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The Dark Energy Spectroscopic Instrument (DESI) is currently measuring the spectra of 40\,million galaxies and quasars, the largest such survey ever made to probe the nature of cosmological dark energy. The 4-meter Mayall telescope at Kitt Peak National Observatory has been adapted for DESI, including the construction of a 3.2-degree diameter prime focus corrector that focuses astronomical light onto a 0.8-meter diameter focal surface with excellent image quality over the DESI bandpass of 360-980nm. The wide-field corrector includes six lenses, as large as 1.1-meters in diameter and as heavy as 237\,kilograms, including two counter-rotating wedged lenses that correct for atmospheric dispersion over Zenith angles from 0 to 60 degrees. The lenses, cells, and barrel assembly all meet precise alignment tolerances on the order of tens of microns. The barrel alignment is maintained throughout a range of observing angles and temperature excursions in the Mayall dome by use of a hexapod, which is itself supported by a new cage, ring, and truss structure. In this paper we describe the design, fabrication, and performance of the new corrector and associated structure, focusing on how they meet DESI requirements. In particular we describe the prescription and specifications of the lenses, design choices and error budgeting of the barrel assembly, stray light mitigations, and integration and test at the Mayall telescope. We conclude with some validation highlights that demonstrate the successful corrector on-sky performance, and list some lessons learned during the multi-year fabrication phase., Comment: 68 pages, 56 figures, 22 tables. Submitted to the Astronomical Journal

The BioNLP Workshop 2023 initiated the launch of a shared task on Problem List Summarization (ProbSum) in January 2023. The aim of this shared task is to attract future research efforts in building NLP models for real-world diagnostic decision support applications, where a system generating relevant and accurate diagnoses will augment the healthcare providers decision-making process and improve the quality of care for patients. The goal for participants is to develop models that generated a list of diagnoses and problems using input from the daily care notes collected from the hospitalization of critically ill patients. Eight teams submitted their final systems to the shared task leaderboard. In this paper, we describe the tasks, datasets, evaluation metrics, and baseline systems. Additionally, the techniques and results of the evaluation of the different approaches tried by the participating teams are summarized., Comment: To appear in the Proceedings of the 5th BioNLP Workshop at ACL

Generative artificial intelligence (AI) is a promising direction for augmenting clinical diagnostic decision support and reducing diagnostic errors, a leading contributor to medical errors. To further the development of clinical AI systems, the Diagnostic Reasoning Benchmark (DR.BENCH) was introduced as a comprehensive generative AI framework, comprised of six tasks representing key components in clinical reasoning. We present a comparative analysis of in-domain versus out-of-domain language models as well as multi-task versus single task training with a focus on the problem summarization task in DR.BENCH (Gao et al., 2023). We demonstrate that a multi-task, clinically trained language model outperforms its general domain counterpart by a large margin, establishing a new state-of-the-art performance, with a ROUGE-L score of 28.55. This research underscores the value of domain-specific training for optimizing clinical diagnostic reasoning tasks., Comment: Accepted to the Proceedings of the 5th Clinical NLP Workshop at ACL

Radiotherapy (RT) toxicities can impair survival and quality-of-life, yet remain under-studied. Real-world evidence holds potential to improve our understanding of toxicities, but toxicity information is often only in clinical notes. We developed natural language processing (NLP) models to identify the presence and severity of esophagitis from notes of patients treated with thoracic RT. We fine-tuned statistical and pre-trained BERT-based models for three esophagitis classification tasks: Task 1) presence of esophagitis, Task 2) severe esophagitis or not, and Task 3) no esophagitis vs. grade 1 vs. grade 2-3. Transferability was tested on 345 notes from patients with esophageal cancer undergoing RT. Fine-tuning PubmedBERT yielded the best performance. The best macro-F1 was 0.92, 0.82, and 0.74 for Task 1, 2, and 3, respectively. Selecting the most informative note sections during fine-tuning improved macro-F1 by over 2% for all tasks. Silver-labeled data improved the macro-F1 by over 3% across all tasks. For the esophageal cancer notes, the best macro-F1 was 0.73, 0.74, and 0.65 for Task 1, 2, and 3, respectively, without additional fine-tuning. To our knowledge, this is the first effort to automatically extract esophagitis toxicity severity according to CTCAE guidelines from clinic notes. The promising performance provides proof-of-concept for NLP-based automated detailed toxicity monitoring in expanded domains., Comment: 17 pages, 6 tables, 1figure, submiting to JCO-CCI for review

Daily progress notes are common types in the electronic health record (EHR) where healthcare providers document the patient's daily progress and treatment plans. The EHR is designed to document all the care provided to patients, but it also enables note bloat with extraneous information that distracts from the diagnoses and treatment plans. Applications of natural language processing (NLP) in the EHR is a growing field with the majority of methods in information extraction. Few tasks use NLP methods for downstream diagnostic decision support. We introduced the 2022 National NLP Clinical Challenge (N2C2) Track 3: Progress Note Understanding - Assessment and Plan Reasoning as one step towards a new suite of tasks. The Assessment and Plan Reasoning task focuses on the most critical components of progress notes, Assessment and Plan subsections where health problems and diagnoses are contained. The goal of the task was to develop and evaluate NLP systems that automatically predict causal relations between the overall status of the patient contained in the Assessment section and its relation to each component of the Plan section which contains the diagnoses and treatment plans. The goal of the task was to identify and prioritize diagnoses as the first steps in diagnostic decision support to find the most relevant information in long documents like daily progress notes. We present the results of 2022 n2c2 Track 3 and provide a description of the data, evaluation, participation and system performance., Comment: To appear in Journal of Biomedical Informatics

