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1. Preparing for the next pandemic via transfer learning from existing diseases with hierarchical multi-modal BERT: a study on COVID-19 outcome prediction

   https://doi.org/10.1038/s41598-022-13072-w  

   Agarwal, Khushbu; Choudhury, Sutanay; Tipirneni, Sindhu; Mukherjee, Pritam; Ham, Colby; Tamang, Suzanne; Baker, Matthew; Tang, Siyi; Kocaman, Veysel; Gevaert, Olivier; et al (June 2022, Scientific Reports)

   Abstract Developing prediction models for emerging infectious diseases from relatively small numbers of cases is a critical need for improving pandemic preparedness. Using COVID-19 as an exemplar, we propose a transfer learning methodology for developing predictive models from multi-modal electronic healthcare records by leveraging information from more prevalent diseases with shared clinical characteristics. Our novel hierarchical, multi-modal model ($${\textsc {TransMED}}$$ $TRANS\mathrm{MED}$) integrates baseline risk factors from the natural language processing of clinical notes at admission, time-series measurements of biomarkers obtained from laboratory tests, and discrete diagnostic, procedure and drug codes. We demonstrate the alignment of$${\textsc {TransMED}}$$ $TRANS\mathrm{MED}$’s predictions with well-established clinical knowledge about COVID-19 through univariate and multivariate risk factor driven sub-cohort analysis.$${\textsc {TransMED}}$$ $TRANS\mathrm{MED}$’s superior performance over state-of-the-art methods shows that leveraging patient data across modalities and transferring prior knowledge from similar disorders is critical for accurate prediction of patient outcomes, and this approach may serve as an important tool in the early response to future pandemics. 

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2. QLBT: a linear Boltzmann transport model for heavy quarks in a quark-gluon plasma of quasi-particles

   https://doi.org/10.1140/epjc/s10052-022-10308-x  

   Liu, Feng-Lei; Xing, Wen-Jing; Wu, Xiang-Yu; Qin, Guang-You; Cao, Shanshan; Wang, Xin-Nian (April 2022, The European Physical Journal C)

   Abstract We develop a new heavy quark transport model, QLBT, to simulate the dynamical propagation of heavy quarks inside the quark-gluon plasma (QGP) created in relativistic heavy-ion collisions. Our QLBT model is based on the linear Boltzmann transport (LBT) model with the ideal QGP replaced by a collection of quasi-particles to account for the non-perturbative interactions among quarks and gluons of the hot QGP. The thermal masses of quasi-particles are fitted to the equation of state from lattice QCD simulations using the Bayesian statistical analysis method. Combining QLBT with our advanced hybrid fragmentation-coalescence hadronization approach, we calculate the nuclear modification factor$$R_\mathrm {AA}$$ $R_{\mathrm{AA}}$and the elliptic flow$$v_2$$ $v_2$ofDmesons at the Relativistic Heavy-Ion Collider and the Large Hadron Collider. By comparing our QLBT calculation to the experimental data on theDmeson$$R_\mathrm {AA}$$ $R_{\mathrm{AA}}$and$$v_2$$ $v_2$, we extract the heavy quark transport parameter$$\hat{q}$$ $\hat{q}$and diffusion coefficient$$D_\mathrm {s}$$ $D_s$in the temperature range of$$1-4~T_\mathrm {c}$$ $1-4T_c$, and compare them with the lattice QCD results and other phenomenological studies. 

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3. Study of baryon number transport dynamics and strangeness conservation effects using Ω-hadron correlations

   https://doi.org/10.1007/s41365-024-01464-8  

   Dong, Wei-Jie; Yu, Xiao-Zhou; Ping, Si-Yuan; Wu, Xia-Tong; Wang, Gang; Huang, Huan-Zhong; Lin, Zi-Wei (July 2024, Nuclear Science and Techniques)

