Enhancing biomedical word embeddings by retrofitting to verb clusters

Verbs play a fundamental role in many biomedical tasks and applications such as relation and event extraction. We hypothesize that performance on many downstream tasks can be improved by aligning the input pretrained embeddings according to semantic verb classes. In this work, we show that by using semantic clusters for verbs, a large lexicon of verb classes derived from biomedical literature, we are able to improve the performance of common pretrained embeddings in downstream tasks by retrofitting them to verb classes. We present a simple and computationally efficient approach using a widely available “off-theshelf” retrofitting algorithm to align pretrained embeddings according to semantic verb clusters. We achieve state-of-the-art results on text classification and relation extraction tasks

Abundance analysis, spectral variability, and search for the presence of a magnetic field in the typical PGa star HD19400

The aim of this study is to carry out an abundance determination, to search for spectral variability and for the presence of a weak magnetic field in the typical PGa star HD19400. High-resolution, high signal-to-noise HARPS spectropolarimetric observations of HD19400 were obtained at three different epochs in 2011 and 2013. For the first time, we present abundances of various elements determined using an ATLAS12 model, including the abundances of a number of elements not analysed by previous studies, such as Ne I, Ga II, and Xe II. Several lines of As II are also present in the spectra of HD19400. To study the variability, we compared the behaviour of the line profiles of various elements. We report on the first detection of anomalous shapes of line profiles belonging to Mn and Hg, and the variability of the line profiles belonging to the elements Hg, P, Mn, Fe, and Ga. We suggest that the variability of the line profiles of these elements is caused by their non-uniform surface distribution, similar to the presence of chemical spots detected in HgMn stars. The search for the presence of a magnetic field was carried out using the moment technique and the SVD method. Our measurements of the magnetic field with the moment technique using 22 Mn II lines indicate the potential existence of a weak variable longitudinal magnetic field on the first epoch. The SVD method applied to the Mn II lines indicates =-76+-25G on the first epoch, and at the same epoch the SVD analysis of the observations using the Fe II lines shows =-91+-35G. The calculated false alarm probability values, 0.008 and 0.003, respectively, are above the value 10^{-3}, indicating no detection.Comment: 13+6 pages, 14 figures, 6+1 tables, including the online-only material, accepted for publication in MNRA

Magnetic field geometry and chemical abundance distribution of the He-strong star CPD -57 3509

The magnetic field of CPD -57 3509 was recently detected in the framework of the BOB (B fields in OB stars) collaboration. We acquired low-resolution spectropolarimetric observations of CPD -57 3509 with FORS2 and high-resolution UVES observations randomly distributed over a few months to search for periodicity, to study the magnetic field geometry, and to determine the surface distribution of silicon and helium. We also obtained supplementary photometric observations at a timeline similar to the spectroscopic and spectropolarimetric observations. A period of 6.36d was detected in the measurements of the mean longitudinal magnetic field. A sinusoidal fit to our measurements allowed us to constrain the magnetic field geometry and estimate the dipole strength in the range of 3.9-4.5kG. Our application of the Doppler imaging technique revealed the presence of He I spots located around the magnetic poles, with a strong concentration at the positive pole and a weaker one around the negative pole. In contrast, high concentration Si III spots are located close to the magnetic equator. Further, our analysis of the spectral variability of CPD -57 3509 on short time scales indicates distinct changes in shape and position of line profiles possibly caused by the presence of beta Cep-like pulsations. A small periodic variability in line with the changes of the magnetic field strength is clearly seen in the photometric data.Comment: 11 pages, 5 tables, 7 figures, accepted for publication in MNRA

Initializing neural networks for hierarchical multi-label text classification

Many tasks in the biomedical domain require the assignment of one or more predefined labels to input text, where the labels are a part of a hierarchical structure (such as a taxonomy). The conventional approach is to use a one-vs.-rest (OVR) classification setup, where a binary classifier is trained for each label in the taxonomy or ontology where all instances not belonging to the class are considered negative examples. The main drawbacks to this approach are that dependencies between classes are not leveraged in the training and classification process, and the additional computational cost of training parallel classifiers. In this paper, we apply a new method for hierarchical multi-label text classification that initializes a neural network model final hidden layer such that it leverages label co-occurrence relations such as hypernymy. This approach elegantly lends itself to hierarchical classifi- cation. We evaluated this approach using two hierarchical multi-label text classification tasks in the biomedical domain using both sentence- and document-level classi- fication. Our evaluation shows promising results for this approach