We present laboratory characterization of kilo-pixel, filled backshort-under-grid (BUG) transition-edge sensor (TES) arrays developed for the Primordial Inflation Polarization ExploreR (PIPER) balloon-borne instrument. PIPER is designed to map the polarization of the CMB on the largest angular scales and characterize dust foregrounds by observing a large fraction of the sky in four frequency bands in the range 200 to 600 GHz. The BUG TES arrays are read out by planar SQUID-based time division multiplexer chips (2dMUX) of matching form factor and hybridized directly with the detector arrays through indium bump bonding. Here, we discuss the performance of the 2dMUX and present measurements of the TES transition temperature, thermal conductance, saturation power, and preliminary noise performance. The detectors achieve saturation power below 1 pW and phonon noise equivalent power (NEP) on the order of a few aW/rtHz. Detector performance is further verified through pre-flight tests in the integrated PIPER receiver, performed in an environment simulating balloon float conditions., Comment: 11 pages, 11 figures

The meaningful use of electronic health records (EHR) continues to progress in the digital era with clinical decision support systems augmented by artificial intelligence. A priority in improving provider experience is to overcome information overload and reduce the cognitive burden so fewer medical errors and cognitive biases are introduced during patient care. One major type of medical error is diagnostic error due to systematic or predictable errors in judgment that rely on heuristics. The potential for clinical natural language processing (cNLP) to model diagnostic reasoning in humans with forward reasoning from data to diagnosis and potentially reduce the cognitive burden and medical error has not been investigated. Existing tasks to advance the science in cNLP have largely focused on information extraction and named entity recognition through classification tasks. We introduce a novel suite of tasks coined as Diagnostic Reasoning Benchmarks, DR.BENCH, as a new benchmark for developing and evaluating cNLP models with clinical diagnostic reasoning ability. The suite includes six tasks from ten publicly available datasets addressing clinical text understanding, medical knowledge reasoning, and diagnosis generation. DR.BENCH is the first clinical suite of tasks designed to be a natural language generation framework to evaluate pre-trained language models. Experiments with state-of-the-art pre-trained generative language models using large general domain models and models that were continually trained on a medical corpus demonstrate opportunities for improvement when evaluated in DR. BENCH. We share DR. BENCH as a publicly available GitLab repository with a systematic approach to load and evaluate models for the cNLP community., Comment: Under review

Automatically summarizing patients' main problems from daily progress notes using natural language processing methods helps to battle against information and cognitive overload in hospital settings and potentially assists providers with computerized diagnostic decision support. Problem list summarization requires a model to understand, abstract, and generate clinical documentation. In this work, we propose a new NLP task that aims to generate a list of problems in a patient's daily care plan using input from the provider's progress notes during hospitalization. We investigate the performance of T5 and BART, two state-of-the-art seq2seq transformer architectures, in solving this problem. We provide a corpus built on top of progress notes from publicly available electronic health record progress notes in the Medical Information Mart for Intensive Care (MIMIC)-III. T5 and BART are trained on general domain text, and we experiment with a data augmentation method and a domain adaptation pre-training method to increase exposure to medical vocabulary and knowledge. Evaluation methods include ROUGE, BERTScore, cosine similarity on sentence embedding, and F-score on medical concepts. Results show that T5 with domain adaptive pre-training achieves significant performance gains compared to a rule-based system and general domain pre-trained language models, indicating a promising direction for tackling the problem summarization task., Comment: Paper is accepted to COLING 2022

A system of 5,020 robotic fiber positioners was installed in 2019 on the Mayall Telescope, at Kitt Peak National Observatory. The robots automatically re-target their optical fibers every 10 - 20 minutes, each to a precision of several microns, with a reconfiguration time less than 2 minutes. Over the next five years, they will enable the newly-constructed Dark Energy Spectroscopic Instrument (DESI) to measure the spectra of 35 million galaxies and quasars. DESI will produce the largest 3D map of the universe to date and measure the expansion history of the cosmos. In addition to the 5,020 robotic positioners and optical fibers, DESI's Focal Plane System includes 6 guide cameras, 4 wavefront cameras, 123 fiducial point sources, and a metrology camera mounted at the primary mirror. The system also includes associated structural, thermal, and electrical systems. In all, it contains over 675,000 individual parts. We discuss the design, construction, quality control, and integration of all these components. We include a summary of the key requirements, the review and acceptance process, on-sky validations of requirements, and lessons learned for future multi-object, fiber-fed spectrographs., Comment: 51 pages, 41 figures

Applying methods in natural language processing on electronic health records (EHR) data is a growing field. Existing corpus and annotation focus on modeling textual features and relation prediction. However, there is a paucity of annotated corpus built to model clinical diagnostic thinking, a process involving text understanding, domain knowledge abstraction and reasoning. This work introduces a hierarchical annotation schema with three stages to address clinical text understanding, clinical reasoning, and summarization. We created an annotated corpus based on an extensive collection of publicly available daily progress notes, a type of EHR documentation that is collected in time series in a problem-oriented format. The conventional format for a progress note follows a Subjective, Objective, Assessment and Plan heading (SOAP). We also define a new suite of tasks, Progress Note Understanding, with three tasks utilizing the three annotation stages. The novel suite of tasks was designed to train and evaluate future NLP models for clinical text understanding, clinical knowledge representation, inference, and summarization., Comment: To appear in 13th Language Resources and Evaluation Conference (LREC 2022)