Filters








37 Hits in 2.1 sec

Groverian Entanglement Measure of Pure Quantum States with Arbitrary Partitions [article]

Yishai Shimoni, Ofer Biham
2007 arXiv   pre-print
The Groverian entanglement measure of pure quantum states of n qubits is generalized to the case in which the qubits are divided into any m < n parties and the entanglement between these parties is evaluated. To demonstrate this measure we apply it to general states of three qubits and to symmetric states with any number of qubits such as the Greenberg-Horne-Zeiliner state and the W state.
arXiv:quant-ph/0702179v1 fatcat:xz2yqnb2vjfadeykcwwhhawhpq

A discriminative approach for finding and characterizing positivity violations using decision trees [article]

Ehud Karavani, Peter Bak, Yishai Shimoni
2019 arXiv   pre-print
The assumption of positivity in causal inference (also known as common support and co-variate overlap) is necessary to obtain valid causal estimates. Therefore, confirming it holds in a given dataset is an important first step of any causal analysis. Most common methods to date are insufficient for discovering non-positivity, as they do not scale for modern high-dimensional covariate spaces, or they cannot pinpoint the subpopulation violating positivity. To overcome these issues, we suggest to
more » ... arness decision trees for detecting violations. By dividing the covariate space into mutually exclusive regions, each with maximized homogeneity of treatment groups, decision trees can be used to automatically detect subspaces violating positivity. By augmenting the method with an additional random forest model, we can quantify the robustness of the violation within each subspace. This solution is scalable and provides an interpretable characterization of the subspaces in which violations occur. We provide a visualization of the stratification rules that define each subpopulation, combined with the severity of positivity violation within it. We also provide an interactive version of the visualization that allows a deeper dive into the properties of each subspace.
arXiv:1907.08127v1 fatcat:ljnip65atfh4nlcspz3mxealla

Towards effect estimation of COVID-19 Non-pharmaceutical Interventions [article]

Vesna Barros, Victor Akinwande, Itay Manes, Osnat Bar-Shira, Celia Cintas, Yishai Shimoni, Michal Rosen-Zvi
2021 Zenodo  
the report: Towards effect estimation of COVID-19 Non-pharmaceutical Interventions Authors: Vesna Barros, Victor Akinwande, Itay Manes, Osnat Bar-Shira, Celia Cintas, Yishai Shimoni, Michal Rosen-Zvi  ... 
doi:10.5281/zenodo.4680686 fatcat:tikgwm6otvgbxdgvf4fzkeatli

Stochastic Analysis of the SOS Response in Escherichia coli

Yishai Shimoni, Shoshy Altuvia, Hanah Margalit, Ofer Biham, Mark Isalan
2009 PLoS ONE  
DNA damage in Escherichia coli evokes a response mechanism called the SOS response. The genetic circuit of this mechanism includes the genes recA and lexA, which regulate each other via a mixed feedback loop involving transcriptional regulation and protein-protein interaction. Under normal conditions, recA is transcriptionally repressed by LexA, which also functions as an auto-repressor. In presence of DNA damage, RecA proteins recognize stalled replication forks and participate in the DNA
more » ... r process. Under these conditions, RecA marks LexA for fast degradation. Generally, such mixed feedback loops are known to exhibit either bi-stability or a single steady state. However, when the dynamics of the SOS system following DNA damage was recently studied in single cells, ordered peaks were observed in the promoter activity of both genes (Friedman et al., 2005, PLoS Biol. 3(7):e238). This surprising phenomenon was masked in previous studies of cell populations. Previous attempts to explain these results harnessed additional genes to the system and deployed complex deterministic mathematical models that were only partially successful in explaining the results. Methodology/Principal Findings: Here we apply stochastic methods, which are better suited for dynamic simulations of single cells. We show that a simple model, involving only the basic components of the circuit, is sufficient to explain the peaks in the promoter activities of recA and lexA. Notably, deterministic simulations of the same model do not produce peaks in the promoter activities. Conclusion/Significance: We conclude that the double negative mixed feedback loop with auto-repression accounts for the experimentally observed peaks in the promoter activities. In addition to explaining the experimental results, this result shows that including additional regulations in a mixed feedback loop may dramatically change the dynamic functionality of this regulatory module. Furthermore, our results suggests that stochastic fluctuations strongly affect the qualitative behavior of important regulatory modules even under biologically relevant conditions, thus emphasizing the importance of stochastic analysis of regulatory circuits.
doi:10.1371/journal.pone.0005363 pmid:19424504 pmcid:PMC2675100 fatcat:6jn6qzevebdjhdwma5m3oylbwu