Cancer Hallmark Text Classification Using Convolutional Neural Networks

Methods based on deep learning approaches have recently achieved state-of-the-art performance in a range of machine learning tasks and are increasingly applied to natural language processing (NLP). Despite strong results in various established NLP tasks involving general domain texts, here is only limited work applying these models to biomedical NLP. In this paper, we consider a Convolutional Neural Network (CNN) approach to biomedical text classification. Evaluation using a recently introduced cancer domain dataset involving the categorization of documents according to the well-established hallmarks of cancer shows that a basic CNN model can achieve a level of performance competitive with a Support Vector Machine (SVM) trained using complex manually engineered features optimized to the task. We further show that simple modifications to the CNN hyperparameters, initialization, and training process allow the model to notably outperform the SVM, establishing a new state of the art result at this task. We make all of the resources and tools introduced in this study available under open licenses from https://cambridgeltl.github.io/cancer-hallmark-cnn/ .The first author is funded by the Commonwealth Scholarship and the Cambridge Trust. This work is supported by Medical Research Council grant MR/M013049/1 and the Google Faculty Award

Lake surface temperature [in “State of the Climate in 2017”]

Observed lake surface water temperature anomalies in 2017 are placed in the context of the recent warming observed in global surface air temperature by collating long-term in situ lake surface temperature observations from some of the world’s best-studied lakes and a satellite-derived global lake surface water temperature dataset. The period 1996–2015, 20 years for which satellite-derived lake temperatures are available, is used as the base period for all lake temperature anomaly calculations

Administration of aromatase inhibitor MPV-2213ad to blue fox vixens (Vulpes lagopus) as a model for contraception in female dogs

The interest in non-surgical approaches to contraception and fertility control in female dogs has increased in recent years. In this study the effect of an aromatase inhibitor (finrozole) was evaluated in fur production animals, farmed blue fox vixens, as a model for contraception in bitches. A total of 80 vixens were divided into 4 groups, receiving orally placebo (A) or finrozole 0.5 mg/kg (B), 3.5 mg/kg (C) or 24.5 mg/kg (D) for 21 consecutive days beginning in the pre-ovulatory period of heat. Monitoring of the vixens included clinical signs of heat, measurement of vaginal electrical resistance (VER) as well as oestradiol and progesterone concentrations in plasma. The approximate relation of the start of treatment to ovulation varied from 11 days before to one day after ovulation provided that the LH peak occurred 0.5 -2 days before the VER peak and ovulation was then estimated to occur 2 days after the LH peak. Seventy vixens were artificially inseminated within 8 h after a 50 Omega decline in vaginal electrical resistance was detected. Ten vixens were not inseminated. Pregnancy was confirmed by transabdominal ultrasound examination and birth of cubs was recorded. The pregnancy rates in the groups were 89.5% (A), 81.3% (B), 55.6% (C) and 52.9% (D). The average number of live born pups in the four groups was 9.4 (A), 7.0 (B), 5.8 (C), and 3.8 (D), respectively. No deleterious effects (for instance malformations) of finrozole on pups could be verified. The administration of finrozole did not have a significant effect on oestradiol parameters and VER values in vixens. Progesterone values were significantly higher in treatment groups compared with the placebo group. The results indicate that pregnancy could be avoided by finrozole provided that doses of >= 3.5 mg/kg were used and the treatment was initiated at least four days before the day of artificial insemination. This corresponds with two to six days before ovulation provided that the LH peak occurred 0.5-2 days before the VER peak and that ovulation then occurred in average 2 days after the LH peak. (C) 2020 The Authors. Published by Elsevier Inc.Peer reviewe

