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Author Correction: AutoTransOP: translating omics signatures without orthologue requirements using deep learning

NPJ systems biology and applications 2024年第1期10卷 148页

作者： Nikolaos Meimetis Krista M Pullen Daniel Y Zhu Avlant Nilsson Trong Nghia Hoang Sara Magliacane Douglas A Lauffenburger Department of Biological Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA. Department of Biology and Biological Engineering Chalmers University of Technology Gothenburg SE 41296 Sweden. School of Electrical Engineering and Computer Science Washington State University Pullman WA 99164-236 USA. Institute of Informatics University of Amsterdam Amsterdam The Netherlands. MIT-IBM Watson AI Lab Cambridge MA 02139 USA. Department of Biological Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA. lauffen@mit.edu.

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Optimal Single Sample Tests for Structured versus Unstructured Network Data 31

Optimal Single Sample Tests for Structured versus Unstructur...

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31st Annual Conference on Learning Theory, COLT 2018

作者： Bresler, Guy Nagaraj, Dheeraj Department of Electrical Engineering and Computer Science MIT United States

We study the problem of testing, using only a single sample, between mean field distributions (like Curie-Weiss, Erdős-Rényi) and structured Gibbs distributions (like Ising model on sparse graphs and Exponential Random Graphs). Our goal is to test without knowing the parameter values of the underlying models: only the structure of dependencies is known. We develop a new approach that applies to both the Ising and Exponential Random Graph settings based on a general and natural statistical test. The test can distinguish the hypotheses with high probability above a certain threshold in the (inverse) temperature parameter, and is optimal in that below the threshold no test can distinguish the hypotheses. The thresholds do not correspond to the presence of long-range order in the models. By aggregating information at a global scale, our test works even at very high temperatures. The proofs are based on distributional approximation and sharp concentration of quadratic forms, when restricted to Hamming spheres. The restriction to Hamming spheres is necessary, since otherwise any scalar statistic is useless without explicit knowledge of the temperature parameter. At the same time, this restriction changes the behavior of the functions under consideration, making it hard to directly apply standard methods (i.e., Stein’s method) for concentration of weakly dependent variables. Instead, we carry out an additional tensorization argument using a Markov chain that respects the symmetry of the Hamming sphere. © 2018 G. Bresler & D. Nagaraj.

关键词： Inverse problems

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Scientific discovery in the age of artificial intelligence

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NATURE 2023年第7978期621卷 E33-E33页

作者： Wang, Hanchen Fu, Tianfan Du, Yuanqi Gao, Wenhao Huang, Kexin Liu, Ziming Chandak, Payal Liu, Shengchao Van Katwyk, Peter Deac, Andreea Anandkumar, Anima Bergen, Karianne Gomes, Carla P. Ho, Shirley Kohli, Pushmeet Lasenby, Joan Leskovec, Jure Liu, Tie-Yan Manrai, Arjun Marks, Debora Ramsundar, Bharath Song, Le Sun, Jimeng Tang, Jian Velickovic, Petar Welling, Max Zhang, Linfeng Coley, Connor W. Bengio, Yoshua Zitnik, Marinka Department of Engineering University of Cambridge Cambridge UK Department of Computing and Mathematical Sciences California Institute of Technology Pasadena CA USA NVIDIA Santa Clara CA USA Department of Computational Science and Engineering Georgia Institute of Technology Atlanta GA USA Department of Computer Science Cornell University Ithaca NY USA Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA USA Department of Computer Science Stanford University Stanford CA USA Department of Physics Massachusetts Institute of Technology Cambridge MA USA Harvard-MIT Program in Health Sciences and Technology Cambridge MA USA Mila – Quebec AI Institute Montreal Quebec Canada Université de Montréal Montreal Quebec Canada HEC Montréal Montreal Quebec Canada CIFAR AI Chair Toronto Ontario Canada Department of Earth Environmental and Planetary Sciences Brown University Providence RI USA Data Science Institute Brown University Providence RI USA Center for Computational Astrophysics Flatiron Institute New York NY USA Department of Astrophysical Sciences Princeton University Princeton NJ USA Department of Physics Carnegie Mellon University Pittsburgh PA USA Department of Physics and Center for Data Science New York University New York NY USA Google DeepMind London UK Department of Computer Science and Technology University of Cambridge Cambridge UK Microsoft Research Beijing China Department of Biomedical Informatics Harvard Medical School Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Harvard Data Science Initiative Cambridge MA USA Kempner Institute for the Study of Natural and Artificial Intelligence Harvard University Cambridge MA USA Department of Systems Biology Harvard Medical School Boston MA USA Deep Forest Sciences Palo Alto CA USA BioMap Beijing China Mo

