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High Entropy Analysis Code
This code describes the process to estimate material properties using elemental properties and machine learning.
Revisiting Huffman Coding: Toward Extreme Performance on Modern GPU Architectures
Today's high-performance computing (HPC) applications are producing vast volumes of data, which are challenging to store and transfer efficiently during the execution, such that data compression is becoming a critical technique to mitigate the storage burden and data movement cost. Huffman coding is arguably the most efficient Entropy coding algorithm in information theory, such that it could be found as a fundamental step in many modern compression algorithms such as DEFLATE. On the other hand, today's HPC applications are more and more relying on the accelerators such as GPU on supercomputers, while Huffman encoding suffers from low throughput on GPUs, resulting in a significant bottleneck in the entire data processing. In this paper, we propose and implement an efficient Huffman encoding approach based on modern GPU architectures, which addresses two key challenges: (1) how to parallelize the entire Huffman encoding algorithm, including codebook construction, and (2) how to fully utilize the high memory-bandwidth feature of modern GPU architectures. The detailed contribution is fourfold. (1) We develop an efficient parallel codebook construction on GPUs that scales effectively with the number of input symbols. (2) We propose a novel reduction based encoding scheme that can efficiently merge the codewords on GPUs. (3) We optimize the overall GPU performance by leveraging the state-of-the-art CUDA APIs such as Cooperative Groups. (4) We evaluate our Huffman encoder thoroughly using six real-world application datasets on two advanced GPUs and compare with our implemented multi-threaded Huffman encoder. Experiments show that our solution can improve the encoding throughput by up to 5.0x and 6.8x on NVIDIA RTX 5000 and V100, respectively, over the state-of-the-art GPU Huffman encoder, and by up to 3.3x over the multi-thread encoder on two 28-core Xeon Platinum 8280 CPUs.
Revisiting Huffman Coding: Toward Extreme Performance on Modern GPU Architectures
Today's high-performance computing (HPC) applications are producing vast volumes of data, which are challenging to store and transfer efficiently during the execution, such that data compression is becoming a critical technique to mitigate the storage burden and data movement cost. Huffman coding is arguably the most efficient Entropy coding algorithm in information theory, such that it could be found as a fundamental step in many modern compression algorithms such as DEFLATE. On the other hand, today's HPC applications are more and more relying on the accelerators such as GPU on supercomputers, while Huffman encoding suffers from low throughput on GPUs, resulting in a significant bottleneck in the entire data processing. In this paper, we propose and implement an efficient Huffman encoding approach based on modern GPU architectures, which addresses two key challenges: (1) how to parallelize the entire Huffman encoding algorithm, including codebook construction, and (2) how to fully utilize the high memory-bandwidth feature of modern GPU architectures. The detailed contribution is fourfold. (1) We develop an efficient parallel codebook construction on GPUs that scales effectively with the number of input symbols. (2) We propose a novel reduction based encoding scheme that can efficiently merge the codewords on GPUs. (3) We optimize the overall GPU performance by leveraging the state-of-the-art CUDA APIs such as Cooperative Groups. (4) We evaluate our Huffman encoder thoroughly using six real-world application datasets on two advanced GPUs and compare with our implemented multithreaded Huffman encoder. Experiments show that our solution can improve the encoding throughput by up to 5.0× and 6.8× on NVIDIA RTX 5000 and V100, respectively, over the state-of-the-art GPU Huffman encoder, and by up to 3.3× over the multithread encoder on two 28-core Xeon Platinum 8280 CPUs.
Thermodynamics of signal transduction systems and fluctuation theorem in a signal cascade
Biochemical chain reactions are signal transduction cascades that can transmit biological information about the intracellular environment. In this study, we modelled a chain reaction as a code string for applying information theory. Herein, we assumed that cell signal transduction selects a strategy to maximize the transduced signal per signal event duration. To investigate the same, we calculated the information transmission capacity of the reaction chain by maximizing the average entropy production rate per reaction time, indicating the idea of the entropy coding method. Moreover, we defined a signal cascade trajectory. Subsequently, we found that the logarithm of the forward and reverse transition ratio per reaction time is equal to the entropy production rate, which derives the form of the fluctuation theorem in signal transduction. Our findings suggest the application of information entropy theory for analysing signal transduction.
