141 research outputs found
Evidence Inference 2.0: More Data, Better Models
How do we most effectively treat a disease or condition? Ideally, we could
consult a database of evidence gleaned from clinical trials to answer such
questions. Unfortunately, no such database exists; clinical trial results are
instead disseminated primarily via lengthy natural language articles. Perusing
all such articles would be prohibitively time-consuming for healthcare
practitioners; they instead tend to depend on manually compiled systematic
reviews of medical literature to inform care.
NLP may speed this process up, and eventually facilitate immediate consult of
published evidence. The Evidence Inference dataset was recently released to
facilitate research toward this end. This task entails inferring the
comparative performance of two treatments, with respect to a given outcome,
from a particular article (describing a clinical trial) and identifying
supporting evidence. For instance: Does this article report that chemotherapy
performed better than surgery for five-year survival rates of operable cancers?
In this paper, we collect additional annotations to expand the Evidence
Inference dataset by 25\%, provide stronger baseline models, systematically
inspect the errors that these make, and probe dataset quality. We also release
an abstract only (as opposed to full-texts) version of the task for rapid model
prototyping. The updated corpus, documentation, and code for new baselines and
evaluations are available at http://evidence-inference.ebm-nlp.com/.Comment: Accepted as workshop paper into BioNLP Updated results from SciBERT
to Biomed RoBERT
Understanding Clinical Trial Reports: Extracting Medical Entities and Their Relations
The best evidence concerning comparative treatment effectiveness comes from
clinical trials, the results of which are reported in unstructured articles.
Medical experts must manually extract information from articles to inform
decision-making, which is time-consuming and expensive. Here we consider the
end-to-end task of both (a) extracting treatments and outcomes from full-text
articles describing clinical trials (entity identification) and, (b) inferring
the reported results for the former with respect to the latter (relation
extraction). We introduce new data for this task, and evaluate models that have
recently achieved state-of-the-art results on similar tasks in Natural Language
Processing. We then propose a new method motivated by how trial results are
typically presented that outperforms these purely data-driven baselines.
Finally, we run a fielded evaluation of the model with a non-profit seeking to
identify existing drugs that might be re-purposed for cancer, showing the
potential utility of end-to-end evidence extraction systems
Multi-messenger searches via IceCube’s high-energy neutrinos and gravitational-wave detections of LIGO/Virgo
We summarize initial results for high-energy neutrino counterpart searches coinciding with gravitational-wave events in LIGO/Virgo\u27s GWTC-2 catalog using IceCube\u27s neutrino triggers. We did not find any statistically significant high-energy neutrino counterpart and derived upper limits on the time-integrated neutrino emission on Earth as well as the isotropic equivalent energy emitted in high-energy neutrinos for each event
In-situ estimation of ice crystal properties at the South Pole using LED calibration data from the IceCube Neutrino Observatory
The IceCube Neutrino Observatory instruments about 1 km3 of deep, glacial ice at the geographic South Pole using 5160 photomultipliers to detect Cherenkov light emitted by charged relativistic particles. A unexpected light propagation effect observed by the experiment is an anisotropic attenuation, which is aligned with the local flow direction of the ice. Birefringent light propagation has been examined as a possible explanation for this effect. The predictions of a first-principles birefringence model developed for this purpose, in particular curved light trajectories resulting from asymmetric diffusion, provide a qualitatively good match to the main features of the data. This in turn allows us to deduce ice crystal properties. Since the wavelength of the detected light is short compared to the crystal size, these crystal properties do not only include the crystal orientation fabric, but also the average crystal size and shape, as a function of depth. By adding small empirical corrections to this first-principles model, a quantitatively accurate description of the optical properties of the IceCube glacial ice is obtained. In this paper, we present the experimental signature of ice optical anisotropy observed in IceCube LED calibration data, the theory and parametrization of the birefringence effect, the fitting procedures of these parameterizations to experimental data as well as the inferred crystal properties.</p
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