Knowledge-based biomedical word sense disambiguation: comparison of approaches

<p>Abstract</p> <p>Background</p> <p>Word sense disambiguation (WSD) algorithms attempt to select the proper sense of ambiguous terms in text. Resources like the UMLS provide a reference thesaurus to be used to annotate the biomedical literature. Statistical learning approaches have produced good results, but the size of the UMLS makes the production of training data infeasible to cover all the domain.</p> <p>Methods</p> <p>We present research on existing WSD approaches based on knowledge bases, which complement the studies performed on statistical learning. We compare four approaches which rely on the UMLS Metathesaurus as the source of knowledge. The first approach compares the overlap of the context of the ambiguous word to the candidate senses based on a representation built out of the definitions, synonyms and related terms. The second approach collects training data for each of the candidate senses to perform WSD based on queries built using monosemous synonyms and related terms. These queries are used to retrieve MEDLINE citations. Then, a machine learning approach is trained on this corpus. The third approach is a graph-based method which exploits the structure of the Metathesaurus network of relations to perform unsupervised WSD. This approach ranks nodes in the graph according to their relative structural importance. The last approach uses the semantic types assigned to the concepts in the Metathesaurus to perform WSD. The context of the ambiguous word and semantic types of the candidate concepts are mapped to Journal Descriptors. These mappings are compared to decide among the candidate concepts. Results are provided estimating accuracy of the different methods on the WSD test collection available from the NLM.</p> <p>Conclusions</p> <p>We have found that the last approach achieves better results compared to the other methods. The graph-based approach, using the structure of the Metathesaurus network to estimate the relevance of the Metathesaurus concepts, does not perform well compared to the first two methods. In addition, the combination of methods improves the performance over the individual approaches. On the other hand, the performance is still below statistical learning trained on manually produced data and below the maximum frequency sense baseline. Finally, we propose several directions to improve the existing methods and to improve the Metathesaurus to be more effective in WSD.</p

Fusion Techniques in Biomedical Information Retrieval

For difficult cases clinicians usually use their experience and also the information found in textbooks to determine a diagnosis. Computer tools can help them supply the relevant information now that much medical knowledge is available in digital form. A biomedical search system such as developed in the Khresmoi project (that this chapter partially reuses) has the goal to fulfil information needs of physicians. This chapter concentrates on information needs for medical cases that contain a large variety of data, from free text, structured data to images. Fusion techniques will be compared to combine the various information sources to supply cases similar to an example case given. This can supply physicians with answers to problems similar to the one they are analyzing and can help in diagnosis and treatment planning

Quantum Computing

Quantum mechanics---the theory describing the fundamental workings of nature---is famously counterintuitive: it predicts that a particle can be in two places at the same time, and that two remote particles can be inextricably and instantaneously linked. These predictions have been the topic of intense metaphysical debate ever since the theory's inception early last century. However, supreme predictive power combined with direct experimental observation of some of these unusual phenomena leave little doubt as to its fundamental correctness. In fact, without quantum mechanics we could not explain the workings of a laser, nor indeed how a fridge magnet operates. Over the last several decades quantum information science has emerged to seek answers to the question: can we gain some advantage by storing, transmitting and processing information encoded in systems that exhibit these unique quantum properties? Today it is understood that the answer is yes. Many research groups around the world are working towards one of the most ambitious goals humankind has ever embarked upon: a quantum computer that promises to exponentially improve computational power for particular tasks. A number of physical systems, spanning much of modern physics, are being developed for this task---ranging from single particles of light to superconducting circuits---and it is not yet clear which, if any, will ultimately prove successful. Here we describe the latest developments for each of the leading approaches and explain what the major challenges are for the future.Comment: 26 pages, 7 figures, 291 references. Early draft of Nature 464, 45-53 (4 March 2010). Published version is more up-to-date and has several corrections, but is half the length with far fewer reference

Photonic quantum technologies

The first quantum technology, which harnesses uniquely quantum mechanical effects for its core operation, has arrived in the form of commercially available quantum key distribution systems that achieve enhanced security by encoding information in photons such that information gained by an eavesdropper can be detected. Anticipated future quantum technologies include large-scale secure networks, enhanced measurement and lithography, and quantum information processors, promising exponentially greater computation power for particular tasks. Photonics is destined for a central role in such technologies owing to the need for high-speed transmission and the outstanding low-noise properties of photons. These technologies may use single photons or quantum states of bright laser beams, or both, and will undoubtably apply and drive state-of-the-art developments in photonics

Structure and catalytic regulatory function of ubiquitin specific protease 11 N-terminal and ubiquitin-like domains

The ubiquitin specific protease 11 (USP11) is implicated in DNA repair, viral RNA replication, and TGFβ signaling. We report the first characterization of the USP11 domain architecture and its role in regulating the enzymatic activity. USP11 consists of an N-terminal "domain present in USPs" (DUSP) and "ubiquitin-like" (UBL) domain, together referred to as DU domains, and the catalytic domain harboring a second UBL domain. Crystal structures of the DU domains show a tandem arrangement with a shortened β-hairpin at the two-domain interface and altered surface characteristics compared to the homologues USP4 and USP15. A conserved VEVY motif is a signature feature at the two-domain interface that shapes a potential protein interaction site. Small angle X-ray scattering and gel filtration experiments are consistent with the USP11DU domains and full-length USP11 being monomeric. Unexpectedly, we reveal, through kinetic assays of a series of deletion mutants, that the catalytic activity of USP11 is not regulated through intramolecular autoinhibition or activation by the N-terminal DU or UBL domains. Moreover, ubiquitin chain cleavage assays with all eight linkages reveal a preference for Lys(63)-, Lys(6)-, Lys(33)-, and Lys(11)-linked chains over Lys(27)-, Lys(29)-, and Lys(48)-linked and linear chains consistent with USP11's function in DNA repair pathways that is mediated by the protease domain. Our data support a model whereby USP11 domains outside the catalytic core domain serve as protein interaction or trafficking modules rather than a direct regulatory function of the proteolytic activity. This highlights the diversity of USPs in substrate recognition and regulation of ubiquitin deconjugation