Benchmarking Framework for Performance-Evaluation of Causal Inference Analysis [article]

Yishai Shimoni, Chen Yanover, Ehud Karavani, Yaara Goldschmnidt
2018 arXiv   pre-print
Causal inference analysis is the estimation of the effects of actions on outcomes. In the context of healthcare data this means estimating the outcome of counter-factual treatments (i.e. including treatments that were not observed) on a patient's outcome. Compared to classic machine learning methods, evaluation and validation of causal inference analysis is more challenging because ground truth data of counter-factual outcome can never be obtained in any real-world scenario. Here, we present a
more » ... omprehensive framework for benchmarking algorithms that estimate causal effect. The framework includes unlabeled data for prediction, labeled data for validation, and code for automatic evaluation of algorithm predictions using both established and novel metrics. The data is based on real-world covariates, and the treatment assignments and outcomes are based on simulations, which provides the basis for validation. In this framework we address two questions: one of scaling, and the other of data-censoring. The framework is available as open source code at https://github.com/IBM-HRL-MLHLS/IBM-Causal-Inference-Benchmarking-Framework
arXiv:1802.05046v2 fatcat:hhcgf5zaoffrdhynbsrvjixqne

Groverian entanglement measure of pure quantum states with arbitrary partitions

Yishai Shimoni, Ofer Biham
2007 Physical Review A. Atomic, Molecular, and Optical Physics  
The Groverian entanglement measure of pure quantum states of n qubits is generalized to the case in which the qubits are divided into any m ≤ n parties and the entanglement between these parties is evaluated. To demonstrate this measure we apply it to general states of three qubits and to symmetric states with any number of qubits such as the Greenberg-Horne-Zeiliner state and the W state.
doi:10.1103/physreva.75.022308 fatcat:i5efnqvzrvenpgerfh7bsapsge

Plato's Cave Algorithm: Inferring Functional Signaling Networks from Early Gene Expression Shadows

Yishai Shimoni, Marc Y. Fink, Soon-gang Choi, Stuart C. Sealfon, Christian von Mering
2010 PLoS Computational Biology  
Improving the ability to reverse engineer biochemical networks is a major goal of systems biology. Lesions in signaling networks lead to alterations in gene expression, which in principle should allow network reconstruction. However, the information about the activity levels of signaling proteins conveyed in overall gene expression is limited by the complexity of gene expression dynamics and of regulatory network topology. Two observations provide the basis for overcoming this limitation: a.
more » ... es induced without de-novo protein synthesis (early genes) show a linear accumulation of product in the first hour after the change in the cell's state; b. The signaling components in the network largely function in the linear range of their stimulus-response curves. Therefore, unlike most genes or most time points, expression profiles of early genes at an early time point provide direct biochemical assays that represent the activity levels of upstream signaling components. Such expression data provide the basis for an efficient algorithm (Plato's Cave algorithm; PLACA) to reverse engineer functional signaling networks. Unlike conventional reverse engineering algorithms that use steady state values, PLACA uses stimulated early gene expression measurements associated with systematic perturbations of signaling components, without measuring the signaling components themselves. Besides the reverse engineered network, PLACA also identifies the genes detecting the functional interaction, thereby facilitating validation of the predicted functional network. Using simulated datasets, the algorithm is shown to be robust to experimental noise. Using experimental data obtained from gonadotropes, PLACA reverse engineered the interaction network of six perturbed signaling components. The network recapitulated many known interactions and identified novel functional interactions that were validated by further experiment. PLACA uses the results of experiments that are feasible for any signaling network to predict the functional topology of the network and to identify novel relationships.
doi:10.1371/journal.pcbi.1000828 pmid:20585619 pmcid:PMC2891706 fatcat:s5so53agtfbfrosruprig7w3da

Regulation of gene expression by small non-coding RNAs: a quantitative view

Yishai Shimoni, Gilgi Friedlander, Guy Hetzroni, Gali Niv, Shoshy Altuvia, Ofer Biham, Hanah Margalit
2007 Molecular Systems Biology  
Regulation of gene expression by small non-coding RNAs Y Shimoni et al the mRNA.  ... 
doi:10.1038/msb4100181 pmid:17893699 pmcid:PMC2013925 fatcat:azmef76hyfd5dijluvestv3qjm