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Microbes as Biosensors

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Microbiology 2020年第1期74卷 337-359页

作者： Maria Eugenia Inda Timothy K. Lu 2Research Laboratory of Electronics Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA 1MIT Synthetic Biology Center Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA email: timlu@mit.edu 3Department of Biological Engineering Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA

The ability to detect disease early and deliver precision therapy would be transformative for the treatment of human illnesses. To achieve these goals, biosensors that can pinpoint when and where diseases emerge are needed. Rapid advances in synthetic biology are enabling us to exploit the information-processing abilities of living cells to diagnose disease and then treat it in a controlled fashion. For example, living sensors could be designed to precisely sense disease biomarkers, such as by-products of inflammation, and to respond by delivering targeted therapeutics in situ. Here, we provide an overview of ongoing efforts in microbial biosensor design, highlight translational opportunities, and discuss challenges for enabling sense-and-respond precision medicines.

关键词： synthetic biology biotechnology biosensor gene circuit biomedical applications diagnosis treatment

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Calibration of Flux Crosstalk in Large-Scale Flux-Tunable Superconducting Quantum Circuits

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PRX Quantum 2021年第4期2卷 040313-040313页

作者： X. Dai D.M. Tennant R. Trappen A.J. Martinez D. Melanson M.A. Yurtalan Y. Tang S. Novikov J.A. Grover S.M. Disseler J.I. Basham R. Das D.K. Kim A.J. Melville B.M. Niedzielski S.J. Weber J.L. Yoder D.A. Lidar A. Lupascu Institute for Quantum Computing and Department of Physics and Astronomy University of Waterloo Waterloo Ontario N2L 3G1 Canada Department of Electrical and Computer Engineering University of Waterloo Waterloo Ontario N2L 3G1 Canada Northrop Grumman Corporation Linthicum Maryland 21090 USA MIT Lincoln Laboratory 244 Wood Street Lexington Massachusetts 02421 USA Departments of Electrical & Computer Engineering Chemistry and Physics and Center for Quantum Information Science & Technology University of Southern California Los Angeles California 90089 USA Waterloo Institute for Nanotechnology University of Waterloo Waterloo Ontario N2L 3G1 Canada

Magnetic flux tunability is an essential feature in most approaches to quantum computing based on superconducting qubits. Independent control of the fluxes in multiple loops is hampered by crosstalk. Calibrating flux crosstalk becomes a challenging task when the circuit elements interact strongly. We present a novel approach to flux crosstalk calibration, which is circuit model independent and relies on an iterative process to gradually improve calibration accuracy. This method allows us to reduce errors due to the inductive coupling between loops. The calibration procedure is automated and implemented on devices consisting of tunable flux qubits and couplers with up to 27 control loops. We devise a method to characterize the calibration error, which is used to show that the errors of the measured crosstalk coefficients are all below 0.17%.

关键词： Adiabatic quantum optimization Quantum information architectures & platforms Quantum information processing Superconducting qubits

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Exploiting sparse semantic HD maps for self-driving vehicle localization

arXiv

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arXiv 2019年

作者： Ma, Wei-Chiu Tartavull, Ignacio Bârsan, Ioan Andrei Wang, Shenlong Bai, Min Mattyus, Gellert Homayounfar, Namdar Lakshmikanth, Shrinidhi Kowshika Pokrovsky, Andrei Urtasun, Raquel Uber Advanced Technologies Group Department of Electrical Engineering and Computer Science MIT Department of Computer Science University of Toronto

