Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Spin and charge effects in Andreev Bound States

We probe experimentally the properties of Andreev states in superconducting weak links based on Indium Arsenide (InAs) nanowires. Andreev states are localized fermionic states that appear at the junction (or weak link) between two superconducting electrodes. They are at the core of the microscopic description of the Josephson effect. InAs nanowires implement finite-length weak links characterized by spin-orbit coupling and electrostatically-tunable conduction properties.By coupling the weak link to a high quality factor microwave resonator, following the circuit quantum electrodynamics (cQED) approach, the Andreev states can be efficiently isolated from external noise, and the resonator frequency readout gives access to their occupation. We model this coupling to achieve optimal sensitivity and to understand in detail the response of the resonator coupled to the weak link.We have performed the microwave spectroscopy of Andreev states, and measured their dependence on the superconducting phase difference. The spectra reveal two effects. The first one is the lifting of the spin degeneracy of the states due to the spin-orbit coupling. This results in spectroscopic lines characterizing the change of the spin state of a single quasiparticle in the weak link. The second one is the influence of Coulomb interactions between quasiparticles, reminiscent of the splitting in singlet and triplet states of two interacting spin-1/2 electrons. Theoretical modeling of finite-length weak links allows to account for these effects.We also characterize the Andreev states by time-resolved measurements. Quantum bits (qubits) are obtained either using the ground state and a state where a pair of quasiparticles is excited; or two states with a quasiparticle in different Andreev states. We have measured the lifetimes and coherence times of these two types of "Andreev qubits".Nous présentons les résultats d’expériences sondant les propriétés des états d’Andreev dans des liens faibles supraconducteurs à base de nanofils d’Arséniure d’Indium (InAs). Les états d’Andreev sont des états fermioniques localisés qui apparaissent à la jonction (ou lien faible) entre deux électrodes supraconductrices. Ils sont au coeur de la description microscopique de l'effet Josephson. Les nanofils d’InAs permettent d’obtenir des liens faibles de longueur finie, caractérisés par un couplage spin-orbite et des propriétés de conduction ajustables électrostatiquement.Par la technique d'électrodynamique quantique en circuit (cQED), qui consiste à coupler le lien faible à un résonateur microonde de fort facteur de qualité, les états d’Andreev peuvent être isolés efficacement du bruit extérieur, et la lecture de la fréquence du résonateur donne accès à leur occupation. Nous modélisons ce couplage pour atteindre une sensibilité optimale et comprendre en détail la réponse du résonateur couplé au lien faible.Nous avons mesuré les spectres des états d’Andreev, et leur dépendance en différence de phase supraconductrice. Ces spectres mettent en évidence deux effets. Le premier est la levée de la dégénérescence de spin des états du fait du couplage spin-orbite. Cela se traduit par des lignes spectroscopiques caractérisant le changement de l'état de spin d'une quasiparticule unique dans le lien faible. Le seconde est l’influence des interactions coulombiennes entre quasiparticules, réminiscentes de la séparation entre états singulet et triplet de deux spins 1/2 en interaction. La modélisation théorique des liens faibles de longueur finie permet de rendre compte de ces effets.Nous caractérisons également les états d’Andreev par des mesures résolues en temps. Des bits quantiques (qubits) sont obtenus soit en utilisant l’état fondamental et un état où une paire de quasiparticules est excitée ; soit deux états avec une quasiparticule dans des états d’Andreev différents. Nous avons mesuré les temps de vie et temps de cohérence de ces deux types de « qubits d’Andreev »

