-domain Pre-training (JMP), a supervised pre-training strategy that simultaneously trains on multiple datasets from different chemical domains, treating each dataset as a unique pre-training task within a multi-task framework. Our combined training dataset consists of sim120M systems from OC20, OC22, ANI-1x, and Transition-1x. We evaluate performance and generalization by fine-tuning over a diverse set of downstream tasks and datasets including: QM9, rMD17, MatBench, QMOF, SPICE, and MD22. JMP demonstrates an average improvement of 59% over training from scratch, and matches or sets state-of-the-art on 34 out of 40 tasks. Our work highlights the potential of pre-training strategies that utilize diverse data to advance property prediction across chemical domains, especially for low-data tasks.

In recent years, groundbreaking advancements in natural language processing have culminated in the emergence of powerful large language models (LLMs), which have showcased remarkable capabilities across a vast array of domains, including the understanding, generation, and translation of natural language, and even tasks that extend beyond language processing. In this report, we delve into the performance of LLMs within the context of scientific discovery, focusing on GPT-4, the state-of-the-art language model. Our investigation spans a diverse range of scientific areas encompassing drug discovery, biology, computational chemistry (density functional theory (DFT) and molecular dynamics (MD)), materials design, and partial differential equations (PDE). Evaluating GPT-4 on scientific tasks is crucial for uncovering its potential across various research domains, validating its domain-specific expertise, accelerating scientific progress, optimizing resource allocation, guiding future model development, and fostering interdisciplinary research. Our exploration methodology primarily consists of expert-driven case assessments, which offer qualitative insights into the model's comprehension of intricate scientific concepts and relationships, and occasionally benchmark testing, which quantitatively evaluates the model's capacity to solve well-defined domain-specific problems. Our preliminary exploration indicates that GPT-4 exhibits promising potential for a variety of scientific applications, demonstrating its aptitude for handling complex problem-solving and knowledge integration tasks. Broadly speaking, we evaluate GPT-4's knowledge base, scientific understanding, scientific numerical calculation abilities, and various scientific prediction capabilities.

We present a straightforward statistical test to detect certain violations of the assumption that the data are Independent and Identically Distributed (IID). The specific form of violation considered is common across real-world applications: whether the examples are ordered in the dataset such that almost adjacent examples tend to have more similar feature values (e.g. due to distributional drift, or attractive interactions between datapoints). Based on a k-Nearest Neighbors estimate, our approach can be used to audit any multivariate numeric data as well as other data types (image, text, audio, etc.) that can be numerically represented, perhaps with model embeddings. Compared with existing methods to detect drift or auto-correlation, our approach is both applicable to more types of data and also able to detect a wider variety of IID violations in practice. Code: https://github.com/cleanlab/cleanlab

The existing search tools for exploring the NASA Astrophysics Data System (ADS) can be quite rich and empowering (e.g., similar and trending operators), but researchers are not yet allowed to fully leverage semantic search. For example, a query for "results from the Planck mission" should be able to distinguish between all the various meanings of Planck (person, mission, constant, institutions and more) without further clarification from the user. At ADS, we are applying modern machine learning and natural language processing techniques to our dataset of recent astronomy publications to train astroBERT, a deeply contextual language model based on research at Google. Using astroBERT, we aim to enrich the ADS dataset and improve its discoverability, and in particular we are developing our own named entity recognition tool. We present here our preliminary results and lessons learned.

Leveraging new data sources is a key step in accelerating the pace of materials design and discovery. To complement the strides in synthesis planning driven by historical, experimental, and computed data, we present an automated method for connecting scientific literature to synthesis insights. Starting from natural language text, we apply word embeddings from language models, which are fed into a named entity recognition model, upon which a conditional variational autoencoder is trained to generate syntheses for arbitrary materials. We show the potential of this technique by predicting precursors for two perovskite materials, using only training data published over a decade prior to their first reported syntheses. We demonstrate that the model learns representations of materials corresponding to synthesis-related properties, and that the model's behavior complements existing thermodynamic knowledge. Finally, we apply the model to perform synthesizability screening for proposed novel perovskite compounds.

In this paper we present SynKB, an open-source, automatically extracted knowledge base of chemical synthesis protocols. Similar to proprietary chemistry databases such as Reaxsys, SynKB allows chemists to retrieve structured knowledge about synthetic procedures. By taking advantage of recent advances in natural language processing for procedural texts, SynKB supports more flexible queries about reaction conditions, and thus has the potential to help chemists search the literature for conditions used in relevant reactions as they design new synthetic routes. Using customized Transformer models to automatically extract information from 6 million synthesis procedures described in U.S. and EU patents, we show that for many queries, SynKB has higher recall than Reaxsys, while maintaining high precision. We plan to make SynKB available as an open-source tool; in contrast, proprietary chemistry databases require costly subscriptions.

Current research on generative language models (GLMs) for automated text scoring (ATS) has focused almost exclusively on querying proprietary models via Application Programming Interfaces (APIs). Yet such practices raise issues around transparency and security, and these methods offer little in the way of efficiency or customizability. With the recent proliferation of smaller, open-source models, there is the option to explore GLMs with computers equipped with modest, consumer-grade hardware, that is, for the "GPU poor." In this study, we analyze the performance and efficiency of open-source, small-scale GLMs for ATS. Results show that GLMs can be fine-tuned to achieve adequate, though not state-of-the-art, performance. In addition to ATS, we take small steps towards analyzing models' capacity for generating feedback by prompting GLMs to explain their scores. Model-generated feedback shows promise, but requires more rigorous evaluation focused on targeted use cases.

The assumption that response and predictor belong to the same statistical unit may be violated in practice. Unbiased estimation and recovery of true label ordering based on unlabeled data are challenging tasks and have attracted increasing attentions in the recent literature. In this paper, we present a relatively complete analysis of label permutation problem for the generalized linear model with multivariate responses. The theory is established under different scenarios, with knowledge of true parameters, with partial knowledge of underlying label permutation matrix and without any knowledge. Our results remove the stringent conditions required by the current literature and are further extended to the missing observation setting which has never been considered in the field of label permutation problem. On computational side, we propose two methods, "maximum likelihood estimation" algorithm and "two-step estimation" algorithm, to accommodate for different settings. When the proportion of permuted labels is moderate, both methods work effectively. Multiple numerical experiments are provided and corroborate our theoretical findings.

Characterizing samples that are difficult to learn from is crucial to developing highly performant ML models. This has led to numerous Hardness Characterization Methods (HCMs) that aim to identify "hard" samples. However, there is a lack of consensus regarding the definition and evaluation of "hardness". Unfortunately, current HCMs have only been evaluated on specific types of hardness and often only qualitatively or with respect to downstream performance, overlooking the fundamental quantitative identification task. We address this gap by presenting a fine-grained taxonomy of hardness types. Additionally, we propose the Hardness Characterization Analysis Toolkit (H-CAT), which supports comprehensive and quantitative benchmarking of HCMs across the hardness taxonomy and can easily be extended to new HCMs, hardness types, and datasets. We use H-CAT to evaluate 13 different HCMs across 8 hardness types. This comprehensive evaluation encompassing over 14K setups uncovers strengths and weaknesses of different HCMs, leading to practical tips to guide HCM selection and future development. Our findings highlight the need for more comprehensive HCM evaluation, while we hope our hardness taxonomy and toolkit will advance the principled evaluation and uptake of data-centric AI methods.

