LLMs Understand Glass-Box Models, Discover Surprises, and Suggest Repairs

We show that large language models (LLMs) are remarkably good at working with interpretable models that decompose complex outcomes into univariate graph-represented components. By adopting a hierarchical approach to reasoning, LLMs can provide comprehensive model-level summaries without ever requiring the entire model to fit in context. This approach enables LLMs to apply their extensive background knowledge to automate common tasks in data science such as detecting anomalies that contradict prior knowledge, describing potential reasons for the anomalies, and suggesting repairs that would remove the anomalies. We use multiple examples in healthcare to demonstrate the utility of these new capabilities of LLMs, with particular emphasis on Generalized Additive Models (GAMs). Finally, we present the package $\texttt{TalkToEBM}$ as an open-source LLM-GAM interface

Late gadolinium enhancement cardiovascular magnetic resonance predicts clinical worsening in patients with pulmonary hypertension

<p>Abstract</p> <p>Background</p> <p>Late gadolinium enhancement (LGE) occurs at the right ventricular (RV) insertion point (RVIP) in patients with pulmonary hypertension (PH) and has been shown to correlate with cardiovascular magnetic resonance (CMR) derived RV indices. However, the prognostic role of RVIP-LGE and other CMR-derived parameters of RV function are not well established. Our aim was to evaluate the predictive value of contrast-enhanced CMR in patients with PH.</p> <p>Methods</p> <p>RV size, ejection fraction (RVEF), and the presence of RVIP-LGE were determined in 58 patients with PH referred for CMR. All patients underwent right heart catheterization, exercise testing, and N-terminal pro-brain natriuretic peptide (NT-proBNP) evaluation; results of which were included in the final analysis if performed within 4 months of the CMR study. Patients were followed for the primary endpoint of time to clinical worsening (death, decompensated right ventricular heart failure, initiation of prostacyclin, or lung transplantation).</p> <p>Results</p> <p>Overall, 40/58 (69%) of patients had RVIP-LGE. Patients with RVIP- LGE had larger right ventricular volume index, lower RVEF, and higher mean pulmonary artery pressure (mPAP), all p < 0.05. During the follow-up period of 10.2 ± 6.3 months, 19 patients reached the primary endpoint. In a univariate analysis, RVIP-LGE was a predictor for adverse outcomes (p = 0.026). In a multivariate analysis, CMR-derived RVEF was an independent predictor of clinical worsening (p = 0.036) along with well-established prognostic parameters such as exercise capacity (p = 0.010) and mPAP (p = 0.001).</p> <p>Conclusions</p> <p>The presence of RVIP-LGE in patients with PH is a marker for more advanced disease and poor prognosis. In addition, this study reveals for the first time that CMR-derived RVEF is an independent non-invasive imaging predictor of adverse outcomes in this patient population.</p

Systemic Disease-Induced Salivary Biomarker Profiles in Mouse Models of Melanoma and Non-Small Cell Lung Cancer

Background: Saliva (oral fluids) is an emerging biofluid poised for detection of clinical diseases. Although the rationale for oral diseases applications (e.g. oral cancer) is intuitive, the rationale and relationship between systemic diseases and saliva biomarkers are unclear. Methodology/Principal Findings: In this study, we used mouse models of melanoma and non-small cell lung cancer and compared the transcriptome biomarker profiles of tumor-bearing mice to those of control mice. Microarray analysis showed that salivary transcriptomes were significantly altered in tumor-bearing mice vs. controls. Significant overlapping among transcriptomes of mouse tumors, serum, salivary glands and saliva suggests that salivary biomarkers have multiple origins. Furthermore, we identified that the expression of two groups of significantly altered transcription factors (TFs) Runx1, Mlxipl, Trim30 and Egr1, Tbx1, Nr1d1 in salivary gland tissue of melanoma-bearing mice can potentially be responsible for 82.6 % of the up-regulated gene expression and 62.5 % of the down-regulated gene expression, respectively, in the saliva o

Host-linked soil viral ecology along a permafrost thaw gradient

Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood1,2,3,4,5,6,7. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans8,9,10, remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling

The Milky Way Bulge: Observed properties and a comparison to external galaxies

The Milky Way bulge offers a unique opportunity to investigate in detail the role that different processes such as dynamical instabilities, hierarchical merging, and dissipational collapse may have played in the history of the Galaxy formation and evolution based on its resolved stellar population properties. Large observation programmes and surveys of the bulge are providing for the first time a look into the global view of the Milky Way bulge that can be compared with the bulges of other galaxies, and be used as a template for detailed comparison with models. The Milky Way has been shown to have a box/peanut (B/P) bulge and recent evidence seems to suggest the presence of an additional spheroidal component. In this review we summarise the global chemical abundances, kinematics and structural properties that allow us to disentangle these multiple components and provide constraints to understand their origin. The investigation of both detailed and global properties of the bulge now provide us with the opportunity to characterise the bulge as observed in models, and to place the mixed component bulge scenario in the general context of external galaxies. When writing this review, we considered the perspectives of researchers working with the Milky Way and researchers working with external galaxies. It is an attempt to approach both communities for a fruitful exchange of ideas.Comment: Review article to appear in "Galactic Bulges", Editors: Laurikainen E., Peletier R., Gadotti D., Springer Publishing. 36 pages, 10 figure