Kullback–Leibler Divergence of an Open-Queuing Network of a Cell-Signal-Transduction Cascade
Queuing networks (QNs) are essential models in operations research, with applications in cloud computing and healthcare systems. However, few studies have analyzed the cell’s biological signal transduction using QN theory. This study entailed the modeling of signal transduction as an open Jackson’s QN (JQN) to theoretically determine cell signal transduction, under the assumption that the signal mediator queues in the cytoplasm, and the mediator is exchanged from one signaling molecule to another through interactions between the signaling molecules. Each signaling molecule was regarded as a network node in the JQN. The JQN Kullback–Leibler divergence (KLD) was defined using the ratio of the queuing time (λ) to the exchange time (μ), λ/μ. The mitogen-activated protein kinase (MAPK) signal-cascade model was applied, and the KLD rate per signal-transduction-period was shown to be conserved when the KLD was maximized. Our experimental study on MAPK cascade supported this conclusion. This result is similar to the entropy-rate conservation of chemical kinetics and entropy coding reported in our previous studies. Thus, JQN can be used as a novel framework to analyze signal transduction.
Quantum error correction in the black hole interior
We study the quantum error correction properties of the black hole interior in a toy model for an evaporating black hole: Jackiw-Teitelboim gravity entangled with a non-gravitational bath. After the Page time, the black hole interior degrees of freedom in this system are encoded in the bath Hilbert space. We use the gravitational path integral to show that the interior density matrix is correctable against the action of quantum operations on the bath which (i) do not have prior access to details of the black hole microstates, and (ii) do not have a large, negative coherent information with respect to the maximally mixed state on the bath, with the lower bound controlled by the black hole entropy and code subspace dimension. Thus, the encoding of the black hole interior in the radiation is robust against generic, low-rank quantum operations. For erasure errors, gravity comes within an O (1) distance of saturating the Singleton bound on the tolerance of error correcting codes. For typical errors in the bath to corrupt the interior, they must have a rank that is a large multiple of the bath Hilbert space dimension, with the precise coefficient set by the black hole entropy and code subspace dimension.
Impact of Misclassification Rates on Compression Efficiency of Red Blood Cell Images of Malaria Infection Using Deep Learning
Malaria is a severe public health problem worldwide, with some developing countries being most affected. Reliable remote diagnosis of malaria infection will benefit from efficient compression of high-resolution microscopic images. This paper addresses a lossless compression of malaria-infected red blood cell images using deep learning. Specifically, we investigate a practical approach where images are first classified before being compressed using stacked autoencoders. We provide probabilistic analysis on the impact of misclassification rates on compression performance in terms of the information-theoretic measure of entropy. We then use malaria infection image datasets to evaluate the relations between misclassification rates and actually obtainable compressed bit rates using Golomb–Rice codes. Simulation results show that the joint pattern classification/compression method provides more efficient compression than several mainstream lossless compression techniques, such as JPEG2000, JPEG-LS, CALIC, and WebP, by exploiting common features extracted by deep learning on large datasets. This study provides new insight into the interplay between classification accuracy and compression bitrates. The proposed compression method can find useful telemedicine applications where efficient storage and rapid transfer of large image datasets is desirable.
Utilizing Amino Acid Composition and Entropy of Potential Open Reading Frames to Identify Protein-Coding Genes
One of the main steps in gene-finding in prokaryotes is determining which open reading frames encode for a protein, and which occur by chance alone. There are many different methods to differentiate the two; the most prevalent approach is using shared homology with a database of known genes. This method presents many pitfalls, most notably the catch that you only find genes that you have seen before. The four most popular prokaryotic gene-prediction programs (GeneMark, Glimmer, Prodigal, Phanotate) all use a protein-coding training model to predict protein-coding genes, with the latter three allowing for the training model to be created ab initio from the input genome. Different methods are available for creating the training model, and to increase the accuracy of such tools, we present here GOODORFS, a method for identifying protein-coding genes within a set of all possible open reading frames (ORFS). Our workflow begins with taking the amino acid frequencies of each ORF, calculating an entropy density profile (EDP), using KMeans to cluster the EDPs, and then selecting the cluster with the lowest variation as the coding ORFs. To test the efficacy of our method, we ran GOODORFS on 14,179 annotated phage genomes, and compared our results to the initial training-set creation step of four other similar methods (Glimmer, MED2, PHANOTATE, Prodigal). We found that GOODORFS was the most accurate (0.94) and had the best F1-score (0.85), while Glimmer had the highest precision (0.92) and PHANOTATE had the highest recall (0.96).
