arXiv subjects

Mu Qiao

Publications and source records attributed to Mu Qiao.

35 records · Page 2Linked to original sources

arXiv2023

BioMedGPT: Open Multimodal Generative Pre-trained Transformer for BioMedicine

Foundation models (FMs) have exhibited remarkable performance across a wide range of downstream tasks in many domains. Nevertheless, general-purpose FMs often face challenges when confronted with domain-specific problems, due to their limited access to the proprietary training data in a particular domain. In biomedicine, there are various biological modalities, such as molecules, proteins, and cells, which are encoded by the language of life and exhibit significant modality gaps with human natural language. In this paper, we introduce BioMedGPT, an open multimodal generative pre-trained transformer (GPT) for biomedicine, to bridge the gap between the language of life and human natural language. BioMedGPT allows users to easily ``communicate'' with diverse biological modalities through free text, which is the first of its kind. BioMedGPT aligns different biological modalities with natural language via a large generative language model, namely, BioMedGPT-LM. We publish BioMedGPT-10B, which unifies the feature spaces of molecules, proteins, and natural language via encoding and alignment. Through fine-tuning, BioMedGPT-10B outperforms or is on par with human and significantly larger general-purpose foundation models on the biomedical QA task. It also demonstrates promising performance in the molecule QA and protein QA tasks, which could greatly accelerate the discovery of new drugs and therapeutic targets. In addition, BioMedGPT-LM-7B is the first large generative language model based on Llama2 in the biomedical domain, therefore is commercial friendly. Both BioMedGPT-10B and BioMedGPT-LM-7B are open-sourced to the research community. In addition, we publish the datasets that are meticulously curated for the alignment of multi-modalities, i.e., PubChemQA and UniProtQA. All the models, codes, and datasets are available at \url{https://github.com/PharMolix/OpenBioMed}.

cs.CE↗

arXiv2023

GNN-Ensemble: Towards Random Decision Graph Neural Networks

Graph Neural Networks (GNNs) have enjoyed wide spread applications in graph-structured data. However, existing graph based applications commonly lack annotated data. GNNs are required to learn latent patterns from a limited amount of training data to perform inferences on a vast amount of test data. The increased complexity of GNNs, as well as a single point of model parameter initialization, usually lead to overfitting and sub-optimal performance. In addition, it is known that GNNs are vulnerable to adversarial attacks. In this paper, we push one step forward on the ensemble learning of GNNs with improved accuracy, generalization, and adversarial robustness. Following the principles of stochastic modeling, we propose a new method called GNN-Ensemble to construct an ensemble of random decision graph neural networks whose capacity can be arbitrarily expanded for improvement in performance. The essence of the method is to build multiple GNNs in randomly selected substructures in the topological space and subfeatures in the feature space, and then combine them for final decision making. These GNNs in different substructure and subfeature spaces generalize their classification in complementary ways. Consequently, their combined classification performance can be improved and overfitting on the training data can be effectively reduced. In the meantime, we show that GNN-Ensemble can significantly improve the adversarial robustness against attacks on GNNs.

cs.LG↗

arXiv2023

Error-Mitigated Quantum Simulation of Interacting Fermions with Trapped Ions

Quantum error mitigation has been extensively explored to increase the accuracy of the quantum circuits in noisy-intermediate-scale-quantum (NISQ) computation, where quantum error correction requiring additional quantum resources is not adopted. Among various error-mitigation schemes, probabilistic error cancellation (PEC) has been proposed as a general and systematic protocol that can be applied to numerous hardware platforms and quantum algorithms. However, PEC has only been tested in two-qubit systems and a superconducting multi-qubit system by learning a sparse error model. Here, we benchmark PEC using up to four trapped-ion qubits. For the benchmark, we simulate the dynamics of interacting fermions with or without spins by applying multiple Trotter steps. By tomographically reconstructing the error model and incorporating other mitigation methods such as positive probability and symmetry constraints, we are able to increase the fidelity of simulation and faithfully observe the dynamics of the Fermi-Hubbard model, including the different behavior of charge and spin of fermions. Our demonstrations can be an essential step for further extending systematic error-mitigation schemes toward practical quantum advantages.

