Chemical-protein relation extraction with ensembles of carefully tuned pretrained language models

The identification of chemical-protein interactions described in the literature is an important task with applications in drug design, precision medicine and biotechnology. Manual extraction of such relationships from the biomedical literature is costly and often prohibitively time-consuming. The BioCreative VII DrugProt shared task provides a benchmark for methods for the automated extraction of chemical-protein relations from scientific text. Here we describe our contribution to the shared task and report on the achieved results. We define the task as a relation classification problem, which we approach with pretrained transformer language models. Upon this basic architecture, we experiment with utilizing textual and embedded side information from knowledge bases as well as additional training data to improve extraction performance. We perform a comprehensive evaluation of the proposed model and the individual extensions including an extensive hyperparameter search leading to 2647 different runs. We find that ensembling and choosing the right pretrained language model are crucial for optimal performance, whereas adding additional data and embedded side information did not improve results. Our best model is based on an ensemble of 10 pretrained transformers and additional textual descriptions of chemicals taken from the Comparative Toxicogenomics Database. The model reaches an F1 score of 79.73% on the hidden DrugProt test set and achieves the first rank out of 107 submitted runs in the official evaluation. Database URL: https://github.com/leonweber/drugprot

Oscillatory Shear Flow-Induced Alignment of Lamellar Melts of Hydrogen-Bonded Comb Copolymer Supramolecules

In this work we present the orientational behavior of comb copolymer-like supramolecules P4VP(PDP)1.0, obtained by hydrogen bonding between poly(4-vinylpyridine) and pentadecylphenol, during large-amplitude oscillatory shear flow experiments over a broad range of frequencies (0.001-10 Hz). The alignment diagram, presenting the macroscopic alignment in T/TODT vs ω/ωc, contains three regions of parallel alignment separated by a region of perpendicular alignment. For our material, the order-disorder temperature TODT = 67 °C and ωc, the frequency above which the distortion of the chain conformation dominates the materials’ viscoelasticity, is around 0.1 Hz at 61 °C. For the first time flipping from a pure transverse alignment via biaxial transverse/perpendicular alignment to a perpendicular alignment as a function of the strain amplitude was found.

Press accept to update now: Individual differences in susceptibility to malevolent interruptions

© 2017 The Authors Increasingly, connected communication technologies have resulted in people being exposed to fraudulent communications by scammers and hackers attempting to gain access to computer systems for malicious purposes. Common influence techniques, such as mimicking authority figures or instilling a sense of urgency, are used to persuade people to respond to malevolent messages by, for example, accepting urgent updates. An ‘accept’ response to a malevolent influence message can result in severe negative consequences for the user and for others, including the organisations they work for. This paper undertakes exploratory research to examine individual differences in susceptibility to fraudulent computer messages when they masquerade as interruptions during a demanding memory recall primary task compared to when they are presented in a post-task phase. A mixed-methods approach was adopted to examine when and why people choose to accept or decline three types of interrupting computer update message (genuine, mimicked, and low authority) and the relative impact of such interruptions on performance of a serial recall memory primary task. Results suggest that fraudulent communications are more likely to be accepted by users when they interrupt a demanding memory-based primary task, that this relationship is impacted by the content of the fraudulent message, and that influence techniques used in fraudulent communications can over-ride authenticity cues when individuals decide to accept an update message. Implications for theories, such as the recently proposed Suspicion, Cognition and Automaticity Model and the Integrated Information Processing Model of Phishing Susceptibility, are discussed

Taking two to tango:fMRI analysis of improvised joint action with physical contact

<div><p>Many forms of joint action involve physical coupling between the participants, such as when moving a sofa together or dancing a tango. We report the results of a novel two-person functional MRI study in which trained couple dancers engaged in bimanual contact with an experimenter standing next to the bore of the magnet, and in which the two alternated between being the leader and the follower of joint improvised movements. Leading showed a general pattern of self-orientation, being associated with brain areas involved in motor planning, navigation, sequencing, action monitoring, and error correction. In contrast, following showed a far more sensory, externally-oriented pattern, revealing areas involved in somatosensation, proprioception, motion tracking, social cognition, and outcome monitoring. We also had participants perform a “mutual” condition in which the movement patterns were pre-learned and the roles were symmetric, thereby minimizing any tendency toward either leading or following. The mutual condition showed greater activity in brain areas involved in mentalizing and social reward than did leading or following. Finally, the analysis of improvisation revealed the dual importance of motor-planning and working-memory areas. We discuss these results in terms of theories of both joint action and improvisation.</p></div