Instrumental variable (IV) methods are used to estimate causal effects in settings with unobserved confounding, where we cannot directly experiment on the treatment variable. Instruments are variables which only affect the outcome indirectly via the treatment variable(s). Most IV applications focus on low-dimensional treatments and crucially require at least as many instruments as treatments. This assumption is restrictive: in the natural sciences we often seek to infer causal effects of high-dimensional treatments (e.g., the effect of gene expressions or microbiota on health and disease), but can only run few experiments with a limited number of instruments (e.g., drugs or antibiotics). In such underspecified problems, the full treatment effect is not identifiable in a single experiment even in the linear case. We show that one can still reliably recover the projection of the treatment effect onto the instrumented subspace and develop techniques to consistently combine such partial estimates from different sets of instruments. We then leverage our combined estimators in an algorithm that iteratively proposes the most informative instruments at each round of experimentation to maximize the overall information about the full causal effect.

Even with various regulations in place across countries and social media platforms (Government of India, 2021; European Parliament and Council of the European Union, 2022, digital abusive speech remains a significant issue. One potential approach to address this challenge is automatic text detoxification, a text style transfer (TST) approach that transforms toxic language into a more neutral or non-toxic form. To date, the availability of parallel corpora for the text detoxification task (Logachevavet al., 2022; Atwell et al., 2022; Dementievavet al., 2024a) has proven to be crucial for state-of-the-art approaches. With this work, we extend parallel text detoxification corpus to new languages -- German, Chinese, Arabic, Hindi, and Amharic -- testing in the extensive multilingual setup TST baselines. Next, we conduct the first of its kind an automated, explainable analysis of the descriptive features of both toxic and non-toxic sentences, diving deeply into the nuances, similarities, and differences of toxicity and detoxification across 9 languages. Finally, based on the obtained insights, we experiment with a novel text detoxification method inspired by the Chain-of-Thoughts reasoning approach, enhancing the prompting process through clustering on relevant descriptive attributes.

The automatic extraction of materials and related properties from the scientific literature is gaining attention in data-driven materials science (Materials Informatics). In this paper, we discuss Grobid-superconductors, our solution for automatically extracting superconductor material names and respective properties from text. Built as a Grobid module, it combines machine learning and heuristic approaches in a multi-step architecture that supports input data as raw text or PDF documents. Using Grobid-superconductors, we built SuperCon2, a database of 40324 materials and properties records from 37700 papers. The material (or sample) information is represented by name, chemical formula, and material class, and is characterized by shape, doping, substitution variables for components, and substrate as adjoined information. The properties include the Tc superconducting critical temperature and, when available, applied pressure with the Tc measurement method.

Probabilistic text generators have been used to produce fake scientific papers for more than a decade. Such nonsensical papers are easily detected by both human and machine. Now more complex AI-powered generation techniques produce texts indistinguishable from that of humans and the generation of scientific texts from a few keywords has been documented. Our study introduces the concept of tortured phrases: unexpected weird phrases in lieu of established ones, such as 'counterfeit consciousness' instead of 'artificial intelligence.' We combed the literature for tortured phrases and study one reputable journal where these concentrated en masse. Hypothesising the use of advanced language models we ran a detector on the abstracts of recent articles of this journal and on several control sets. The pairwise comparisons reveal a concentration of abstracts flagged as 'synthetic' in the journal. We also highlight irregularities in its operation, such as abrupt changes in editorial timelines. We substantiate our call for investigation by analysing several individual dubious articles, stressing questionable features: tortured writing style, citation of non-existent literature, and unacknowledged image reuse. Surprisingly, some websites offer to rewrite texts for free, generating gobbledegook full of tortured phrases. We believe some authors used rewritten texts to pad their manuscripts. We wish to raise the awareness on publications containing such questionable AI-generated or rewritten texts that passed (poor) peer review. Deception with synthetic texts threatens the integrity of the scientific literature.

Hallucination is a well-known phenomenon in text generated by large language models (LLMs). The existence of hallucinatory responses is found in almost all application scenarios e.g., summarization, question-answering (QA) etc. For applications requiring high reliability (e.g., customer-facing assistants), the potential existence of hallucination in LLM-generated text is a critical problem. The amount of hallucination can be reduced by leveraging information retrieval to provide relevant background information to the LLM. However, LLMs can still generate hallucinatory content for various reasons (e.g., prioritizing its parametric knowledge over the context, failure to capture the relevant information from the context, etc.). Detecting hallucinations through automated methods is thus paramount. To facilitate research in this direction, we introduce a sophisticated dataset, DelucionQA, that captures hallucinations made by retrieval-augmented LLMs for a domain-specific QA task. Furthermore, we propose a set of hallucination detection methods to serve as baselines for future works from the research community. Analysis and case study are also provided to share valuable insights on hallucination phenomena in the target scenario.

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows.

This article presents Individual Conditional Expectation (ICE) plots, a tool for visualizing the model estimated by any supervised learning algorithm. Classical partial dependence plots (PDPs) help visualize the average partial relationship between the predicted response and one or more features. In the presence of substantial interaction effects, the partial response relationship can be heterogeneous. Thus, an average curve, such as the PDP, can obfuscate the complexity of the modeled relationship. Accordingly, ICE plots refine the partial dependence plot by graphing the functional relationship between the predicted response and the feature for individual observations. Specifically, ICE plots highlight the variation in the fitted values across the range of a covariate, suggesting where and to what extent heterogeneities might exist. In addition to providing a plotting suite for exploratory analysis, we include a visual test for additive structure in the data generating model. Through simulated examples and real data sets, we demonstrate how ICE plots can shed light on estimated models in ways PDPs cannot. Procedures outlined are available in the R package ICEbox.

We develop a novel way to probe subgalactic-scale matter distribution with diffractive lensing on gravitational waves. Five-year observations from Einstein Telescope and DECIGO are expected to probe k= 10^5sim 10^8 ,{rm Mpc}^{-1} down to P(k) = 10^{-16} sim 10^{-14} ,{rm Mpc}^3 level. These results can be interpreted in terms of primordial black holes in the range M_{rm PBH} gtrsim 10^{-3}M_odot down to f_{rm PBH} = 10^{-6} level, or QCD axion minihalos in the range m_a = 10^{-3} sim 10^{-12} ,{rm eV}. A key result of the paper is the approximate relation between the scale k and the gravitational wave frequency f, derived in an ensemble of `multi-lensing' events. This relation enables direct measurement of the power spectrum at specific scales, with sensitivities characterized by model-independent kernels delta P(k). Additionally, we delineate the statistical properties of `multi-lensing' based on the `Fresnel number' N_F. When N_F cal O(1), the statistical significance can be approximately calculated by Variance of lensing effects, which is directly related to the power spectrum among other moments of matter distribution.

