The Shaky Foundations of Clinical Foundation Models: A Survey of Large Language Models and Foundation Models for EMRs

The successes of foundation models such as ChatGPT and AlphaFold have spurred significant interest in building similar models for electronic medical records (EMRs) to improve patient care and hospital operations. However, recent hype has obscured critical gaps in our understanding of these models' capabilities. We review over 80 foundation models trained on non-imaging EMR data (i.e. clinical text and/or structured data) and create a taxonomy delineating their architectures, training data, and potential use cases. We find that most models are trained on small, narrowly-scoped clinical datasets (e.g. MIMIC-III) or broad, public biomedical corpora (e.g. PubMed) and are evaluated on tasks that do not provide meaningful insights on their usefulness to health systems. In light of these findings, we propose an improved evaluation framework for measuring the benefits of clinical foundation models that is more closely grounded to metrics that matter in healthcare.Comment: Reformatted figures, updated contribution

Fall, Recovery and Characterization of the Novato L6 Chondrite Breccia

The Novato L6 chondrite fragmental breccia fell in California on 17 October 2012, and was recovered after the Cameras for Allsky Meteor Surveillance (CAMS) project determined the meteor's trajectory between 95 and 45 km altitude. The final fragmentation at 33 1 km altitude was exceptionally well documented by digital photographs. The first sample was recovered before rain hit the area. First results from a consortium study of the meteorite's characterization, cosmogenic and radiogenic nuclides, origin and conditions of the fall are presented. Some meteorites did not retain fusion crust and show evidence of spallation. Before entry, the meteoroid was 35+/-5 cm in diameter (mass 80+/-35 kg) with a cosmic ray exposure age of 9+/-1 Ma, if it had a one-stage exposure history. However, based on the cosmogenic nuclide inventory, a two-stage exposure history is more likely, with lower shielding in the last few Ma. Thermoluminescence data suggest a collision event within the last approx. 0.1 Ma. Novato likely belonged to the class of shocked L chondrites that have a common shock age of 470 Ma, based on the U,Th-He age of 460+/-220 Ma. The measured orbits of Novato, Jesenice and Innisfree are consistent with a proposed origin of these shocked L chondrites in the Gefion asteroid family, but leave open the possibility that they came to us directly from the 5:2 mean motion resonance with Jupiter. Novato experienced a stronger compaction than did other L6 chondrites of shock-stage S4. Despite this, a freshly broken surface shows a wide range of organic compounds

Ancient Lowland Maya neighborhoods: Average Nearest Neighbor analysis and kernel density models, environments, and urban scale

Many humans live in large, complex political centers, composed of multi-scalar communities including neighborhoods and districts. Both today and in the past, neighborhoods form a fundamental part of cities and are defined by their spatial, architectural, and material elements. Neighborhoods existed in ancient centers of various scales, and multiple methods have been employed to identify ancient neighborhoods in archaeological contexts. However, the use of different methods for neighborhood identification within the same spatiotemporal setting results in challenges for comparisons within and between ancient societies. Here, we focus on using a single method—combining Average Nearest Neighbor (ANN) and Kernel Density (KD) analyses of household groups—to identify potential neighborhoods based on clusters of households at 23 ancient centers across the Maya Lowlands. While a one-size-fits all model does not work for neighborhood identification everywhere, the ANN/KD method provides quantifiable data on the clustering of ancient households, which can be linked to environmental zones and urban scale. We found that centers in river valleys exhibited greater household clustering compared to centers in upland and escarpment environments. Settlement patterns on flat plains were more dispersed, with little discrete spatial clustering of households. Furthermore, we categorized the ancient Maya centers into discrete urban scales, finding that larger centers had greater variation in household spacing compared to medium-sized and smaller centers. Many larger political centers possess heterogeneity in household clustering between their civic-ceremonial cores, immediate hinterlands, and far peripheries. Smaller centers exhibit greater household clustering compared to larger ones. This paper quantitatively assesses household clustering among nearly two dozen centers across the Maya Lowlands, linking environment and urban scale to settlement patterns. The findings are applicable to ancient societies and modern cities alike; understanding how humans form multi-scalar social groupings, such as neighborhoods, is fundamental to human experience and social organization

Sorghum Genome Sequencing by Methylation Filtration

Sorghum bicolor is a close relative of maize and is a staple crop in Africa and much of the developing world because of its superior tolerance of arid growth conditions. We have generated sequence from the hypomethylated portion of the sorghum genome by applying methylation filtration (MF) technology. The evidence suggests that 96% of the genes have been sequence tagged, with an average coverage of 65% across their length. Remarkably, this level of gene discovery was accomplished after generating a raw coverage of less than 300 megabases of the 735-megabase genome. MF preferentially captures exons and introns, promoters, microRNAs, and simple sequence repeats, and minimizes interspersed repeats, thus providing a robust view of the functional parts of the genome. The sorghum MF sequence set is beneficial to research on sorghum and is also a powerful resource for comparative genomics among the grasses and across the entire plant kingdom. Thousands of hypothetical gene predictions in rice and Arabidopsis are supported by the sorghum dataset, and genomic similarities highlight evolutionarily conserved regions that will lead to a better understanding of rice and Arabidopsis

Improved performance of crystal structure solution from powder diffraction data through parameter tuning of a simulated annealing algorithm

Significant gains in the performance of the simulated annealing algorithm in the DASH software package have been realised by using the irace automatic configuration tool to optimise the values of three key simulated annealing parameters. Specifically, the success rate in finding the global minimum in intensity chi squared space is improved by up to an order of magnitude. The general applicability of these revised simulated annealing parameters is demonstrated using the crystal structure determinations of over 100 powder diffraction data sets

Organics Captured from Comet Wild 2 by the Stardust Spacecraft

Organics found in Comet Wild 2 samples show a heterogeneous and unequilibrated distribution in abundance and composition. Some are similar, but not identical, to those in interplanetary dust particles (IDPs) and carbonaceous meteorites. A new class of aromatic-poor organic material is also present. The organics are rich in O and N compared to meteoritic organics. Aromatic compounds are present, but the samples tend to be relatively poorer in aromatics than meteorites and IDPs. D and 15N suggest that some organics have an interstellar/protostellar heritage. While the variable extent of modification of these materials by impact capture is not yet fully constrained, a remarkably diverse suite of organic compounds is present and identifiable within the returned samples