Multi-Scale Stochastic Simulation of Diffusion-Coupled Agents and Its Application to Cell Culture Simulation

Yishai Shimoni, German Nudelman, Fernand Hayot, Stuart C. Sealfon, Giuseppe Chirico
2011 PLoS ONE  
Many biological systems consist of multiple cells that interact by secretion and binding of diffusing molecules, thus coordinating responses across cells. Techniques for simulating systems coupling extracellular and intracellular processes are very limited. Here we present an efficient method to stochastically simulate diffusion processes, which at the same time allows synchronization between internal and external cellular conditions through a modification of Gillespie's chemical reaction
more » ... thm. Individual cells are simulated as independent agents, and each cell accurately reacts to changes in its local environment affected by diffusing molecules. Such a simulation provides time-scale separation between the intracellular and extra-cellular processes. We use our methodology to study how human monocyte-derived dendritic cells alert neighboring cells about viral infection using diffusing interferon molecules. A subpopulation of the infected cells reacts early to the infection and secretes interferon into the extra-cellular medium, which helps activate other cells. Findings predicted by our simulation and confirmed by experimental results suggest that the early activation is largely independent of the fraction of infected cells and is thus both sensitive and robust. The concordance with the experimental results supports the value of our method for overcoming the challenges of accurately simulating multiscale biological signaling systems.
doi:10.1371/journal.pone.0029298 pmid:22216238 pmcid:PMC3244460 fatcat:osydppg74nfappmzbj4l7tcsui

A causal inference approach for estimating effects of non-pharmaceutical interventions during Covid-19 pandemic [article]

Vesna Barros, Itay Manes, Victor Akinwande, Celia Cintas, Osnat Bar-Shira, Michal Ozery-Flato, Yishai Shimoni, Michal Rosen-Zvi
2022 medRxiv   pre-print
AbstractIn response to the outbreak of the coronavirus disease 2019 (Covid-19), governments worldwide have introduced multiple restriction policies, known as non-pharmaceutical interventions (NPIs). However, the relative impact of control measures and the long-term causal contribution of each NPI are still a topic of debate. We present a method to rigorously study the effectiveness of interventions on the rate of the time-varying reproduction number Rt and on human mobility, considered here as
more » ... proxy measure of policy adherence and social distancing. We frame our model using a causal inference approach to quantify the impact of five governmental interventions introduced until June 2020 to control the outbreak in 113 countries: confinement, school closure, mask wearing, cultural closure, and work restrictions. Our results indicate that mobility changes are more accurately predicted when compared to reproduction number. All NPIs, except for mask wearing, significantly affected human mobility trends. From these, schools and cultural closure mandates showed the largest effect on social distancing. We also found that closing schools, issuing face mask usage, and work-from-home mandates also caused a persistent reduction on Rt after their initiation, which was not observed with the other social distancing measures. Our results are robust and consistent across different model specifications and can shed more light on the impact of individual NPIs.
doi:10.1101/2022.02.28.22271671 fatcat:zaunf3rulvg5fiaqbif5y7rrgm

Groverian measure of entanglement for mixed states

Daniel Shapira, Yishai Shimoni, Ofer Biham
2006 Physical Review A. Atomic, Molecular, and Optical Physics  
The Groverian entanglement measure introduced earlier for pure quantum states [O. Biham, M.A. Nielsen and T. Osborne, Phys. Rev. A 65, 062312 (2002)] is generalized to the case of mixed states, in a way that maintains its operational interpretation. The Groverian measure of a mixed state of n qubits is obtained by a purification procedure into a pure state of 2n qubits, followed by an optimization process based on Uhlmann's theorem, before the resulting state is fed into Grover's search
more » ... m. The Groverian measure, expressed in terms of the maximal success probability of the algorithm, provides an operational measure of entanglement of both pure and mixed quantum states of multiple qubits. These results may provide further insight into the role of entanglement in making quantum algorithms powerful.
doi:10.1103/physreva.73.044301 fatcat:p7hvg5cmqncxza2wnp32tvdb3q