Entanglement wedge reconstruction and the information paradox
When absorbing boundary conditions are used to evaporate a black hole in AdS/CFT, we show that there is a phase transition in the location of the quantum Ryu-Takayanagi surface, at precisely the Page time. The new RT surface lies slightly inside the event horizon, at an infalling time approximately the scrambling time β/2 π logS BH into the past. We can immediately derive the Page curve, using the Ryu-Takayanagi formula, and the Hayden-Preskill decoding criterion, using entanglement wedge reconstruction. Because part of the interior is now encoded in the early Hawking radiation, the decreasing entanglement entropy of the black hole is exactly consistent with the semiclassical bulk entanglement of the late-time Hawking modes, despite the absence of a firewall.By studying the entanglement wedge of highly mixed states, we can understand the state dependence of the interior reconstructions. A crucial role is played by the existence of tiny, non-perturbative errors in entanglement wedge reconstruction. Directly after the Page time, interior operators can only be reconstructed from the Hawking radiation if the initial state of the black hole is known. As the black hole continues to evaporate, reconstructions become possible that simultaneously work for a large class of initial states. Using similar techniques, we generalise Hayden-Preskill to show how the amount of Hawking radiation required to reconstruct a large diary, thrown into the black hole, depends on both the energy and the entropy of the diary. Finally we argue that, before the evaporation begins, a single, state-independent interior reconstruction exists for any code space of microstates with entropy strictly less than the Bekenstein-Hawking entropy, and show that this is sufficient state dependence to avoid the AMPSS typical-state firewall paradox.
Channel capacity: limitation of entropy rate during cell signal transduction
Cellular signal transduction is mediated through chain activation reactions involving signalling molecules. Information thermodynamics may be a promising approach for quantifying signal transduction. A cell signal is transduced through the signal molecule activation as a step of a signal transduction cascade. In each step, two types of entropy can be defined. First, the signal transduction was defined using thermodynamic entropy production during the chemical activation of signal molecules. Second, the chronology was described as a code string, and the logarithm of the number of signal code strings corresponded to the information entropy. Finally, the total entropy during signal transduction was determined by summing the two entropies. When maximising the total entropy, the total entropy rate per signalling molecule concentration was found to be consistent independently of each transduction step (i.e., signal molecule types). Consequently, the speed limit of the entropy rate can be calculated, providing the capacity, which is an essential property of the signal transduction cascade. The theory introduced here is expected to provide a basic framework for understanding new methods of discovering signal cascades and intracellular signal transduction.
A fault-tolerant neutral-atom architecture for universal quantum computation
Quantum error correction (QEC) is essential for the realization of large-scale quantum computers. However, owing to the complexity of operating on the encoded ‘logical’ qubits, understanding the physical principles for building fault-tolerant quantum devices and combining them into efficient architectures is an outstanding scientific challenge. Here we use reconfigurable arrays of up to 448 neutral atoms to implement the key elements of a universal, fault-tolerant quantum processing architecture and experimentally explore their underlying working mechanisms. We first use surface codes to study how repeated QEC suppresses errors, demonstrating 2.14(13)x below-threshold performance in a four-round characterization circuit by leveraging atom loss detection and machine learning decoding. We then investigate logical entanglement using transversal gates and lattice surgery and extend it to universal logic through transversal teleportation with three-dimensional [[15,1,3]] codes, enabling arbitrary-angle synthesis with polylogarithmic overhead. Finally, we develop mid-circuit qubit reuse16, increasing experimental cycle rates by two orders of magnitude and enabling deep-circuit protocols with dozens of logical qubits and hundreds of logical teleportations with [[7,1,3]] and high-rate [[16,6,4]] codes while maintaining constant internal entropy. Our experiments show key principles for efficient architecture design, involving the interplay between quantum logic and entropy removal, judiciously using physical entanglement in logic gates and magic state generation, and leveraging teleportations for universality and physical qubit reset. These results establish foundations for scalable, universal error-corrected processing and its practical implementation in neutral atom systems.
