What Makes a Top-Performing Precision Medicine Search Engine? Tracing Main System Features in a Systematic Way

From 2017 to 2019 the Text REtrieval Conference (TREC) held a challenge task on precision medicine using documents from medical publications (PubMed) and clinical trials. Despite lots of performance measurements carried out in these evaluation campaigns, the scientific community is still pretty unsure about the impact individual system features and their weights have on the overall system performance. In order to overcome this explanatory gap, we first determined optimal feature configurations using the Sequential Model-based Algorithm Configuration (SMAC) program and applied its output to a BM25-based search engine. We then ran an ablation study to systematically assess the individual contributions of relevant system features: BM25 parameters, query type and weighting schema, query expansion, stop word filtering, and keyword boosting. For evaluation, we employed the gold standard data from the three TREC-PM installments to evaluate the effectiveness of different features using the commonly shared infNDCG metric.Comment: Accepted for SIGIR2020, 10 page

CMS physics technical design report : Addendum on high density QCD with heavy ions

Peer reviewe

Multi-messenger observations of a binary neutron star merger

On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ~1.7 s with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of 40+8-8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 Mo. An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ~40 Mpc) less than 11 hours after the merger by the One- Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ~10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position ~9 and ~16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta

Multi-messenger Observations of a Binary Neutron Star Merger

On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ∼ 1.7 {{s}} with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of {40}-8+8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 {M}ȯ . An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ∼ 40 {{Mpc}}) less than 11 hours after the merger by the One-Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ∼10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position ∼ 9 and ∼ 16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC 4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta.</p

Clinical reports information retrieval

Narrativas clínicas são normalmente escritas em linguagem natural devido a seu poder descritivo e facilidade de comunicação entre os especialistas. Processar esses dados para fins de descoberta de conhecimento e coleta de estatísticas exige técnicas de extração de informações, com alguns resultados já apresentados na literatura para o domínio jornalístico, mas ainda raras no domínio médico. O presente trabalho visa desenvolver um classificador de laudos de anatomia patológica que seja capaz de inferir a topografia e a morfologia de um câncer na Classificação Internacional de Doenças para Oncologia (CID-O). Dados fornecidos pelo A.C. Camargo Cancer Center em São Paulo foram utilizados para treinamento e validação. Técnicas de processamento de linguagem natural (PLN) aliadas a classificadores bayesianos foram exploradas na busca de qualidade da recuperação da informação, avaliada por meio da medida-F2. Valores acima de 74% para o grupo topográfico e de 61% para o grupo morfológico são relatados, com pequena contribuição das técnicas de PLN e suavização. Os resultados corroboram trabalhos similares e demonstram a necessidade de retreinamento das ferramentas de PLN no domínio médico.Clinical reports are usually written in natural language due to its descriptive power and ease of communication among specialists. Processing data for knowledge discovery and statistical analysis requires information retrieval techniques, already established for newswire texts, but still rare in the medical subdomain. The present work aims at developing an automated classifier of pathology reports, which should be able to infer the topography and the morphology classes of a cancer using codes of the International Classification of Diseases for Oncology (ICD-O). Data provided by the A.C. Camargo Cancer Center located in Sao Paulo was used for training and validation. Techniques of natural language processing (NLP) and Bayes classifiers were used in search for information retrieval quality, evaluated by F2-score. Measures upper than 74% in the topographic group and 61% in the morphologic group are reported, with small contribution from NLP or smoothing techniques. The results agree with similar studies and show that a retraining of NLP tools in the medical domain is necessary

An Ontology for TNM Clinical Stage Inference

Abstract. TNM is a classification system for assessment of progression stage of malignant tumors. The physician, upon patient examination, classifies a tumor using three variables: T, N and M. Definitions of values for T, N and M depend on the tumor topography (or body part), specified as ICD-O codes. These values are then used to infer the Clinical Stage (CS) and reflect the disease progression, which can be 0 (no malignant tumor), IS (in situ), I, II, III, or IV. The rules for inference are different for each topography and may depend on other factors such as age. With the objective of evaluating missing CS information on A. C. Camargo Cancer Center databases, we developed an open ontology to represent TNM concepts and rules for CS inference. It was designed to be easily expansible and fast to compute

Southern Ocean upwelling, Earth’s obliquity, and late Pleistocene glacial-interglacial atmospheric CO2 change

info:eu-repo/semantics/nonPublishe