We present an open-source database of superconducting quantum device designs that may be used as the starting point for customized devices. Each design can be generated programmatically using the open-source Qiskit Metal package, and simulated using finite-element electromagnetic solvers. We present a robust workflow for achieving high accuracy on design simulations. Many designs in the database are experimentally validated, showing excellent agreement between simulated and measured parameters. Our database includes a front-end interface that allows users to generate ``best-guess'' designs based on desired circuit parameters. This project lowers the barrier to entry for research groups seeking to make a new class of devices by providing them a well-characterized starting point from which to refine their designs.

We show evidence of particle acceleration at GEV energies associated directly with protons from the prompt emission of a long-duration M6-class solar flare on July 17, 2023, rather than from protons acceleration by shocks from its associated Coronal Mass Ejection (CME), which erupted with a speed of 1342 km/s. Solar Energetic Particles (SEP) accelerated by the blast have reached Earth, up to an almost S3 (strong) category of a radiation storm on the NOAA scale. Also, we show a temporal correlation between the fast rising of GOES-16 proton and muon excess at ground level in the count rate of the New-Tupi muon detector at the central SAA region. A Monte Carlo spectral analysis based on muon excess at New-Tupi is consistent with the acceleration of electrons and protons (ions) up to relativistic energies (GeV energy range) in the impulsive phase of the flare. In addition, we present another two marginal particle excesses (with low confidence) at ground-level detectors in correlation with the solar flare prompt emission.

Large language models (LLMs) frequently generate non-factual content, known as hallucinations. Existing retrieval-augmented-based hallucination detection approaches typically address this by framing it as a classification task, evaluating hallucinations based on their consistency with retrieved evidence. However, this approach usually lacks detailed explanations for these evaluations and does not assess the reliability of these explanations. Furthermore, deficiencies in retrieval systems can lead to irrelevant or partially relevant evidence retrieval, impairing the detection process. Moreover, while real-world hallucination detection requires analyzing multiple pieces of evidence, current systems usually treat all evidence uniformly without considering its relevance to the content. To address these challenges, we introduce Halu-J, a critique-based hallucination judge with 7 billion parameters. Halu-J enhances hallucination detection by selecting pertinent evidence and providing detailed critiques. Our experiments indicate that Halu-J outperforms GPT-4o in multiple-evidence hallucination detection and matches its capability in critique generation and evidence selection. We also introduce ME-FEVER, a new dataset designed for multiple-evidence hallucination detection. Our code and dataset can be found in https://github.com/GAIR-NLP/factool .

Automated computational analysis of the vast chemical space is critical for numerous fields of research such as drug discovery and material science. Representation learning techniques have recently been employed with the primary objective of generating compact and informative numerical expressions of complex data. One approach to efficiently learn molecular representations is processing string-based notations of chemicals via natural language processing (NLP) algorithms. Majority of the methods proposed so far utilize SMILES notations for this purpose; however, SMILES is associated with numerous problems related to validity and robustness, which may prevent the model from effectively uncovering the knowledge hidden in the data. In this study, we propose SELFormer, a transformer architecture-based chemical language model that utilizes a 100% valid, compact and expressive notation, SELFIES, as input, in order to learn flexible and high-quality molecular representations. SELFormer is pre-trained on two million drug-like compounds and fine-tuned for diverse molecular property prediction tasks. Our performance evaluation has revealed that, SELFormer outperforms all competing methods, including graph learning-based approaches and SMILES-based chemical language models, on predicting aqueous solubility of molecules and adverse drug reactions. We also visualized molecular representations learned by SELFormer via dimensionality reduction, which indicated that even the pre-trained model can discriminate molecules with differing structural properties. We shared SELFormer as a programmatic tool, together with its datasets and pre-trained models. Overall, our research demonstrates the benefit of using the SELFIES notations in the context of chemical language modeling and opens up new possibilities for the design and discovery of novel drug candidates with desired features.

Symbolic equations are at the core of scientific discovery. The task of discovering the underlying equation from a set of input-output pairs is called symbolic regression. Traditionally, symbolic regression methods use hand-designed strategies that do not improve with experience. In this paper, we introduce the first symbolic regression method that leverages large scale pre-training. We procedurally generate an unbounded set of equations, and simultaneously pre-train a Transformer to predict the symbolic equation from a corresponding set of input-output-pairs. At test time, we query the model on a new set of points and use its output to guide the search for the equation. We show empirically that this approach can re-discover a set of well-known physical equations, and that it improves over time with more data and compute.

We present a systematic study of the BVRI colours of novae over the course of their eruptions. Where possible, interstellar reddening was measured using the equivalent widths of Diffuse Interstellar Bands (DIBs). Some novae lack spectra with sufficient resolution and signal-to-noise ratios; therefore, we supplement as necessary with 3D and 2D dust maps. Utilising only novae with DIB- or 3D-map-based E(B-V), we find an average intrinsic (B-V)_0 colour of novae at V-band light curve peak of 0.18 with a standard deviation of 0.31, based on a sample of 23 novae. When the light curve has declined by 2 magnitudes (t_2), we find an average (B-V)_0 = -0.02 with a standard deviation of 0.19. These average colours are consistent with previous findings, although the spreads are larger than previously found due to more accurate reddening estimates. We also examined the intrinsic (R-I)_0 and (V-R)_0 colours across our sample. These colours behave similarly to (B-V)_0, except that the (V-R)_0 colour gets redder after peak, likely due to the contributions of emission line flux. We searched for correlations between nova colours and t_2, peak V-band absolute magnitude, and GeV gamma-ray luminosity, but find no statistically significant correlations. Nova colours can therefore be used as standard "crayons" to estimate interstellar reddening from photometry alone, with 0.2--0.3 mag uncertainty. We present a novel Bayesian strategy for estimating distances to Galactic novae based on these E(B-V) measurements, independent of assumptions about luminosity, built using 3D dust maps and a stellar mass model of the Milky Way.

An amplitude analysis of B^-rightarrow D^- D^0 K_S^0 decays is performed using proton-proton collision data, corresponding to an integrated luminosity of 9,fb^{-1}, collected with the LHCb detector at center-of-mass energies of 7, 8, and 13,Tekern -0.1em V. A resonant structure of spin-parity 0^+ is observed in the D^0 K_S^0 invariant-mass spectrum with a significance of 5.3,sigma. The mass and width of the state, modeled with a Breit-Wigner lineshape, are determined to be 2883pm11pm6,Mekern -0.1em V!/c^2 and 87_{-47}^{+22}pm6,Mekern -0.1em V respectively, where the first uncertainties are statistical and the second systematic. These properties and the quark content are consistent with those of the open-charm tetraquark state T_{cs 0}^{*}(2870)^0 observed previously in the D^+ K^- final state of the B^-rightarrow D^- D^+ K^- decay. This result confirms the existence of the T_{cs 0}^{*}(2870)^0 state in a new decay mode. The T_{cs1}^{*}(2900)^0 state, reported in the B^-rightarrow D^- D^+ K^- decay, is also searched for in the D^0 K_S^0 invariant-mass spectrum of the B^- rightarrow D^- D^0 K_S^0 decay, without finding evidence for it.