   Abstract In nuclear collisions at RHIC energies, an excess of$$\Omega$$ $\Omega$hyperons over$$\bar{\Omega }$$ $\overline{\Omega }$is observed, indicating that$$\Omega$$ $\Omega$has a net baryon number despitesand$$\bar{s}$$ $\overline{s}$quarks being produced in pairs. The baryon number in$$\Omega$$ $\Omega$may have been transported from the incident nuclei and/or produced in the baryon-pair production of$$\Omega$$ $\Omega$with other types of anti-hyperons such as$$\bar{\Xi }$$ $\overline{\Xi }$. To investigate these two scenarios, we propose to measure the correlations between$$\Omega$$ $\Omega$andKand between$$\Omega$$ $\Omega$and anti-hyperons. We use two versions, the default and string-melting, of a multiphase transport (AMPT) model to illustrate the method for measuring the correlation and to demonstrate the general shape of the correlation. We present the$$\Omega$$ $\Omega$-hadron correlations from simulated Au+Au collisions at$$\sqrt{s_\text{NN}} = 7.7$$ $\sqrt{s_{\text{NN}}}=7.7$and$$14.6 \ \textrm{GeV}$$ $14.6\text{GeV}$and discuss the dependence on the collision energy and on the hadronization scheme in these two AMPT versions. These correlations can be used to explore the mechanism of baryon number transport and the effects of baryon number and strangeness conservation on nuclear collisions. 

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4. Identifying a stochastic clock network with light entrainment for single cells of Neurospora crassa

   https://doi.org/10.1038/s41598-020-72213-1  

   Caranica, C.; Al-Omari, A.; Schüttler, H. -B.; Arnold, J. (September 2020, Scientific Reports)

   Abstract Stochastic networks for the clock were identified by ensemble methods using genetic algorithms that captured the amplitude and period variation in single cell oscillators ofNeurosporacrassa. The genetic algorithms were at least an order of magnitude faster than ensemble methods using parallel tempering and appeared to provide a globally optimum solution from a random start in the initial guess of model parameters (i.e., rate constants and initial counts of molecules in a cell). The resulting goodness of fit$${x}^{2}$$ $x^2$was roughly halved versus solutions produced by ensemble methods using parallel tempering, and the resulting$${x}^{2}$$ $x^2$per data point was only$${\chi }^{2}/n$$ ${\chi }^2/n$= 2,708.05/953 = 2.84. The fitted model ensemble was robust to variation in proxies for “cell size”. The fitted neutral models without cellular communication between single cells isolated by microfluidics provided evidence for onlyoneStochastic Resonance at one common level of stochastic intracellular noise across days from 6 to 36 h of light/dark (L/D) or in a D/D experiment. When the light-driven phase synchronization was strong as measured by the Kuramoto (K), there was degradation in the single cell oscillations away from the stochastic resonance. The rate constants for the stochastic clock network are consistent with those determined on a macroscopic scale of 10⁷cells. 

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5. An Efficient ZK Compiler from SIMD Circuits to General Circuits

   https://doi.org/10.1007/s00145-024-09531-4  

   Bui, Dung; Chu, Haotian; Couteau, Geoffroy; Wang, Xiao; Weng, Chenkai; Yang, Kang; Yu, Yu (January 2025, Journal of Cryptology)

   Abstract We propose a generic compiler that can convert any zero-knowledge (ZK) proof for SIMD circuits to general circuits efficiently, and an extension that can preserve the space complexity of the proof systems. Our compiler can immediately produce new results improving upon state of the art.By plugging in our compiler to Antman, an interactive sublinear-communication protocol, we improve the overall communication complexity for general circuits from$$\mathcal {O}(C^{3/4})$$ $O\left(C^{3/4}\right)$to$$\mathcal {O}(C^{1/2})$$ $O\left(C^{1/2}\right)$. Our implementation shows that for a circuit of size$$2^{27}$$ $2^{27}$, it achieves up to$$83.6\times $$ $83.6\times$improvement on communication compared to the state-of-the-art implementation. Its end-to-end running time is at least$$70\%$$ $70\%$faster in a 10Mbps network.Using the recent results on compressed$$\varSigma $$ $\Sigma$-protocol theory, we obtain a discrete-log-based constant-round zero-knowledge argument with$$\mathcal {O}(C^{1/2})$$ $O\left(C^{1/2}\right)$communication and common random string length, improving over the state of the art that has linear-size common random string and requires heavier computation.We improve the communication of a designatedn-verifier zero-knowledge proof from$$\mathcal {O}(nC/B+n^2B^2)$$ $O(nC/B+n^2{B}^2)$to$$\mathcal {O}(nC/B+n^2)$$ $O(nC/B+n^2)$.To demonstrate the scalability of our compilers, we were able to extract a commit-and-prove SIMD ZK from Ligero and cast it in our framework. We also give one instantiation derived from LegoSNARK, demonstrating that the idea of CP-SNARK also fits in our methodology. 

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