Ultrafast all-optical switching by single photons

An outstanding goal in quantum optics is the realization of fast optical non-linearities at the single-photon level. Such non-linearities would allow for the realization of optical devices with new functionalities such as a single-photon switch/transistor or a controlled-phase gate, which could form the basis of future quantum optical technologies. While non-linear optics effects at the single-emitter level have been demonstrated in different systems, including atoms coupled to Fabry-Perot or toroidal micro-cavities, super-conducting qubits in strip-line resonators or quantum dots (QDs) in nano-cavities, none of these experiments so far has demonstrated single-photon switching on ultrafast timescales. Here, we demonstrate that in a strongly coupled QD-cavity system the presence of a single photon on one of the fundamental polariton transitions can turn on light scattering on a transition from the first to the second Jaynes-Cummings manifold with a switching time of 20 ps. As an additional device application, we use this non-linearity to implement a single-photon pulse-correlator. Our QD-cavity system could form the building-block of future high-bandwidth photonic networks operating in the quantum regime

Quantum nonlinear optics with single photons enabled by strongly interacting atoms

The realization of strong nonlinear interactions between individual light quanta (photons) is a long-standing goal in optical science and engineering, being of both fundamental and technological significance. In conventional optical materials, the nonlinearity at light powers corresponding to single photons is negligibly weak. Here we demonstrate a medium that is nonlinear at the level of individual quanta, exhibiting strong absorption of photon pairs while remaining transparent to single photons. The quantum nonlinearity is obtained by coherently coupling slowly propagating photons to strongly interacting atomic Rydberg states in a cold, dense atomic gas. Our approach paves the way for quantum-by-quantum control of light fields, including single-photon switching, all-optical deterministic quantum logic and the realization of strongly correlated many-body states of light.National Science Foundation (U.S.)MIT-Harvard Center for Ultracold AtomsUnited States. Air Force Office of Scientific Research. Multidisciplinary University Research Initiative (Quantum Memories

All-optical routing and switching for three-dimensional photonic circuitry

The ability to efficiently transmit and rapidly process huge amounts of data has become almost indispensable to our daily lives. It turned out that all-optical networks provide a very promising platform to deal with this task. Within such networks opto-optical switches, where light is directed by light, are a crucial building block for an effective operation. In this article, we present an experimental analysis of the routing and switching behaviour of light in two-dimensional evanescently coupled waveguide arrays of Y- and T-junction geometries directly inscribed into fused silica using ultrashort laser pulses. These systems have the fundamental advantage of supporting three-dimensional network topologies, thereby breaking the limitations on complexity associated with planar structures while maintaining a high dirigibility of the light. Our results show how such arrays can be used to control the flow of optical signals within integrated photonic circuits

The Impact of Hydrogen Bonding on Amide 1H Chemical Shift Anisotropy Studied by Cross-Correlated Relaxation and Liquid Crystal NMR Spectroscopy

Site-specific (1)H chemical shift anisotropy (CSA) tensors have been derived for the well-ordered backbone amide moieties in the B3 domain of protein G (GB3). Experimental input data include residual chemical shift anisotropy (RCSA), measured in six mutants that align differently relative to the static magnetic field when dissolved in a liquid crystalline Pf1 suspension, and cross-correlated relaxation rates between the (1)H(N) CSA tensor and either the (1)H-(15)N, the (1)H-(13)C&#39;, or the (1)H-(13)C(alpha) dipolar interactions. Analyses with the assumption that the (1)H(N) CSA tensor is symmetric with respect to the peptide plane (three-parameter fit) or without this premise (five-parameter fit) yield very similar results, confirming the robustness of the experimental input data, and that, to a good approximation, one of the principal components orients orthogonal to the peptide plane. (1)H(N) CSA tensors are found to deviate strongly from axial symmetry, with the most shielded tensor component roughly parallel to the N-H vector, and the least shielded component orthogonal to the peptide plane. DFT calculations on pairs of N-methyl acetamide and acetamide in H-bonded geometries taken from the GB3 X-ray structure correlate with experimental data and indicate that H-bonding effects dominate variations in the (1)H(N) CSA. Using experimentally derived (1)H(N) CSA tensors, the optimal relaxation interference effect needed for narrowest (1)H(N) TROSY line widths is found at similar to 1200 MHz

Nanophotonic quantum phase switch with a single atom

By analogy to transistors in classical electronic circuits, quantum optical switches are important elements of quantum circuits and quantum networks1, 2, 3. Operated at the fundamental limit where a single quantum of light or matter controls another field or material system4, such a switch may enable applications such as long-distance quantum communication5, distributed quantum information processing2 and metrology6, and the exploration of novel quantum states of matter7. Here, by strongly coupling a photon to a single atom trapped in the near field of a nanoscale photonic crystal cavity, we realize a system in which a single atom switches the phase of a photon and a single photon modifies the atom’s phase. We experimentally demonstrate an atom-induced optical phase shift8 that is nonlinear at the two-photon level9, a photon number router that separates individual photons and photon pairs into different output modes10, and a single-photon switch in which a single ‘gate’ photon controls the propagation of a subsequent probe field11, 12. These techniques pave the way to integrated quantum nanophotonic networks involving multiple atomic nodes connected by guided light.Physic