Statistical Properties of Galactic Starlight Polarization

We present a statistical analysis of Galactic interstellar polarization from the largest compilation available of starlight data. The data comprises ~ 9300 stars of which we have selected ~ 5500 for our analysis. We find a nearly linear growth of mean polarization degree with extinction. The amplitude of this correlation shows that interstellar grains are not fully aligned with the Galactic magnetic field, which can be interpreted as the effect of a large random component of the field. In agreement with earlier studies of more limited scope, we estimate the ratio of the uniform to the random plane-of-the-sky components of the magnetic field to be B_u/B_r = 0.8. Moreover, a clear correlation exists between polarization degree and polarization angle what provides evidence that the magnetic field geometry follows Galactic structures on large-scales. The angular power spectrum C_l of the starlight polarization degree for Galactic plane data (|b| < 10 deg) is consistent with a power-law, C_l ~ l^{-1.5} (where l ~ 180 deg/\theta is the multipole order), for all angular scales \theta > 10 arcmin. An investigation of sparse and inhomogeneous sampling of the data shows that the starlight data analyzed traces an underlying polarized continuum that has the same power spectrum slope, C_l ~ l^{-1.5}. Our findings suggest that starlight data can be safely used for the modeling of Galactic polarized continuum emission at other wavelengths.Comment: 31 pages, 11 figures. Minor corrections and some clarifications included. Matches version accepted for publication by the Astrophysical Journa

Comparing apples and oranges: assessment of the relative video quality in the presence of different types of distortions

<p>Abstract</p> <p>Video quality assessment is essential for the performance analysis of visual communication applications. Objective metrics can be used for estimating the relative quality differences, but they typically give reliable results only if the compared videos contain similar types of quality distortion. However, video compression typically produces different kinds of visual artifacts than transmission errors. In this article, we focus on a novel subjective quality assessment method that is suitable for comparing different types of quality distortions. The proposed method has been used to evaluate how well different objective quality metrics estimate the relative subjective quality levels for content with different types of quality distortions. Our conclusion is that none of the studied objective metrics works reliably for assessing the co-impact of compression artifacts and transmission errors on the subjective quality. Nevertheless, we have observed that the objective metrics' tendency to either over- or underestimate the perceived impact of transmission errors has a high correlation with the spatial and temporal activity levels of the content. Therefore, our results can be useful for improving the performance of objective metrics in the presence of both source and channel distortions.</p

Promoting Parents' Use of Non-Pharmacological Methods and Assessment of Children's Postoperative Pain at Home

Background: Parents have reported challenges in assessing their child's postoperative pain at home.Aims: The purpose of this study was to evaluate the usefulness of the parental use of the Parents' Postoperative Pain Measure -tool (PPPM) on 1-3 -year-old children's non-pharmacological pain alleviation at home.Methodology: This was a non-randomized, prospective study with two parallel groups, where the parents in the intervention group were provided with PPPM in addition to a pain diary consisting of a verbal pain scale. The data were collected from 50 parents whose children had undergone day surgery in three Finnish university hospitals between January 2006 and June 2007. Parents completed questionnaires consisting of background information, verbal pain rating scale and a sub-scale measuring parents' use of non-pharmacological methods in children's postoperative pain alleviation.Results: Most children had mild postoperative pain after discharge, but in some children pain was moderate or severe. Non-pharmacological interventions were used commonly for pain alleviation in both groups, including holding the child in lap, comforting the child and spending time with the child more than usual during the recovery period after discharge. However, the use of non-pharmacological pain alleviation methods was 15% more common in the intervention group than in the control group. Parents of the intervention group had carried the child (p=0.04) and used distraction (p=0.05) more commonly than parents in control group. No group differences were found in parental assessments of the helpfulness of non-pharmacological pain alleviation methods.Conclusions: Children's pain remains under-treated and their pain alleviation can be promoted by providing the parents pain assessment tools, such as PPPM, to be used at home. The results can be utilized to further improve children's pain alleviation. More parental education is needed to promote their skills to alleviate the child's pain. Further research of the usefulness of the PPPM using larger samples is needed