In this paper we propose a novel semantic localization algorithm that exploits multiple sensors and has precision on the order of a few centimeters. Our approach does not require detailed knowledge about the appearance of the world, and our maps require orders of magnitude less storage than maps utilized by traditional geometry- and LiDAR intensity-based localizers. This is important as self-driving cars need to operate in large environments. Towards this goal, we formulate the problem in a Bayesian filtering framework, and exploit lanes, traffic signs, as well as vehicle dynamics to localize robustly with respect to a sparse semantic map. We validate the effectiveness of our method on a new highway dataset consisting of 312km of roads. Our experiments show that the proposed approach is able to achieve 0.05m lateral accuracy and 1.12m longitudinal accuracy on average while taking up only 0.3% of the storage required by previous LiDAR intensity-based approaches. Copyright © 2019, The Authors. All rights reserved.

关键词： Semantics

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Quantum lattice representation for the curl equations of Maxwell equations

arXiv

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arXiv 2021年

作者： Vahala, George Hawthorne, John Vahala, Linda Ram, Abhay K. Soe, Min Department of Physics William & Mary WilliamsburgVA23185 United States Department of Electrical & Computer Engineering Old Dominion University NorfolkVA12319 United States Plasma Science and Fusion Center MIT CambridgeMA02139 United States Department of Mathematics and Physical Sciences Rogers State University ClaremoreOK74017 United States

A quantum lattice representation (QLA) is devised for the initial value problem of one-dimensional (1D) propagation of an electromagnetic disturbance in a scalar dielectric medium satisfying directly only the two curl equations of Maxwell. It si found that only 4 qubits/node are required. The collision, streaming, and potential operators are determined so as to recover the two curl equations to second order. Both polarizations are considered. © 2021, CC BY.

关键词： Initial value problems

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Cell trajectory modulation: rapid microfluidic biophysical profiling of CAR T cell functional phenotypes

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Nature Communications 2025年第1期16卷 1-15页

作者： Zeming, Kerwin Kwek Quek, Kai Yun Sin, Wei-Xiang Teo, Denise Bei Lin Cheung, Ka-Wai Goh, Chin Ren Kairi, Faris Lee, Elizabeth Lim, Francesca Lorraine Wei Inng Seng, Michaela Su-Fern Soh, Shui Yen Birnbaum, Michael E. Han, Jongyoon Critical Analytics for Manufacturing of Personalized Medicine Singapore-MIT Alliance for Research and Technology (SMART) Singapore Singapore Department of Haematology Singapore General Hospital Singapore Singapore SingHealth Duke-NUS Oncology Academic Clinical Programme Sing Health Duke-NUS Academic Medical Centre Singapore Singapore SingHealth Duke-NUS Cell Therapy Centre SingHealth Duke-NUS Academic Medical Centre Singapore Singapore Department of Paediatric Hematology and Oncology KK Women’s and Children’s Hospital Singapore Singapore Department of Biological Engineering Massachusetts Institute of Technology Cambridge MA United States Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA United States Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA United States

Chimeric Antigen Receptor (CAR) T cell therapy is a pivotal treatment for hematological malignancies. However, CAR T cell products exhibit batch-to-batch variability in cell number, quality, and in vivo efficacy due to donor-to-donor heterogeneity, and pre/post-manufacturing processes, and the manufacturing of such products necessitates careful testing, both post-manufacturing and pre-infusion. Here, we introduce the Cell Trajectory Modulation (CTM) assay, a microfluidic, label-free approach for the rapid evaluation of the functional attributes of CAR T cells based on biophysical features (i.e., size, deformability). CTM assay correlates with phenotypic metrics, including CD4:CD8 ratio, memory subtypes, and cytotoxic activity. Validated across multiple donors and culture platforms, the CTM assay requires fewer than 10,000 cells and delivers results within 10 minutes. Compared to labeled flow cytometry processing, the CTM assay offers real-time data to guide adaptive manufacturing workflows. Thus, the CTM assay offers an improvement over existing phenotypic assessments, marking a step forward in advancing CAR T cell therapy manufacturing. © The Author(s) 2025.