Effets de spin et de charge dans les états liés d'Andreev

Nous présentons les résultats d’expériences sondant les propriétés des états d’Andreev dans des liens faibles supraconducteurs à base de nanofils d’Arséniure d’Indium (InAs). Les états d’Andreev sont des états fermioniques localisés qui apparaissent à la jonction (ou lien faible) entre deux électrodes supraconductrices. Ils sont au coeur de la description microscopique de l'effet Josephson. Les nanofils d’InAs permettent d’obtenir des liens faibles de longueur finie, caractérisés par un couplage spin-orbite et des propriétés de conduction ajustables électrostatiquement.Par la technique d'électrodynamique quantique en circuit (cQED), qui consiste à coupler le lien faible à un résonateur microonde de fort facteur de qualité, les états d’Andreev peuvent être isolés efficacement du bruit extérieur, et la lecture de la fréquence du résonateur donne accès à leur occupation. Nous modélisons ce couplage pour atteindre une sensibilité optimale et comprendre en détail la réponse du résonateur couplé au lien faible.Nous avons mesuré les spectres des états d’Andreev, et leur dépendance en différence de phase supraconductrice. Ces spectres mettent en évidence deux effets. Le premier est la levée de la dégénérescence de spin des états du fait du couplage spin-orbite. Cela se traduit par des lignes spectroscopiques caractérisant le changement de l'état de spin d'une quasiparticule unique dans le lien faible. Le seconde est l’influence des interactions coulombiennes entre quasiparticules, réminiscentes de la séparation entre états singulet et triplet de deux spins 1/2 en interaction. La modélisation théorique des liens faibles de longueur finie permet de rendre compte de ces effets.Nous caractérisons également les états d’Andreev par des mesures résolues en temps. Des bits quantiques (qubits) sont obtenus soit en utilisant l’état fondamental et un état où une paire de quasiparticules est excitée ; soit deux états avec une quasiparticule dans des états d’Andreev différents. Nous avons mesuré les temps de vie et temps de cohérence de ces deux types de « qubits d’Andreev ».We probe experimentally the properties of Andreev states in superconducting weak links based on Indium Arsenide (InAs) nanowires. Andreev states are localized fermionic states that appear at the junction (or weak link) between two superconducting electrodes. They are at the core of the microscopic description of the Josephson effect. InAs nanowires implement finite-length weak links characterized by spin-orbit coupling and electrostatically-tunable conduction properties.By coupling the weak link to a high quality factor microwave resonator, following the circuit quantum electrodynamics (cQED) approach, the Andreev states can be efficiently isolated from external noise, and the resonator frequency readout gives access to their occupation. We model this coupling to achieve optimal sensitivity and to understand in detail the response of the resonator coupled to the weak link.We have performed the microwave spectroscopy of Andreev states, and measured their dependence on the superconducting phase difference. The spectra reveal two effects. The first one is the lifting of the spin degeneracy of the states due to the spin-orbit coupling. This results in spectroscopic lines characterizing the change of the spin state of a single quasiparticle in the weak link. The second one is the influence of Coulomb interactions between quasiparticles, reminiscent of the splitting in singlet and triplet states of two interacting spin-1/2 electrons. Theoretical modeling of finite-length weak links allows to account for these effects.We also characterize the Andreev states by time-resolved measurements. Quantum bits (qubits) are obtained either using the ground state and a state where a pair of quasiparticles is excited; or two states with a quasiparticle in different Andreev states. We have measured the lifetimes and coherence times of these two types of "Andreev qubits"