This study is dedicated to assessing the capabilities of large language models (LLMs) such as GPT-3.5-Turbo, GPT-4, and GPT-4-Turbo in extracting structured information from scientific documents in materials science. To this end, we primarily focus on two critical tasks of information extraction: (i) a named entity recognition (NER) of studied materials and physical properties and (ii) a relation extraction (RE) between these entities. Due to the evident lack of datasets within Materials Informatics (MI), we evaluated using SuperMat, based on superconductor research, and MeasEval, a generic measurement evaluation corpus. The performance of LLMs in executing these tasks is benchmarked against traditional models based on the BERT architecture and rule-based approaches (baseline). We introduce a novel methodology for the comparative analysis of intricate material expressions, emphasising the standardisation of chemical formulas to tackle the complexities inherent in materials science information assessment. For NER, LLMs fail to outperform the baseline with zero-shot prompting and exhibit only limited improvement with few-shot prompting. However, a GPT-3.5-Turbo fine-tuned with the appropriate strategy for RE outperforms all models, including the baseline. Without any fine-tuning, GPT-4 and GPT-4-Turbo display remarkable reasoning and relationship extraction capabilities after being provided with merely a couple of examples, surpassing the baseline. Overall, the results suggest that although LLMs demonstrate relevant reasoning skills in connecting concepts, specialised models are currently a better choice for tasks requiring extracting complex domain-specific entities like materials. These insights provide initial guidance applicable to other materials science sub-domains in future work.

Neural Information Retrieval (NIR) has significantly improved upon heuristic-based IR systems. Yet, failures remain frequent, the models used often being unable to retrieve documents relevant to the user's query. We address this challenge by proposing a lightweight abstention mechanism tailored for real-world constraints, with particular emphasis placed on the reranking phase. We introduce a protocol for evaluating abstention strategies in a black-box scenario, demonstrating their efficacy, and propose a simple yet effective data-driven mechanism. We provide open-source code for experiment replication and abstention implementation, fostering wider adoption and application in diverse contexts.

From the dynamics of a broad class of classical mean-field glass models one may obtain a quantum model with finite zero-temperature entropy, a quantum transition at zero temperature, and a time-reparametrization (quasi-)invariance in the dynamical equations for correlations. The low eigenvalue spectrum of the resulting quantum model is directly related to the structure and exploration of metastable states in the landscape of the original classical glass model. This mapping reveals deep connections between classical glasses and the properties of SYK-like models.

Classification is an important aspect of hyperspectral images processing and application. At present, the researchers mostly use the classic airborne hyperspectral imagery as the benchmark dataset. However, existing datasets suffer from three bottlenecks: (1) low spatial resolution; (2) low labeled pixels proportion; (3) low degree of subclasses distinction. In this paper, a new benchmark dataset named the Wuhan UAV-borne hyperspectral image (WHU-Hi) dataset was built for hyperspectral image classification. The WHU-Hi dataset with a high spectral resolution (nm level) and a very high spatial resolution (cm level), which we refer to here as H2 imager. Besides, the WHU-Hi dataset has a higher pixel labeling ratio and finer subclasses. Some start-of-art hyperspectral image classification methods benchmarked the WHU-Hi dataset, and the experimental results show that WHU-Hi is a challenging dataset. We hope WHU-Hi dataset can become a strong benchmark to accelerate future research.

Public trust in science depends on honest and factual communication of scientific papers. However, recent studies have demonstrated a tendency of news media to misrepresent scientific papers by exaggerating their findings. Given this, we present a formalization of and study into the problem of exaggeration detection in science communication. While there are an abundance of scientific papers and popular media articles written about them, very rarely do the articles include a direct link to the original paper, making data collection challenging. We address this by curating a set of labeled press release/abstract pairs from existing expert annotated studies on exaggeration in press releases of scientific papers suitable for benchmarking the performance of machine learning models on the task. Using limited data from this and previous studies on exaggeration detection in science, we introduce MT-PET, a multi-task version of Pattern Exploiting Training (PET), which leverages knowledge from complementary cloze-style QA tasks to improve few-shot learning. We demonstrate that MT-PET outperforms PET and supervised learning both when data is limited, as well as when there is an abundance of data for the main task.

In recent decades, chemistry publications and patents have increased rapidly. A significant portion of key information is embedded in molecular structure figures, complicating large-scale literature searches and limiting the application of large language models in fields such as biology, chemistry, and pharmaceuticals. The automatic extraction of precise chemical structures is of critical importance. However, the presence of numerous Markush structures in real-world documents, along with variations in molecular image quality, drawing styles, and noise, significantly limits the performance of existing optical chemical structure recognition (OCSR) methods. We present MolParser, a novel end-to-end OCSR method that efficiently and accurately recognizes chemical structures from real-world documents, including difficult Markush structure. We use a extended SMILES encoding rule to annotate our training dataset. Under this rule, we build MolParser-7M, the largest annotated molecular image dataset to our knowledge. While utilizing a large amount of synthetic data, we employed active learning methods to incorporate substantial in-the-wild data, specifically samples cropped from real patents and scientific literature, into the training process. We trained an end-to-end molecular image captioning model, MolParser, using a curriculum learning approach. MolParser significantly outperforms classical and learning-based methods across most scenarios, with potential for broader downstream applications. The dataset is publicly available.

The Kramers-Kronig relations are a pivotal foundation of linear optics and atomic physics, embedding a physical connection between the real and imaginary components of any causal response function. A mathematically equivalent, but simpler, approach instead utilises the Hilbert transform. In a previous study, the Hilbert transform was applied to absorption spectra in order to infer the sole refractive index of an atomic medium in the absence of an external magnetic field. The presence of a magnetic field causes the medium to become birefringent and dichroic, and therefore it is instead characterised by two refractive indices. In this study, we apply the same Hilbert transform technique to independently measure both refractive indices of a birefringent atomic medium, leading to an indirect measurement of atomic magneto-optical rotation. Key to this measurement is the insight that inputting specific light polarisations into an atomic medium induces absorption associated with only one of the refractive indices. We show this is true in two configurations, commonly referred to in literature as the Faraday and Voigt geometries, which differ by the magnetic field orientation with respect to the light wavevector. For both cases, we measure the two refractive indices independently for a Rb thermal vapour in a 0.6 T magnetic field, finding excellent agreement with theory. This study further emphasises the application of the Hilbert transform to the field of quantum and atomic optics in the linear regime.

In this work, we introduce ChemBFN, a language model that handles chemistry tasks based on Bayesian flow networks working on discrete data. A new accuracy schedule is proposed to improve the sampling quality by significantly reducing the reconstruction loss. We show evidence that our method is appropriate for generating molecules with satisfied diversity even when a smaller number of sampling steps is used. A classifier-free guidance method is adapted for conditional generation. It is also worthwhile to point out that after generative training, our model can be fine-tuned on regression and classification tasks with the state-of-the-art performance, which opens the gate of building all-in-one models in a single module style. Our model has been open sourced at https://github.com/Augus1999/bayesian-flow-network-for-chemistry.