quant-ph↗

arXiv2022

Scalable and Programmable Phononic Network with Trapped Ions

Controllable bosonic systems can provide post-classical computational power with sub-universal quantum computational capability. A network that consists of a number of bosons evolving through beam-splitters and phase-shifters between different modes, has been proposed and applied to demonstrate quantum advantages. While the network has been implemented mostly in optical systems with photons, recently alternative realizations have been explored, where major limitations in photonic systems such as photon loss, and probabilistic manipulation can be addressed. Phonons, the quantized excitations of vibrational modes, of trapped ions can be a promising candidate to realize the bosonic network. Here, we experimentally demonstrate a minimal-loss phononic network that can be programmed and in which any phononic states are deterministically prepared and detected. We realize the network with up to four collective-vibrational modes, which can be straightforwardly extended to reveal quantum advantage. We benchmark the performance of the network with an exemplary algorithm of tomography for arbitrary multi-mode states with a fixed total phonon number. We obtain reconstruction fidelities of 94.5 $\pm$ 1.95 % and 93.4 $\pm$ 3.15 % for single-phonon and two-phonon states, respectively. Our experiment demonstrates a clear and novel pathway to scale up a phononic network for various quantum information processing beyond the limitations of classical and other quantum systems.

quant-ph↗

arXiv2022

Observing frustrated quantum magnetism in two-dimensional ion crystals

Two-dimensional (2D) quantum magnetism is a paradigm in strongly correlated many-body physics. The understanding of 2D quantum magnetism can be expedited by employing a controllable quantum simulator that faithfully maps 2D-spin Hamiltonians. The 2D quantum simulators can exhibit exotic phenomena such as frustrated quantum magnetism and topological order and can be used to show quantum computational advantages. Many experimental platforms are being developed, including Rydberg atoms and superconducting annealers. However, with trapped-ion systems, which showed the most advanced controllability and quantum coherence, quantum magnetism was explored in one-dimensional chains. Here, we report simulations of frustrated quantum magnetism with 2D ion crystals. We create a variety of spin-spin interactions for quantum magnets, including those that exhibit frustration by driving different vibrational modes and adiabatically prepare the corresponding ground states. The experimentally measured ground states are consistent with the theoretical predictions and are highly degenerate for geometrically frustrated spin models in two dimensions. Quantum coherence of the ground states is probed by reversing the time evolution of the B-field to the initial value and then measuring the extent to which the remaining state coincides with the initial state. Our results open the door for quantum simulations with 2D ion crystals.

quant-ph↗

arXiv2022

Towards a New Science of Disinformation

How can we best address the dangerous impact that deep learning-generated fake audios, photographs, and videos (a.k.a. deepfakes) may have in personal and societal life? We foresee that the availability of cheap deepfake technology will create a second wave of disinformation where people will receive specific, personalized disinformation through different channels, making the current approaches to fight disinformation obsolete. We argue that fake media has to be seen as an upcoming cybersecurity problem, and we have to shift from combating its spread to a prevention and cure framework where users have available ways to verify, challenge, and argue against the veracity of each piece of media they are exposed to. To create the technologies behind this framework, we propose that a new Science of Disinformation is needed, one which creates a theoretical framework both for the processes of communication and consumption of false content. Key scientific and technological challenges facing this research agenda are listed and discussed in the light of state-of-art technologies for fake media generation and detection, argument finding and construction, and how to effectively engage users in the prevention and cure processes.

cs.CY↗

arXiv2021

Significant-loophole-free test of Kochen-Specker contextuality using two species of atomic-ions

Quantum measurements cannot be thought of as revealing preexisting results, even when they do not disturb any other measurement in the same trial. This feature is called contextuality and is crucial for the quantum advantage in computing. Here, we report the first observation of quantum contextuality simultaneously free of the detection, sharpness and compatibility loopholes. The detection and sharpness loopholes are closed by adopting a hybrid two-ion system and highly efficient fluorescence measurements offering a detection efficiency of $100\%$ and a measurement repeatability $>98\%$. The compatibility loophole is closed by targeting correlations between observables for two different ions in a Paul trap, a $^{171}\mathrm{Yb}^{+}$ ion and a $^{138}\mathrm{Ba}^{+}$ ion, chosen so measurements on each ion use different operation laser wavelengths, fluorescence wavelengths, and detectors. The experimental results show a violation of the bound for the most adversarial noncontextual models and open a new way to certify quantum systems.

quant-ph↗

arXiv2021

Dual-view Snapshot Compressive Imaging via Optical Flow Aided Recurrent Neural Network

Dual-view snapshot compressive imaging (SCI) aims to capture videos from two field-of-views (FoVs) using a 2D sensor (detector) in a single snapshot, achieving joint FoV and temporal compressive sensing, and thus enjoying the advantages of low-bandwidth, low-power, and low-cost. However, it is challenging for existing model-based decoding algorithms to reconstruct each individual scene, which usually require exhaustive parameter tuning with extremely long running time for large scale data. In this paper, we propose an optical flow-aided recurrent neural network for dual video SCI systems, which provides high-quality decoding in seconds. Firstly, we develop a diversity amplification method to enlarge the differences between scenes of two FoVs, and design a deep convolutional neural network with dual branches to separate different scenes from the single measurement. Secondly, we integrate the bidirectional optical flow extracted from adjacent frames with the recurrent neural network to jointly reconstruct each video in a sequential manner. Extensive results on both simulation and real data demonstrate the superior performance of our proposed model in a short inference time. The code and data are available at https://github.com/RuiyingLu/OFaNet-for-Dual-view-SCI.