From Adiabatic to Dispersive Readout of Quantum Circuits

International audienceSpectral properties of a quantum circuit are efficiently read out by monitoring the resonance frequency shift it induces in a microwave resonator coupled to it. When the two systems are strongly detuned, theory attributes the shift to an effective resonator capacitance or inductance that depends on the quantum circuit state. At small detuning, the shift arises from the exchange of virtual photons, as described by the Jaynes-Cummings model. Here we present a theory bridging these two limits and illustrate, with several examples, its necessity for a general description of quantum circuits readout. Circuit Quantum Electrodynamics (cQED) is at the heart of most advanced superconducting quantum technologies. Different types of superconducting qubits can be strongly coupled to microwave resonators thus achieving regimes and phenomenena which cannot be reached within the realm of quantum optics [1]. More recently, strong coupling between microwave resonators and a variety of other quantum systems not necessarily involving superconductors has been achieved [2], extending further the realm of cQED. In all these applications the measurement of the qubit or the hybrid device state is achieved by monitoring the resonator properties. Theoretically , two regimes have been approached using disconnected descriptions [3]: the dispersive regime, where the qubit-resonator detuning is larger than the coupling strength yet small enough to allow the exchange of virtual photons, and the adiabatic regime, where the de-tuning is sufficiently large for virtual processes to be strongly suppressed. The dispersive regime, which describes level repulsion between those of the quantum circuit and of the resonator, is typically dealt with using a Jaynes-Cummings Hamiltonian within different levels of approximation [3-10]. In contrast, the adiabatic regime accounts for the renormalization of the resonator capaci-tance/inductance by the effective capacitance of the circuit , including its "quantum capacitance" [11, 12], or its effective inductance [13, 14], which modifies the resonator frequency [15, 16]. However, there is no actual border between these two regimes which could justify a separate treatment, as illustrated by recent experiments on hybrid cQED setups [17] that reveal features of both regimes for the same device. This situation claims for a unified description of quantum circuits readout, going beyond the standard Jaynes-Cummings model, which could be applied to different types of devices over a large range of parameters. * Corresponding author : [email protected] In the present Letter we derive a general expression for the resonator frequency shift when coupled to a generic quantum circuit. This expression naturally interpolates between the adiabatic and the dispersive regimes, thus allowing to clarify their origin from the same coupling Hamiltonian. In addition our formalism is not restricted to the usual two-level approximations but any multilevel situation can be described on the same footing. We illustrate the importance of the different terms in our expression by analyzing well-known models like a short single channel superconducting weak link hosting Andreev states, the RF-SQUID and the Cooper pair box. Resonator-quantum circuit coupling.-The system we consider comprises a resonant circuit and a quantum circuit coupled through phase or charge fluctuations as depicted in Figs. 1(a), 2(a) and in the inset of Fig. 3. The resonant circuit is represented as a lumped-element LC resonator with bare resonance frequency f r = ω r /2π, with ω r = 1/ √ L r C r. Introducing the photon annihilation (creation) operators a (a †), it can be described by the Hamiltonian H r = ω r a † a. On the other hand, the quantum circuit Hamiltonian,Ĥ qc (x), depends on a dimensionless control parameter x, corresponding to an excess charge on a capacitor or a flux through a loop. We denote by |Φ i (x) the eigenstates of the uncoupled quantum circuit,Ĥ qc (x)|Φ i (x) = E i (x)|Φ i (x). Flux (charge) fluctuations in the resonator lead to x → x 0 +x r , wherex r = λ(s a + s * a †) with a coupling constant λ, depending on a coupling scheme [19], and s = 1 (−i). We assume λ 1 in accordance with experiments. The resonator-quantum circuit coupling HamiltonianĤ c is obtained by expandingĤ qc (x 0 +x r) up to second order inx rĤ c (x 0) =x rĤ qc (x 0) +x 2 r 2Ĥ qc (x 0), (1) where the prime stands for the derivative with respect to x. The Hamiltonian describing resonator, quantu

Circuit-QED with phase-biased Josephson weak links

International audienceBy coupling a superconducting weak link to a microwave resonator, recent experiments probed the spectrum and achieved the quantum manipulation of Andreev states in various systems. However, the quantitative understanding of the response of the resonator to changes in the occupancy of the Andreev levels, which are of fermionic nature, is missing. Here, using Bogoliubov-de Gennes formalism to describe the weak link and a general formulation of the coupling to the resonator, we calculate the shift of the resonator frequency as a function of the levels occupancy and describe how transitions are induced by phase or electric field microwave drives. We apply this formalism to analyze recent experimental results obtained using circuit-QED techniques on superconducting atomic contacts and semiconducting nanowire Josephson junctions

Understanding the Origins of Higher Capacities at Faster Rates in Lithium-Excess Li_<i>x</i>Ni_{2–4<i>x</i>/3}Sb_<i>x</i>/3O₂

The lithium-excess Li_<i>x</i>Ni_{2–4<i>x</i>/3}Sb_<i>x</i>/3O₂ (LNSO) materials were previously shown to demonstrate higher capacities and improved cyclability with increasing lithium content. While the performance trend is promising, observed capacities are much lower than theoretical capacities, pointing to a need for further understanding of active redox processes in these materials. In this work, we study the electrochemical behavior of the LNSO materials as a function of lithium content and at slow and fast rates. Surprisingly, Li_1.15Ni_0.47Sb_0.38O₂ (LNSO-15) exhibits higher discharge capacities at faster rates and traverses distinct voltage curves at slow and fast rates. To understand these two peculiarities, we characterize the redox activity of nickel, antimony, and oxygen at different rates. While experiments confirm some nickel redox activity and oxygen loss, these two mechanisms cannot account for all observed capacity. We propose that the balance of the observed capacity may be due to reversible oxygen redox and that the rate-dependent voltage curve features may derive from irreversible nickel migration occurring on slow charge. As future high energy density cathodes are likely to contain both lithium excess and high nickel content, both of these findings have important implications for the development of novel high capacity cathode materials