Modern cosmological surveys are delivering datasets characterized by unprecedented quality and statistical completeness; this trend is expected to continue into the future as new ground- and space-based surveys come online. In order to maximally extract cosmological information from these observations, matching theoretical predictions are needed. At low redshifts, the surveys probe the nonlinear regime of structure formation where cosmological simulations are the primary means of obtaining the required information. The computational cost of sufficiently resolved large-volume simulations makes it prohibitive to run very large ensembles. Nevertheless, precision emulators built on a tractable number of high-quality simulations can be used to build very fast prediction schemes to enable a variety of cosmological inference studies. We have recently introduced the Mira-Titan Universe simulation suite designed to construct emulators for a range of cosmological probes. The suite covers the standard six cosmological parameters {omega_m,omega_b, sigma_8, h, n_s, w_0} and, in addition, includes massive neutrinos and a dynamical dark energy equation of state, {omega_{nu}, w_a}. In this paper we present the final emulator for the matter power spectrum based on 111 cosmological simulations, each covering a (2.1Gpc)^3 volume and evolving 3200^3 particles. An additional set of 1776 lower-resolution simulations and TimeRG perturbation theory results for the power spectrum are used to cover scales straddling the linear to mildly nonlinear regimes. The emulator provides predictions at the two to three percent level of accuracy over a wide range of cosmological parameters and is publicly released as part of this paper.

Based on the established task of identifying boosted, hadronically decaying top quarks, we compare a wide range of modern machine learning approaches. Unlike most established methods they rely on low-level input, for instance calorimeter output. While their network architectures are vastly different, their performance is comparatively similar. In general, we find that these new approaches are extremely powerful and great fun.

The advent of artificial intelligence (AI) has enabled a comprehensive exploration of materials for various applications. However, AI models often prioritize frequently encountered materials in the scientific literature, limiting the selection of suitable candidates based on inherent physical and chemical properties. To address this imbalance, we have generated a dataset of 1,494,017 natural language-material paragraphs based on combined OQMD, Materials Project, JARVIS, COD and AFLOW2 databases, which are dominated by ab initio calculations and tend to be much more evenly distributed on the periodic table. The generated text narratives were then polled and scored by both human experts and ChatGPT-4, based on three rubrics: technical accuracy, language and structure, and relevance and depth of content, showing similar scores but with human-scored depth of content being the most lagging. The merger of multi-modality data sources and large language model (LLM) holds immense potential for AI frameworks to help the exploration and discovery of solid-state materials for specific applications.

The efficient exploration of chemical space to design molecules with intended properties enables the accelerated discovery of drugs, materials, and catalysts, and is one of the most important outstanding challenges in chemistry. Encouraged by the recent surge in computer power and artificial intelligence development, many algorithms have been developed to tackle this problem. However, despite the emergence of many new approaches in recent years, comparatively little progress has been made in developing realistic benchmarks that reflect the complexity of molecular design for real-world applications. In this work, we develop a set of practical benchmark tasks relying on physical simulation of molecular systems mimicking real-life molecular design problems for materials, drugs, and chemical reactions. Additionally, we demonstrate the utility and ease of use of our new benchmark set by demonstrating how to compare the performance of several well-established families of algorithms. Surprisingly, we find that model performance can strongly depend on the benchmark domain. We believe that our benchmark suite will help move the field towards more realistic molecular design benchmarks, and move the development of inverse molecular design algorithms closer to designing molecules that solve existing problems in both academia and industry alike.

In this paper, we present the current progress of the project Verif.ai, an open-source scientific generative question-answering system with referenced and verified answers. The components of the system are (1) an information retrieval system combining semantic and lexical search techniques over scientific papers (PubMed), (2) a fine-tuned generative model (Mistral 7B) taking top answers and generating answers with references to the papers from which the claim was derived, and (3) a verification engine that cross-checks the generated claim and the abstract or paper from which the claim was derived, verifying whether there may have been any hallucinations in generating the claim. We are reinforcing the generative model by providing the abstract in context, but in addition, an independent set of methods and models are verifying the answer and checking for hallucinations. Therefore, we believe that by using our method, we can make scientists more productive, while building trust in the use of generative language models in scientific environments, where hallucinations and misinformation cannot be tolerated.

Novel machine learning methods for tabular data generation are often developed on small datasets which do not match the scale required for scientific applications. We investigate a recent proposal to use XGBoost as the function approximator in diffusion and flow-matching models on tabular data, which proved to be extremely memory intensive, even on tiny datasets. In this work, we conduct a critical analysis of the existing implementation from an engineering perspective, and show that these limitations are not fundamental to the method; with better implementation it can be scaled to datasets 370x larger than previously used. Our efficient implementation also unlocks scaling models to much larger sizes which we show directly leads to improved performance on benchmark tasks. We also propose algorithmic improvements that can further benefit resource usage and model performance, including multi-output trees which are well-suited to generative modeling. Finally, we present results on large-scale scientific datasets derived from experimental particle physics as part of the Fast Calorimeter Simulation Challenge. Code is available at https://github.com/layer6ai-labs/calo-forest.

We reanalyze the spectral lag data for GRB 160625B using frequentist inference in order to constrain the energy scale (E_{QG}) of Lorentz Invariance Violation (LIV). For this purpose, we use profile likelihood to deal with the astrophysical nuisance parameters. This is in contrast to Bayesian inference implemented in previous works, where marginalization was carried out over the nuisance parameters. We show that with profile likelihood, we do not find a global minimum for chi^2 as a function of E_{QG} below the Planck scale for both linear and quadratic models of LIV, whereas bounded credible intervals were previously obtained using Bayesian inference. Therefore, we can set one-sided lower limits in a straightforward manner. We find that E_{QG} geq 2.55 times 10^{16} GeV and E_{QG} geq 1.85 times 10^7 GeV at 95\% c.l., for linear and quadratic LIV, respectively. Therefore, this is the first proof-of-principles application of profile likelihood method to the analysis of GRB spectral lag data to constrain LIV.

We present the RODEM Jet Datasets, a comprehensive collection of simulated large-radius jets designed to support the development and evaluation of machine-learning algorithms in particle physics. These datasets encompass a diverse range of jet sources, including quark/gluon jets, jets from the decay of W bosons, top quarks, and heavy new-physics particles. The datasets provide detailed substructure information, including jet kinematics, constituent kinematics, and track displacement details, enabling a wide range of applications in jet tagging, anomaly detection, and generative modelling.

Recent years have seen the advent of molecular simulation datasets that are orders of magnitude larger and more diverse. These new datasets differ substantially in four aspects of complexity: 1. Chemical diversity (number of different elements), 2. system size (number of atoms per sample), 3. dataset size (number of data samples), and 4. domain shift (similarity of the training and test set). Despite these large differences, benchmarks on small and narrow datasets remain the predominant method of demonstrating progress in graph neural networks (GNNs) for molecular simulation, likely due to cheaper training compute requirements. This raises the question -- does GNN progress on small and narrow datasets translate to these more complex datasets? This work investigates this question by first developing the GemNet-OC model based on the large Open Catalyst 2020 (OC20) dataset. GemNet-OC outperforms the previous state-of-the-art on OC20 by 16% while reducing training time by a factor of 10. We then compare the impact of 18 model components and hyperparameter choices on performance in multiple datasets. We find that the resulting model would be drastically different depending on the dataset used for making model choices. To isolate the source of this discrepancy we study six subsets of the OC20 dataset that individually test each of the above-mentioned four dataset aspects. We find that results on the OC-2M subset correlate well with the full OC20 dataset while being substantially cheaper to train on. Our findings challenge the common practice of developing GNNs solely on small datasets, but highlight ways of achieving fast development cycles and generalizable results via moderately-sized, representative datasets such as OC-2M and efficient models such as GemNet-OC. Our code and pretrained model weights are open-sourced.