eess.IV↗

arXiv2021

Double-EIT Ground-State Cooling of Stationary Two-Dimensional Ion Lattices

We theoretically and experimentally investigate double electromagnetically induced transparency (double-EIT) cooling of two-dimensional ion crystals confined in a Paul trap. The double-EIT ground-state cooling is observed for \Yb ions with clock state, for which EIT cooling has not been realized like many other ions with a simple $Λ$-scheme. A cooling rate of $\dot{\bar n}=34~(\pm1.8)~\rm{ms}^{-1}$ and a cooling limit of $\bar n=0.06~(\pm 0.059)$ are observed for a single ion. The measured cooling rate and limit are consistent with theoretical predictions. We apply double-EIT cooling to the transverse modes of two-dimensional (2D) crystals with up to 12 ions. In our 2D crystals, the micromotion and the transverse mode directions are perpendicular, which makes them decoupled. Therefore, the cooling on transverse modes is not disturbed by micromotion, which is confirmed in our experiment. For the center of mass mode of a 12 ions crystal, we observe a cooling rate and a cooling limit that are consistent with those of a single ion, including heating rates proportional to the number of ions. This method can be extended to other hyperfine qubits, and near ground-state cooling of stationary 2D crystals with large numbers of ions may advance the field of quantum information sciences.

quant-ph↗

arXiv2020

Single ion-qubit exceeding one hour coherence time

Realizing a long coherence time quantum memory is a major challenge of current quantum technology. Here, we report a single \Yb ion-qubit memory with over one hour coherence time, an order of improvement compared to the state-of-the-art record. The long coherence time memory is realized by addressing various technical challenges such as ambient magnetic-field noise, phase noise and leakage of the microwave oscillator. Moreover, systematically study the decoherence process of our quantum memory by quantum process tomography, which enables to apply the strict criteria of quantum coherence, relative entropy of coherence. We also benchmark our quantum memory by its ability in preserving quantum information, i.e., the robustness of quantum memory, which clearly shows that over 6000 s, our quantum memory preserves non-classical quantum information. Our results verify the stability of the quantum memory in hours level and indicate its versatile applicability in various scenarios.

quant-ph↗

arXiv2020

Snapshot Interferometric 3D Imaging by Compressive Sensing and Deep Learning

We demonstrate single-shot compressive three-dimensional (3D) $(x, y, z)$ imaging based on interference coding. The depth dimension of the object is encoded into the interferometric spectra of the light field, resulting a $(x, y, λ)$ datacube which is subsequently measured by a single-shot spectrometer. By implementing a compression ratio up to $400$, we are able to reconstruct $1G$ voxels from a 2D measurement. Both an optimization based compressive sensing algorithm and a deep learning network are developed for 3D reconstruction from a single 2D coded measurement. Due to the fast acquisition speed, our approach is able to capture volumetric activities at native camera frame rates, enabling 4D (volumetric-temporal) visualization of dynamic scenes.

eess.IV↗

arXiv2020

A realistic phase screen model for forward multiple-scattering media

Existing random phase screen (RPS) models for forward multiple-scattering media fail to incorporate ballistic light. In this letter, we redesign the angular spectrum of the screen by means of Monte-Carlo simulation based on an assumption that a single screen should represent all the scattering events a photon experiences between two adjacent screens. Three examples demonstrate that the proposed model exhibits more realistic optical properties than conventional RPS models in terms of attenuation of ballistic light, evolution of beam profile and angular memory effect. The proposed model also provides the flexibility to balance the computing accuracy, speed and memory usage by tuning the screen spacing.

physics.optics↗

arXiv2020

Temporal Tensor Transformation Network for Multivariate Time Series Prediction

Multivariate time series prediction has applications in a wide variety of domains and is considered to be a very challenging task, especially when the variables have correlations and exhibit complex temporal patterns, such as seasonality and trend. Many existing methods suffer from strong statistical assumptions, numerical issues with high dimensionality, manual feature engineering efforts, and scalability. In this work, we present a novel deep learning architecture, known as Temporal Tensor Transformation Network, which transforms the original multivariate time series into a higher order of tensor through the proposed Temporal-Slicing Stack Transformation. This yields a new representation of the original multivariate time series, which enables the convolution kernel to extract complex and non-linear features as well as variable interactional signals from a relatively large temporal region. Experimental results show that Temporal Tensor Transformation Network outperforms several state-of-the-art methods on window-based predictions across various tasks. The proposed architecture also demonstrates robust prediction performance through an extensive sensitivity analysis.