UV Star Formation Rates in the Local Universe

We measure star formation rates of ~50,000 optically-selected galaxies in the local universe (z~0.1), spanning a range from gas-rich dwarfs to massive ellipticals. We obtain dust-corrected SFRs by fitting the GALEX (UV) and SDSS (optical) photometry to a library of population synthesis models that include dust attenuation. For star-forming galaxies, our UV-based SFRs compare remarkably well with those derived from SDSS H alpha. Deviations from perfect agreement between these two methods are due to differences in the dust attenuation estimates. In contrast to H alpha, UV provides reliable SFRs for galaxies with weak or no H alpha emission, and where H alpha is contaminated with an emission from an AGN. We use full-SED SFRs to calibrate a simple prescription that uses GALEX UV magnitudes to produce good SFRs for normal star-forming galaxies. The specific SFR is considered as a function of stellar mass for (1) star-forming galaxies with no AGN, (2) those hosting an AGN, and for (3) galaxies without H alpha emission. We find that the three have distinct star formation histories, with AGN lying intermediate between the star-forming and the quiescent galaxies. Normal star forming galaxies (without an AGN) lie on a relatively narrow linear sequence. Remarkably, galaxies hosting a strong AGN appear to represent the massive continuation of this sequence. Weak AGN, while also massive, have lower SFR, sometimes extending to the realm of quiescent galaxies. We propose an evolutionary sequence for massive galaxies that smoothly connects normal star-forming galaxies to quiescent (red sequence) galaxies via strong and weak AGN. We confirm that some galaxies with no H alpha emission show signs of SF in the UV. We derive a UV-based cosmic SFR density at z=0.1 with smaller total error than previous measurements (abridged).Comment: Accepted for publication in ApJ (Special GALEX Supplement issue - Dec 2007). v2: Typo in Eq. 2 correcte

Second Data Release of the COSMOS Lyman-alpha Mapping and Tomographic Observation: The First 3D Maps of the Detailed Cosmic Web at 2.05<z<2.55

We present the second data release of the COSMOS Lyman-Alpha Mapping And Tomography Observations (CLAMATO) Survey conducted with the LRIS spectrograph on the Keck-I telescope. This project used Lyman-alpha forest absorption in the spectra of faint star forming galaxies and quasars at z ~ 2-3 to trace neutral hydrogen in the intergalactic medium. In particular, we use 320 objects over a footprint of ~0.2 deg^2 to reconstruct the absorption field at 2.05 < z < 2.55 at ~2 h^{-1}Mpc resolution. We apply a Wiener filtering technique to the observed data to reconstruct three dimensional maps of the field over a volume of 4.1 x 10^5 comoving cubic Mpc. In addition to the filtered flux maps, for the first time we infer the underlying dark matter field through a forward modeling framework from a joint likelihood of galaxy and Lyman-alpha forest data, finding clear examples of the detailed cosmic web consisting of cosmic voids, sheets, filaments, and nodes. In addition to traditional figures, we present a number of interactive three dimensional models to allow exploration of the data and qualitative comparisons to known galaxy surveys. We find that our inferred over-densities are consistent with those found from galaxy fields. Our reduced spectra, extracted Lyman-alpha forest pixel data, and reconstructed tomographic maps are available publicly at https://doi.org/10.5281/zenodo.5842842Comment: 20 pages, 15 figures. Data is available at https://doi.org/10.5281/zenodo.5842842 arXiv admin note: text overlap with arXiv:1710.0289

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals.

Large-scale deep-coverage whole-genome sequencing (WGS) is now feasible and offers potential advantages for locus discovery. We perform WGS in 16,324 participants from four ancestries at mean depth &gt;29X and analyze genotypes with four quantitative traits-plasma total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol, and triglycerides. Common variant association yields known loci except for few variants previously poorly imputed. Rare coding variant association yields known Mendelian dyslipidemia genes but rare non-coding variant association detects no signals. A high 2M-SNP LDL-C polygenic score (top 5th percentile) confers similar effect size to a monogenic mutation (~30 mg/dl higher for each); however, among those with severe hypercholesterolemia, 23% have a high polygenic score and only 2% carry a monogenic mutation. At these sample sizes and for these phenotypes, the incremental value of WGS for discovery is limited but WGS permits simultaneous assessment of monogenic and polygenic models to severe hypercholesterolemia

Spectral Identification of Lighting Type and Character

We investigated the optimal spectral bands for the identification of lighting types and the estimation of four major indices used to measure the efficiency or character of lighting. To accomplish these objectives we collected high-resolution emission spectra (350 to 2,500 nm) for forty-three different lamps, encompassing nine of the major types of lamps used worldwide. The narrow band emission spectra were used to simulate radiances in eight spectral bands including the human eye photoreceptor bands (photopic, scotopic, and “meltopic”) plus five spectral bands in the visible and near-infrared modeled on bands flown on the Landsat Thematic Mapper (TM). The high-resolution continuous spectra are superior to the broad band combinations for the identification of lighting type and are the standard for calculation of Luminous Efficacy of Radiation (LER), Correlated Color Temperature (CCT) and Color Rendering Index (CRI). Given the high cost that would be associated with building and flying a hyperspectral sensor with detection limits low enough to observe nighttime lights we conclude that it would be more feasible to fly an instrument with a limited number of broad spectral bands in the visible to near infrared. The best set of broad spectral bands among those tested is blue, green, red and NIR bands modeled on the band set flown on the Landsat Thematic Mapper. This set provides low errors on the identification of lighting types and reasonable estimates of LER and CCT when compared to the other broad band set tested. None of the broad band sets tested could make reasonable estimates of Luminous Efficacy (LE) or CRI. The photopic band proved useful for the estimation of LER. However, the three photoreceptor bands performed poorly in the identification of lighting types when compared to the bands modeled on the Landsat Thematic Mapper. Our conclusion is that it is feasible to identify lighting type and make reasonable estimates of LER and CCT using four or more spectral bands with minimal spectral overlap spanning the 0.4 to 1.0 um region

Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.

The original version of this article contained an error in the name of the author Ramachandran S. Vasan, which was incorrectly given as Vasan S. Ramachandran. This has now been corrected in both the PDF and HTML versions of the article