Accurate and comprehensive material databases extracted from research papers are critical for materials science and engineering but require significant human effort to develop. In this paper we present a simple method of extracting materials data from full texts of research papers suitable for quickly developing modest-sized databases. The method requires minimal to no coding, prior knowledge about the extracted property, or model training, and provides high recall and almost perfect precision in the resultant database. The method is fully automated except for one human-assisted step, which typically requires just a few hours of human labor. The method builds on top of natural language processing and large general language models but can work with almost any such model. The language models GPT-3/3.5, bart and DeBERTaV3 are evaluated here for comparison. We provide a detailed detailed analysis of the methods performance in extracting bulk modulus data, obtaining up to 90% precision at 96% recall, depending on the amount of human effort involved. We then demonstrate the methods broader effectiveness by developing a database of critical cooling rates for metallic glasses.

Depression has proven to be a significant public health issue, profoundly affecting the psychological well-being of individuals. If it remains undiagnosed, depression can lead to severe health issues, which can manifest physically and even lead to suicide. Generally, Diagnosing depression or any other mental disorder involves conducting semi-structured interviews alongside supplementary questionnaires, including variants of the Patient Health Questionnaire (PHQ) by Clinicians and mental health professionals. This approach places significant reliance on the experience and judgment of trained physicians, making the diagnosis susceptible to personal biases. Given that the underlying mechanisms causing depression are still being actively researched, physicians often face challenges in diagnosing and treating the condition, particularly in its early stages of clinical presentation. Recently, significant strides have been made in Artificial neural computing to solve problems involving text, image, and speech in various domains. Our analysis has aimed to leverage these state-of-the-art (SOTA) models in our experiments to achieve optimal outcomes leveraging multiple modalities. The experiments were performed on the Extended Distress Analysis Interview Corpus Wizard of Oz dataset (E-DAIC) corpus presented in the Audio/Visual Emotion Challenge (AVEC) 2019 Challenge. The proposed solutions demonstrate better results achieved by Proprietary and Open-source Large Language Models (LLMs), which achieved a Root Mean Square Error (RMSE) score of 3.98 on Textual Modality, beating the AVEC 2019 challenge baseline results and current SOTA regression analysis architectures. Additionally, the proposed solution achieved an accuracy of 71.43% in the classification task. The paper also includes a novel audio-visual multi-modal network that predicts PHQ-8 scores with an RMSE of 6.51.

Hallucination plagues even frontier LLMs--but how bad is it really for summarizing academic papers? We evaluate Factored Verification, a simple automated method for detecting hallucinations in abstractive summaries. This method sets a new SotA on hallucination detection in the summarization task of the HaluEval benchmark, achieving 76.2% accuracy. We then use this method to estimate how often language models hallucinate when summarizing across multiple academic papers and find 0.62 hallucinations in the average ChatGPT (16k) summary, 0.84 for GPT-4, and 1.55 for Claude 2. We ask models to self-correct using Factored Critiques and find that this lowers the number of hallucinations to 0.49 for ChatGPT, 0.46 for GPT-4, and 0.95 for Claude 2. The hallucinations we find are often subtle, so we advise caution when using models to synthesize academic papers.

In the era of proliferation of large language and image generation models, the phenomenon of "model collapse" refers to the situation whereby as a model is trained recursively on data generated from previous generations of itself over time, its performance degrades until the model eventually becomes completely useless, i.e the model collapses. In this work, we study this phenomenon in the setting of high-dimensional regression and obtain analytic formulae which quantitatively outline this phenomenon in a broad range of regimes. In the special case of polynomial decaying spectral and source conditions, we obtain modified scaling laws which exhibit new crossover phenomena from fast to slow rates. We also propose a simple strategy based on adaptive regularization to mitigate model collapse. Our theoretical results are validated with experiments.

This paper explores the potential of contextualized word embeddings (CWEs) as a new tool in the history, philosophy, and sociology of science (HPSS) for studying contextual and evolving meanings of scientific concepts. Using the term "Planck" as a test case, I evaluate five BERT-based models with varying degrees of domain-specific pretraining, including my custom model Astro-HEP-BERT, trained on the Astro-HEP Corpus, a dataset containing 21.84 million paragraphs from 600,000 articles in astrophysics and high-energy physics. For this analysis, I compiled two labeled datasets: (1) the Astro-HEP-Planck Corpus, consisting of 2,900 labeled occurrences of "Planck" sampled from 1,500 paragraphs in the Astro-HEP Corpus, and (2) a physics-related Wikipedia dataset comprising 1,186 labeled occurrences of "Planck" across 885 paragraphs. Results demonstrate that the domain-adapted models outperform the general-purpose ones in disambiguating the target term, predicting its known meanings, and generating high-quality sense clusters, as measured by a novel purity indicator I developed. Additionally, this approach reveals semantic shifts in the target term over three decades in the unlabeled Astro-HEP Corpus, highlighting the emergence of the Planck space mission as a dominant sense. The study underscores the importance of domain-specific pretraining for analyzing scientific language and demonstrates the cost-effectiveness of adapting pretrained models for HPSS research. By offering a scalable and transferable method for modeling the meanings of scientific concepts, CWEs open up new avenues for investigating the socio-historical dynamics of scientific discourses.

We study regressions with multiple treatments and a set of controls that is flexible enough to purge omitted variable bias. We show that these regressions generally fail to estimate convex averages of heterogeneous treatment effects -- instead, estimates of each treatment's effect are contaminated by non-convex averages of the effects of other treatments. We discuss three estimation approaches that avoid such contamination bias, including the targeting of easiest-to-estimate weighted average effects. A re-analysis of nine empirical applications finds economically and statistically meaningful contamination bias in observational studies; contamination bias in experimental studies is more limited due to smaller variability in propensity scores.

We present final natural system optical (ugriBV) and near-infrared (YJH) photometry of 134 supernovae (SNe) with probable white dwarf progenitors that were observed in 2004-2009 as part of the first stage of the Carnegie Supernova Project (CSP-I). The sample consists of 123 Type Ia SNe, 5 Type Iax SNe, 2 super-Chandrasekhar SN candidates, 2 Type Ia SNe interacting with circumstellar matter, and 2 SN 2006bt-like events. The redshifts of the objects range from z = 0.0037 to 0.0835; the median redshift is 0.0241. For 120 (90%) of these SNe, near-infrared photometry was obtained. Average optical extinction coefficients and color terms are derived and demonstrated to be stable during the five CSP-I observing campaigns. Measurements of the CSP-I near-infrared bandpasses are also described, and near-infrared color terms are estimated through synthetic photometry of stellar atmosphere models. Optical and near-infrared magnitudes of local sequences of tertiary standard stars for each supernova are given, and a new calibration of Y-band magnitudes of the Persson et al. (1998) standards in the CSP-I natural system is presented.