cs.LG↗

arXiv2019

Realization of two-dimensional crystal of ions in a monolithic Paul trap

We present a simple Paul trap that stably accommodates up to a couple of dozens of \ensuremath{^{171}\mathrm{Yb}^+~} ions in a stationary two-dimensional lattice. The trap is constructed on a single plate of gold-plated laser-machined alumina and can produce a pancake-like pseudo-potential that makes ions form a self-assembly two-dimensional crystal which locates on the plane composed of axial and one of the transverse axes with around 5 $μ$m spacing. We use Raman laser beams to coherently manipulate these ion-qubits where the net propagation direction is perpendicular to the plane of the crystal and micromotion. We perform the coherent operations and study the spectrum of vibrational modes through globally addressed Raman laser-beams on a dozen of ions in the two-dimensional crystal. We measure the amplitude of micro-motion by comparing the strengths of carrier and micro-motion sideband transitions with three ions, where the micro-motion amplitude is similar to that of a single ion. The spacings of ions are small enough for large coupling strengths, which is a favorable condition for two-dimensional quantum simulation.

quant-ph↗

arXiv2019

Randomness expansion secured by quantum contextuality

The output randomness from a random number generator can be certified by observing the violation of quantum contextuality inequalities based on the Kochen-Specker theorem. Contextuality can be tested in a single quantum system, which significantly simplifies the experimental requirements to observe the violation comparing to the ones based on nonlocality tests. However, it is not yet resolved how to ensure compatibilities for sequential measurements that is required in contextuality tests. Here, we employ a modified Klyachko-Can-Binicioğlu-Shumovsky contextuality inequality, which can ease the strict compatibility requirement on measurements. On a trapped single \Ba ion system, we experimentally demonstrate violation of the contextuality inequality and realize self-testing quantum random number expansion by closing detection loopholes. We perform $1.29 \times 10^8$ trials of experiments and extract the randomness of $8.06 \times 10^5$ bits with a speed of 270 bits s$^{-1}$. Our demonstration paves the way for the practical high-speed spot-checking quantum random number expansion and other secure information processing applications.

quant-ph↗

arXiv2017

StackInsights: Cognitive Learning for Hybrid Cloud Readiness

Hybrid cloud is an integrated cloud computing environment utilizing a mix of public cloud, private cloud, and on-premise traditional IT infrastructures. Workload awareness, defined as a detailed full range understanding of each individual workload, is essential in implementing the hybrid cloud. While it is critical to perform an accurate analysis to determine which workloads are appropriate for on-premise deployment versus which workloads can be migrated to a cloud off-premise, the assessment is mainly performed by rule or policy based approaches. In this paper, we introduce StackInsights, a novel cognitive system to automatically analyze and predict the cloud readiness of workloads for an enterprise. Our system harnesses the critical metrics across the entire stack: 1) infrastructure metrics, 2) data relevance metrics, and 3) application taxonomy, to identify workloads that have characteristics of a) low sensitivity with respect to business security, criticality and compliance, and b) low response time requirements and access patterns. Since the capture of the data relevance metrics involves an intrusive and in-depth scanning of the content of storage objects, a machine learning model is applied to perform the business relevance classification by learning from the meta level metrics harnessed across stack. In contrast to traditional methods, StackInsights significantly reduces the total time for hybrid cloud readiness assessment by orders of magnitude.

cs.LG↗

arXiv2015

Gaussian Mixture Models with Component Means Constrained in Pre-selected Subspaces

We investigate a Gaussian mixture model (GMM) with component means constrained in a pre-selected subspace. Applications to classification and clustering are explored. An EM-type estimation algorithm is derived. We prove that the subspace containing the component means of a GMM with a common covariance matrix also contains the modes of the density and the class means. This motivates us to find a subspace by applying weighted principal component analysis to the modes of a kernel density and the class means. To circumvent the difficulty of deciding the kernel bandwidth, we acquire multiple subspaces from the kernel densities based on a sequence of bandwidths. The GMM constrained by each subspace is estimated; and the model yielding the maximum likelihood is chosen. A dimension reduction property is proved in the sense of being informative for classification or clustering. Experiments on real and simulated data sets are conducted to examine several ways of determining the subspace and to compare with the reduced rank mixture discriminant analysis (MDA). Our new method with the simple technique of spanning the subspace only by class means often outperforms the reduced rank MDA when the subspace dimension is very low, making it particularly appealing for visualization.

stat.ML↗