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Error mitigation via stabilizer measurement emulation

arXiv

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arXiv 2021年

作者： Greene, Ami Kjaergaard, M. Schwartz, M.E. Samach, G.O. Bengtsson, A. McNally, C. O’Keeffe, M. Kim, D.K. Marvian, M. Melville, A. Niedzielski, B.M. Vepsäläinen, A. Winik, R. Yoder, J. Rosenberg, D. Lloyd, S. Orlando, T.P. Marvian, I. Gustavsson, S. Oliver, W.D. Research Laboratory of Electronics Massachusetts Institute of Technology CambridgeMA02139 United States MIT Lincoln Laboratory LexingtonMA02421 United States Microtechnology and Nanoscience Chalmers University of Technology GöteborgSE-412 96 Sweden Department of Mechanical Engineering Massachusetts Institute of Technology CambridgeMA02139 United States Departments of Physics & Electrical and Computer Engineering Duke University DurhamNC27708 United States Department of Physics Massachusetts Institute of Technology CambridgeMA02139 United States Department of Electrical Engineering & Computer Science Massachusetts Institute of Technology CambridgeMA02139 United States

Dynamical decoupling (DD) is a widely-used quantum control technique that takes advantage of temporal symmetries in order to partially suppress quantum errors without the need resource-intensive error detection and correction protocols. This and other open-loop error mitigation techniques are critical for quantum information processing in the era of Noisy Intermediate-Scale Quantum technology. However, despite its utility, dynamical decoupling does not address errors which occur at unstructured times during a circuit, including certain commonly-encountered noise mechanisms such as cross-talk and imperfectly calibrated control pulses. Here, we introduce and demonstrate an alternative technique — ‘quantum measurement emulation’ (QME) — that effectively emulates the measurement of stabilizer operators via stochastic gate application, leading to a first-order insensitivity to coherent errors. The QME protocol enables error suppression based on the stabilizer code formalism without the need for costly measurements and feedback, and it is particularly well-suited to discrete coherent errors that are challenging for DD to address. Copyright © 2021, The Authors. All rights reserved.

关键词： Errors

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Broadband Squeezed Microwaves and Amplification with a Josephson Traveling-Wave Parametric Amplifier

arXiv

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arXiv 2022年

作者： Qiu, Jack Y. Grimsmo, Arne Peng, Kaidong Kannan, Bharath Lienhard, Benjamin Sung, Youngkyu Krantz, Philip Bolkhovsky, Vladimir Calusine, Greg Kim, David Melville, Alex Niedzielski, Bethany M. Yoder, Jonilyn Schwartz, Mollie E. Orlando, Terry P. Siddiqi, Irfan Gustavsson, Simon O'Brien, Kevin P. Oliver, William D. Research Laboratory of Electronics Massachusetts Institute of Technology CambridgeMA02139 United States Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA02139 United States ARC Centre of Excellence for Engineered Quantum Systems School of Physics The University of Sydney SydneyNSW2006 Australia MIT Lincoln Laboratory 244 Wood Street LexingtonMA02420 United States Quantum Nanoelectronics Laboratory BerkeleyCA94720 United States Department of Physics Massachusetts Institute of Technology CambridgeMA02139 United States

Squeezing of the electromagnetic vacuum is an essential metrological technique used to reduce quantum noise in applications spanning gravitational wave detection, biological microscopy, and quantum information science. In superconducting circuits, the resonator-based Josephson-junction parametric amplifiers conventionally used to generate squeezed microwaves are constrained by a narrow bandwidth and low dynamic range. In this work, we develop a dual-pump, broadband Josephson traveling-wave parametric amplifier that combines a phase-sensitive extinction ratio of 56 dB with single-mode squeezing on par with the best resonator-based squeezers. We also demonstrate two-mode squeezing at microwave frequencies with bandwidth in the gigahertz range that is almost two orders of magnitude wider than that of contemporary resonator-based squeezers. Our amplifier is capable of simultaneously creating entangled microwave photon pairs with large frequency separation, with potential applications including high-fidelity qubit readout, quantum illumination and teleportation. Copyright © 2022, The Authors. All rights reserved.

关键词： Parametric amplifiers

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