The lack of freely available standardized datasets represents an aggravating factor during the development and testing the performance of novel computational techniques in exposure assessment and dosimetry research. This hinders progress as researchers are required to generate numerical data (field, power and temperature distribution) anew using simulation software for each exposure scenario. Other than being time consuming, this approach is highly susceptible to errors that occur during the configuration of the electromagnetic model. To address this issue, in this paper, the limited available data on the incident power density and resultant maximum temperature rise on the skin surface considering various steady-state exposure scenarios at 10-90 GHz have been statistically modeled. The synthetic data have been sampled from the fitted statistical multivariate distribution with respect to predetermined dosimetric constraints. We thus present a comprehensive and open-source dataset compiled of the high-fidelity numerical data considering various exposures to a realistic source. Furthermore, different surrogate models for predicting maximum temperature rise on the skin surface were fitted based on the synthetic dataset. All surrogate models were tested on the originally available data where satisfactory predictive performance has been demonstrated. A simple technique of combining quadratic polynomial and tensor-product spline surrogates, each operating on its own cluster of data, has achieved the lowest mean absolute error of 0.058 {\deg}C. Therefore, overall experimental results indicate the validity of the proposed synthetic dataset.

Retrieval-augmented language models are being increasingly tasked with subjective, contentious, and conflicting queries such as "is aspartame linked to cancer". To resolve these ambiguous queries, one must search through a large range of websites and consider "which, if any, of this evidence do I find convincing?". In this work, we study how LLMs answer this question. In particular, we construct ConflictingQA, a dataset that pairs controversial queries with a series of real-world evidence documents that contain different facts (e.g., quantitative results), argument styles (e.g., appeals to authority), and answers (Yes or No). We use this dataset to perform sensitivity and counterfactual analyses to explore which text features most affect LLM predictions. Overall, we find that current models rely heavily on the relevance of a website to the query, while largely ignoring stylistic features that humans find important such as whether a text contains scientific references or is written with a neutral tone. Taken together, these results highlight the importance of RAG corpus quality (e.g., the need to filter misinformation), and possibly even a shift in how LLMs are trained to better align with human judgements.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

Aims: The aim of the present study is to explore how to disentangle energy-dependent time delays due to a possible Lorentz invariance violation (LIV) at Planck scale from intrinsic delays expected in standard blazar flares. Methods: We first characterise intrinsic time delays in BL Lacs and Flat Spectrum Radio Quasars in standard one-zone time-dependent synchrotron self-Compton or external Compton models, during flares produced by particle acceleration and cooling processes. We simulate families of flares with both intrinsic and external LIV-induced energy-dependent delays. Discrimination between intrinsic and LIV delays is then investigated in two different ways. A technique based on Euclidean distance calculation between delays obtained in the synchrotron and in the inverse-Compton spectral bumps is used to assess their degree of correlation. A complementary study is performed using spectral hardness versus intensity diagrams in both energy ranges. Results: We show that the presence of non-negligible LIV effects, which essentially act only at very high energies (VHE), can drastically reduce the strong correlation expected between the X-ray and the VHE gamma-ray emission in leptonic scenarios. The LIV phenomenon can then be hinted at measuring the Euclidean distance d_{E} from simultaneous X-ray and gamma-ray flare monitoring. Large values of minimal distance d_{E,min} would directly indicate the influence of non-intrinsic time delays possibly due to LIV in SSC flares. LIV effects can also significantly modify the VHE hysteresis patterns in hardness-intensity diagrams and even change their direction of rotation as compared to the X-ray behaviour. Both observables could be used to discriminate between LIV and intrinsic delays, provided high quality flare observations are available.

In the marketing field, understanding consumer heterogeneity, which is the internal or psychological difference among consumers that cannot be captured by behavioral logs, has long been a critical challenge. However, a number of consumers today usually post their evaluation on the specific product on the online platform, which can be the valuable source of such unobservable differences among consumers. Several previous studies have shown the validity of the analysis on text modality, but on the other hand, such analyses may not necessarily demonstrate sufficient predictive accuracy for text alone, as they may not include information readily available from cross-sectional data, such as consumer profile data. In addition, recent advances in machine learning techniques, such as large-scale language models (LLMs) and multimodal learning have made it possible to deal with the various kind of dataset simultaneously, including textual data and the traditional cross-sectional data, and the joint representations can be effectively obtained from multiple modalities. Therefore, this study constructs a product evaluation model that takes into account consumer heterogeneity by multimodal learning of online product reviews and consumer profile information. We also compare multiple models using different modalities or hyper-parameters to demonstrate the robustness of multimodal learning in marketing analysis.

We describe the design and performance of the near-infrared (1.51--1.70 micron), fiber-fed, multi-object (300 fibers), high resolution (R = lambda/delta lambda ~ 22,500) spectrograph built for the Apache Point Observatory Galactic Evolution Experiment (APOGEE). APOGEE is a survey of ~ 10^5 red giant stars that systematically sampled all Milky Way populations (bulge, disk, and halo) to study the Galaxy's chemical and kinematical history. It was part of the Sloan Digital Sky Survey III (SDSS-III) from 2011 -- 2014 using the 2.5 m Sloan Foundation Telescope at Apache Point Observatory, New Mexico. The APOGEE-2 survey is now using the spectrograph as part of SDSS-IV, as well as a second spectrograph, a close copy of the first, operating at the 2.5 m du Pont Telescope at Las Campanas Observatory in Chile. Although several fiber-fed, multi-object, high resolution spectrographs have been built for visual wavelength spectroscopy, the APOGEE spectrograph is one of the first such instruments built for observations in the near-infrared. The instrument's successful development was enabled by several key innovations, including a "gang connector" to allow simultaneous connections of 300 fibers; hermetically sealed feedthroughs to allow fibers to pass through the cryostat wall continuously; the first cryogenically deployed mosaic volume phase holographic grating; and a large refractive camera that includes mono-crystalline silicon and fused silica elements with diameters as large as ~ 400 mm. This paper contains a comprehensive description of all aspects of the instrument including the fiber system, optics and opto-mechanics, detector arrays, mechanics and cryogenics, instrument control, calibration system, optical performance and stability, lessons learned, and design changes for the second instrument.

This paper proposes a method for the automatic creation of variables (in the case of regression) that complement the information contained in the initial input vector. The method works as a pre-processing step in which the continuous values of the variable to be regressed are discretized into a set of intervals which are then used to define value thresholds. Then classifiers are trained to predict whether the value to be regressed is less than or equal to each of these thresholds. The different outputs of the classifiers are then concatenated in the form of an additional vector of variables that enriches the initial vector of the regression problem. The implemented system can thus be considered as a generic pre-processing tool. We tested the proposed enrichment method with 5 types of regressors and evaluated it in 33 regression datasets. Our experimental results confirm the interest of the approach.