Entangled quantum states generated by Shor's factoring algorithm

Yishai Shimoni, Daniel Shapira, Ofer Biham
2005 Physical Review A. Atomic, Molecular, and Optical Physics  
The intermediate quantum states of multiple qubits, generated during the operation of Shor's factoring algorithm are analyzed. Their entanglement is evaluated using the Groverian measure. It is found that the entanglement is generated during the pre-processing stage of the algorithm and remains nearly constant during the quantum Fourier transform stage. The entanglement is found to be correlated with the speedup achieved by the quantum algorithm compared to classical algorithms.
doi:10.1103/physreva.72.062308 fatcat:2tfqvkbjyfhjzeuteiwuvra7p4

Trends in clinical characteristics and associations of severe non-respiratory events related to SARS-CoV-2 [article]

Tal El-Hay, Ehud Karavani, Asaf Perez, Matan Ninio, Sivan Ravid, Michal Chorev, Michal Rosen-Zvi, Tal Patalon, Yishai Shimoni, Anil Jain
2021 medRxiv   pre-print
The 2019 novel coronavirus (SARS-CoV-2) is reported to result in both respiratory and non-respiratory severe health outcomes, but quantitative assessment of the risk - while adjusting for underlying risk driven by comorbidities - is not yet established. Methods: A retrospective observational study using electronic health records of 9,344,021 individuals across the U.S. with at-least 1 year of clinical history and followed up throughout 2020. Results: 131,329 individuals were associated with
more » ... -CoV-2 infection by January 6, 2021 in three distinct surges. While the age and number of preexisting conditions had decreased throughout the pandemic, the characteristics of those who experienced severe health events did not. During the second surge, between June 7 and November 18, 2020, 425,988 individuals in the base cohort were admitted to emergency rooms or hospitals. Among them, 15,486 were detected with SAR-CoV-2 within few days of admission. Significant adjusted odds ratios were observed between SARS-CoV-2 infection and the following severe health events: respiratory (4.38, 95% confidence interval 4.16-4.62), bacterial pneumonia (3.25, 2.76-3.83), sepsis (1.71, 1.53-1.91), renal (1.69, 1.57-1.83), hematologic/immune (1.32, 1.20-1.45), and neurological (1.23, 1.09-1.38). Conclusions: SARS-CoV-2 infection among hospitalized patients is associated with non-negligible increased risk of severe events including multiple non-respiratory ones. These associations, which complement recent studies, are persistent even after accounting for sources of selection and confounding bias, increasing the confidence they are not spurious.
doi:10.1101/2021.03.24.21251900 fatcat:4t5ndty6cffkvmy4fhr5as2peq

Formation of multipartite entanglement using random quantum gates

Yonatan Most, Yishai Shimoni, Ofer Biham
2007 Physical Review A. Atomic, Molecular, and Optical Physics  
The formation of multipartite quantum entanglement by repeated operation of one and two qubit gates is examined. The resulting entanglement is evaluated using two measures: the average bipartite entanglement and the Groverian measure. A comparison is made between two geometries of the quantum register: a one dimensional chain in which two-qubit gates apply only locally between nearest neighbors and a non-local geometry in which such gates may apply between any pair of qubits. More specifically,
more » ... we use a combination of random single qubit rotations and a fixed two-qubit gate such as the controlled-phase gate. It is found that in the non-local geometry the entanglement is generated at a higher rate. In both geometries, the Groverian measure converges to its asymptotic value more slowly than the average bipartite entanglement. These results are expected to have implications on different proposed geometries of future quantum computers with local and non-local interactions between the qubits.
doi:10.1103/physreva.76.022328 fatcat:uao3o6mbtzh43cy7t7ls6mctcm

Analysis of Grover's quantum search algorithm as a dynamical system

Ofer Biham, Daniel Shapira, Yishai Shimoni
2003 Physical Review A. Atomic, Molecular, and Optical Physics  
Grover's quantum search algorithm is analyzed for the case in which the initial state is an arbitrary pure quantum state |ϕ> of n qubits. It is shown that the optimal time to perform the measurement is independent of | ϕ>, namely, it is identical to the optimal time in the original algorithm in which | ϕ > = | 0>, with the same number of marked states, r. The probability of success P_ s is obtained, in terms of the amplitudes of the state | ϕ>, and is shown to be independent of r. A class of
more » ... tes, which includes fixed points and cycles of the Grover iteration operator is identified. The relevance of these results in the context of using the success probability as an entanglement measure is discussed. In particular, the Groverian entanglement measure, previously limited to a single marked state, is generalized to the case of several marked states.
doi:10.1103/physreva.68.022326 fatcat:33cdyrmombhdpo444uqvo7rqcm
« Previous Showing results 1 — 15 out of 37 results