Coordination Cost and Super-Efficiency in Teamwork: The Role of Communication, Psychological States, Cardiovascular Responses, and Brain Rhythms

To advance knowledge on the psychophysiological markers of “coordination cost” in team settings, we explored differences in meta-communication patterns (i.e., silence, speaking, listening, and overlap), perceived psychological states (i.e., core affect, attention, efficacy beliefs), heart rate variability (i.e., RMSSD), and brain rhythms (i.e., alpha, beta and theta absolute power) across three studies involving 48 male dyads (Mage = 21.30; SD = 2.03). Skilled participants cooperatively played three consecutive FIFA-17 (Xbox) games in a dyad against the computer, or competed against the computer in a solo condition and a dyad condition. We observed that playing in a team, in contrast to playing alone, was associated with higher alpha peak and global efficiency in the brain and, at the same time, led to an increase in focused attention as evidenced by participants’ higher theta activity in the frontal lobe. Moreover, we observed that overtime participants’ brain dynamics moved towards a state of “neural-efficiency” or “flow”, characterized by increased theta and beta activity in the frontal lobe, and high alpha activity across the whole brain. Our findings advance the literature by demonstrating that (1) the notion of coordination cost can be captured at the neural level in the initial stages of team development; (2) by decreasing the costs of switching between tasks, teamwork increases both individuals’ attentional focus and global neural efficiency; and (3) communication dynamics become more proficient and individuals’ brain patterns change towards neural efficiency over time, likely due to team learning and decreases in intra-team conflict

Ethical issues in autologous stem cell transplantation (ASCT) in advanced breast cancer: A systematic literature review

BACKGROUND: An effectiveness assessment on ASCT in locally advanced and metastatic breast cancer identified serious ethical issues associated with this intervention. Our objective was to systematically review these aspects by means of a literature analysis. METHODS: We chose the reflexive Socratic approach as the review method using Hofmann's question list, conducted a comprehensive literature search in biomedical, psychological and ethics bibliographic databases and screened the resulting hits in a 2-step selection process. Relevant arguments were assembled from the included articles, and were assessed and assigned to the question list. Hofmann's questions were addressed by synthesizing these arguments. RESULTS: Of the identified 879 documents 102 included arguments related to one or more questions from Hofmann's question list. The most important ethical issues were the implementation of ASCT in clinical practice on the basis of phase-II trials in the 1990s and the publication of falsified data in the first randomized controlled trials (Bezwoda fraud), which caused significant negative effects on recruiting patients for further clinical trials and the doctor-patient relationship. Recent meta-analyses report a marginal effect in prolonging disease-free survival, accompanied by severe harms, including death. ASCT in breast cancer remains a stigmatized technology. Reported health-related-quality-of-life data are often at high risk of bias in favor of the survivors. Furthermore little attention has been paid to those patients who were dying. CONCLUSIONS: The questions were addressed in different degrees of completeness. All arguments were assignable to the questions. The central ethical dimensions of ASCT could be discussed by reviewing the published literature

Search for Eccentric Black Hole Coalescences during the Third Observing Run of LIGO and Virgo

Despite the growing number of confident binary black hole coalescences observed through gravitational waves so far, the astrophysical origin of these binaries remains uncertain. Orbital eccentricity is one of the clearest tracers of binary formation channels. Identifying binary eccentricity, however, remains challenging due to the limited availability of gravitational waveforms that include effects of eccentricity. Here, we present observational results for a waveform-independent search sensitive to eccentric black hole coalescences, covering the third observing run (O3) of the LIGO and Virgo detectors. We identified no new high-significance candidates beyond those that were already identified with searches focusing on quasi-circular binaries. We determine the sensitivity of our search to high-mass (total mass $M>70$ $M_\odot$) binaries covering eccentricities up to 0.3 at 15 Hz orbital frequency, and use this to compare model predictions to search results. Assuming all detections are indeed quasi-circular, for our fiducial population model, we place an upper limit for the merger rate density of high-mass binaries with eccentricities $0 < e \leq 0.3$ at $0.33$ Gpc$^{-3}$ yr$^{-1}$ at 90\% confidence level.Comment: 24 pages, 5 figure