Generative models trained on internet-scale data are capable of generating novel and realistic texts, images, and videos. A natural next question is whether these models can advance science, for example by generating novel stable materials. Traditionally, models with explicit structures (e.g., graphs) have been used in modeling structural relationships in scientific data (e.g., atoms and bonds in crystals), but generating structures can be difficult to scale to large and complex systems. Another challenge in generating materials is the mismatch between standard generative modeling metrics and downstream applications. For instance, common metrics such as the reconstruction error do not correlate well with the downstream goal of discovering stable materials. In this work, we tackle the scalability challenge by developing a unified crystal representation that can represent any crystal structure (UniMat), followed by training a diffusion probabilistic model on these UniMat representations. Our empirical results suggest that despite the lack of explicit structure modeling, UniMat can generate high fidelity crystal structures from larger and more complex chemical systems, outperforming previous graph-based approaches under various generative modeling metrics. To better connect the generation quality of materials to downstream applications, such as discovering novel stable materials, we propose additional metrics for evaluating generative models of materials, including per-composition formation energy and stability with respect to convex hulls through decomposition energy from Density Function Theory (DFT). Lastly, we show that conditional generation with UniMat can scale to previously established crystal datasets with up to millions of crystals structures, outperforming random structure search (the current leading method for structure discovery) in discovering new stable materials.

Existing approaches to multilingual text detoxification are hampered by the scarcity of parallel multilingual datasets. In this work, we introduce a pipeline for the generation of multilingual parallel detoxification data. We also introduce SynthDetoxM, a manually collected and synthetically generated multilingual parallel text detoxification dataset comprising 16,000 high-quality detoxification sentence pairs across German, French, Spanish and Russian. The data was sourced from different toxicity evaluation datasets and then rewritten with nine modern open-source LLMs in few-shot setting. Our experiments demonstrate that models trained on the produced synthetic datasets have superior performance to those trained on the human-annotated MultiParaDetox dataset even in data limited setting. Models trained on SynthDetoxM outperform all evaluated LLMs in few-shot setting. We release our dataset and code to help further research in multilingual text detoxification.

Neutron tagging in Gadolinium-doped water may play a significant role in reducing backgrounds from atmospheric neutrinos in next generation proton-decay searches using megaton-scale Water Cherenkov detectors. Similar techniques might also be useful in the detection of supernova neutrinos. Accurate determination of neutron tagging efficiencies will require a detailed understanding of the number of neutrons produced by neutrino interactions in water as a function of momentum transferred. We propose the Atmospheric Neutrino Neutron Interaction Experiment (ANNIE), designed to measure the neutron yield of atmospheric neutrino interactions in gadolinium-doped water. An innovative aspect of the ANNIE design is the use of precision timing to localize interaction vertices in the small fiducial volume of the detector. We propose to achieve this by using early production of LAPPDs (Large Area Picosecond Photodetectors). This experiment will be a first application of these devices demonstrating their feasibility for Water Cherenkov neutrino detectors.

Neutron tagging in Gadolinium-doped water may play a significant role in reducing backgrounds from atmospheric neutrinos in next generation proton-decay searches using megaton-scale Water Cherenkov detectors. Similar techniques might also be useful in the detection of supernova neutrinos. Accurate determination of neutron tagging efficiencies will require a detailed understanding of the number of neutrons produced by neutrino interactions in water as a function of momentum transferred. We propose the Atmospheric Neutrino Neutron Interaction Experiment (ANNIE), designed to measure the neutron yield of atmospheric neutrino interactions in gadolinium-doped water. An innovative aspect of the ANNIE design is the use of precision timing to localize interaction vertices in the small fiducial volume of the detector. We propose to achieve this by using early production of LAPPDs (Large Area Picosecond Photodetectors). This experiment will be a first application of these devices demonstrating their feasibility for Water Cherenkov neutrino detectors.

A recent study shows that if the power spectra (PS) of accreting compact objects consist of a combination of Lorentzian functions that are coherent in different energy bands but incoherent with each other, the same is true for the Real and Imaginary parts of the cross spectrum (CS). Using this idea, we discovered imaginary quasi-periodic oscillations (QPOs) in NICER observations of the black hole candidate MAXI J1820+070. The imaginary QPOs appear as narrow features with a small Real and large Imaginary part in the CS but are not significantly detected in the PS when they overlap in frequency with other variability components. The coherence function drops and the phase lags increase abruptly at the frequency of the imaginary QPO. We show that the multi-Lorentzian model that fits the PS and CS of the source in two energy bands correctly reproduces the lags and the coherence, and that the narrow drop of the coherence is caused by the interaction of the imaginary QPO with other variability components. The imaginary QPO appears only in the decay of the outburst, during the transition from the high-soft to the low-hard state of MAXI J1820+070, and its frequency decreases from approximately 5 Hz to around 1 Hz as the source spectrum hardens. We also analysed the earlier observations of the transition, where no narrow features were seen, and we identified a QPO in the PS that appears to evolve into the imaginary QPO as the source hardens. As for the type-B and C QPOs in this source, the rms spectrum of the imaginary QPO increases with energy. The lags of the imaginary QPO are similar to those of the type-B and C QPOs above 2 keV but differ from the lags of those other QPOs below that energy. While the properties of this imaginary QPO resemble those of type-C QPOs, we cannot rule out that it is a new type of QPO.

Without accurate transcription of numerical data in scientific documents, a scientist cannot draw accurate conclusions. Unfortunately, the process of copying numerical data from one paper to another is prone to human error. In this paper, we propose to meet this challenge through the novel task of automatic table verification (AutoTV), in which the objective is to verify the accuracy of numerical data in tables by cross-referencing cited sources. To support this task, we propose a new benchmark, arXiVeri, which comprises tabular data drawn from open-access academic papers on arXiv. We introduce metrics to evaluate the performance of a table verifier in two key areas: (i) table matching, which aims to identify the source table in a cited document that corresponds to a target table, and (ii) cell matching, which aims to locate shared cells between a target and source table and identify their row and column indices accurately. By leveraging the flexible capabilities of modern large language models (LLMs), we propose simple baselines for table verification. Our findings highlight the complexity of this task, even for state-of-the-art LLMs like OpenAI's GPT-4. The code and benchmark will be made publicly available.

We present Chandra ACIS imaging spectroscopy results for the extended (1.5"-8") hard X-ray emission of the Compton thick (CT) Seyfert NGC 5728. We find spectrally and spatially-resolved features in the Fe Kalpha complex (5.0-7.5 keV), redward and blueward of the neutral 6.4 keV line in the extended bicone. The [red, blue] features have [6.5sigma, 5.3sigma] significance, with an equivalent width = [2.0 keV, 2.5 keV], much higher than in the nuclear spectrum. These energies imply line-of-sight velocities of ~19,000-42,000 km s^{-1} for the red wing, and ~ -28,000 km s^{-1} for the blue wing, if the emission is due to neutral Fe Kalpha. These red and blue wings are radially extended ~6"(1.2 kpc), and ~5"(1 kpc), respectively, as confirmed by narrow-band X-ray imaging. Our models discard the possibility that the red wing could arise from a Compton shoulder, and show that the flux in the blue wing is unlikely to arise (at ~3sigma significance) from a blend of Fe Kbeta and highly ionized Fe lines.