NEREL-BIO: a dataset of biomedical abstracts annotated with nested named entities.

MOTIVATION: This article describes NEREL-BIO-an annotation scheme and corpus of PubMed abstracts in Russian and smaller number of abstracts in English. NEREL-BIO extends the general domain dataset NEREL by introducing domain-specific entity types. NEREL-BIO annotation scheme covers both general and biomedical domains making it suitable for domain transfer experiments. NEREL-BIO provides annotation for nested named entities as an extension of the scheme employed for NEREL. Nested named entities may cross entity boundaries to connect to shorter entities nested within longer entities, making them harder to detect. RESULTS: NEREL-BIO contains annotations for 700+ Russian and 100+ English abstracts. All English PubMed annotations have corresponding Russian counterparts. Thus, NEREL-BIO comprises the following specific features: annotation of nested named entities, it can be used as a benchmark for cross-domain (NEREL → NEREL-BIO) and cross-language (English → Russian) transfer. We experiment with both transformer-based sequence models and machine reading comprehension models and report their results. AVAILABILITY AND IMPLEMENTATION: The dataset and annotation guidelines are freely available at https://github.com/nerel-ds/NEREL-BIO.

Statistics of transmitted power in multichannel dissipative ergodic structures.

We use the random matrix theory (RMT) to study the probability distribution function and moments of the wave power transmitted inside systems with ergodic wave motion. The results describe either open multichannel systems or their closed counterparts with local-in-space internal dissipation. We concentrate on the regime of broken time-reversal invariance and employ two different analytical approaches: the exact supersymmetry method and a simpler technique that uses RMT eigenstatistics for closed nondissipative systems as an input. The results of the supersymmetric method were confirmed by numerical simulation. The simpler method is found to be adequate for closed systems with uniform dissipation, or in the limit of a large number of weak local dampers.

Variance of transmitted power in multichannel dissipative ergodic structures invariant under time reversal.

We use random matrix theory (RMT) to study the first two moments of the wave power transmitted in time-reversal invariant systems having ergodic motion. Dissipation is modeled by a number of loss channels of variable coupling strength. To make a connection with ultrasonic experiments on ergodic elastodynamic billiards, the channels injecting and collecting the waves are assumed to be negligibly coupled to the medium and to contribute essentially no dissipation. Within the RMT model we calculate the quantities of interest exactly, employing the supersymmetry technique. This approach is found to be more accurate than another method based on simplifying naive assumptions for the statistics of the eigenfrequencies and the eigenfunctions. The results of the supersymmetric method are confirmed by Monte Carlo numerical simulation and are used to reveal a possible source of the disagreement between the predictions of the naive theory and ultrasonic measurements.

Photon emission from a driven single-molecule source: a renormalization group approach.

The photon emission from a single molecule driven simultaneously by a laser and a slow electric radio frequency (rf) field is studied. We use a non-Hermitian Hamiltonian approach which accounts for the radiative decay of a two-level system modeling the single-molecule source. We apply the renormalization group method for differential equations to obtain long time solution of the corresponding Schrodinger equation, which allows us to calculate the average waiting time for the first photon emission. Then, we analyze the conditions for suppression and enhancement of photon emission in this dissipative two-level system. In particular we derive a transcendental equation, which yields the nontrivial rf field control parameters, for which enhancement and suppression of photon emission occurs. For finite values of radiative decay rate an abrupt transition to the state when both situations are indistinguishable is found for certain values of the rf field parameters. Our results are shown to be in agreement with the available experiments [Ch. Brunel et al., Phys. Rev. Lett. 81, 2679 (1998)].

Nonexponential dissipation in a lossy elastodynamic billiard: comparison with Porter-Thomas and random matrix predictions.

We study the dissipation of diffuse ultrasonic energy in a reverberant body coupled to a waveguide, an analog for a mesoscopic electron in a quantum dot. A simple model predicts a Porter-Thomas distribution of level widths and corresponding nonexponential dissipation, a behavior largely confirmed by measurements. For the case of fully open channels, however, measurements deviate from this model to a statistically significant degree. A random matrix supersymmetric calculation is found to accurately model the observed behaviors at all coupling strengths.