Simulation of the NaGd(MoO{sub 4}){sub 2}–NaEu(MoO{sub 4}){sub 2} and Na{sub 2}Gd{sub 4}(MoO{sub 4}){sub 7}–Na{sub 2}Eu{sub 4}(MoO{sub 4}){sub 7} Solid Solutions by the Interatomic Potential Method
Simulation of the solid solutions in the system of double sodium–gadolinium and sodium–europium molybdates, which are promising matrices for solid state lasers and phosphors has been carried out by the method of interatomic potentials. Two types of solid solutions have been studied, one of which contains finite components corresponding to the stoichiometric NaGd(MoO{sub 4}){sub 2}–NaEu(MoO{sub 4}){sub 2} compositions with statistical distribution of cations in the crystal lattice. Another object is a cation-deficient Na{sub 2}Gd{sub 4}(MoO{sub 4}){sub 7}–Na{sub 2}Eu{sub 4}(MoO{sub 4}){sub 7} system, in which we have examined the variants of statistical distribution and partial ordering of cations over structural positions. Atomistic simulation has been performed using the GULP 4.0.1 software package (General Utility Lattice Program). It is shown that when we pass from sodium-gadolinium molybdate to sodium-europium molybdate, both of stoichiometric and cation-deficient compositions, an increase in the unit cell volume is observed, while the density of the crystal, the energy of interatomic interactions in the structure, the vibrational entropy and the heat capacity decrease along with increasing europium content. The energy of interatomic interactions in the structure for cation-deficient solid solutions is less than for stoichiometric ones. Other aforementioned characteristics for cation-deficient solid solutions have greater values than for stoichiometric ones. The role of cluster europium centers in concentration quenching in NaGd(MoO{sub 4}){sub 2}–NaEu(MoO{sub 4}){sub 2} solid solutions has been examined.
Entanglement spectra of stabilizer codes: A window into gapped quantum phases of matter
The entanglement spectrum (ES) provides a barometer of quantum entanglement and encodes physical information beyond that contained in the entanglement entropy. In this paper, we explore the ES of stabilizer codes, which furnish exactly solvable models for a plethora of gapped quantum phases of matter. Studying the ES for stabilizer Hamiltonians in the presence of arbitrary weak local perturbations thus allows us to develop a general framework within which the entanglement features of gapped topological phases can be computed and contrasted. In particular, we study models harboring fracton order, both type-I and type-II, and compare the resulting ES with that of both conventional topological order and of (strong) subsystem symmetry protected topological (SSPT) states. We find that nonlocal surface stabilizers (NLSS), a set of symmetries of the Hamiltonian which form on the boundary of the entanglement cut, act as purveyors of universal nonlocal features appearing in the entanglement spectrum. While in conventional topological orders and fracton orders, the NLSS retain a form of topological invariance with respect to the entanglement cut, subsystem symmetric systems—fracton and SSPT phases—additionally show a nontrivial geometric dependence on the entanglement cut, corresponding to the subsystem symmetry. This sheds further light on the interplay between geometric and topological effects in fracton phases of matter and demonstrates that strong SSPT phases harbour a measure of quasilocal entanglement beyond that encountered in conventional SPT phases. Here, we further show that a version of the edge-entanglement correspondence, established earlier for gapped two-dimensional topological phases, also holds for gapped three-dimensional fracton models.
QUESTS: Quick Uncertainty and Entropy from STructural Similarity
QUESTS provides a strategy to quantify the uncertainty and the information content (entropy) of datasets of atomistic simulations. The code implements the calculation of a descriptor, compares information contents of datasets, verifies whether given structures are contained in specific datasets, and more. This code base enables better design of training sets for machine learning force fields as well as understanding some thermodynamic properties of materials.
Codebase release r1.1 for SmoQyDEAC.jl
We introduce the SmoQyDEAC.jl package, a Julia implementation of the Differential Evolution Analytic Continuation (DEAC) algorithm [N. S. Nichols et al., Phys. Rev. E 106, 025312 (2022)] for analytically continuing noisy imaginary time correlation functions to the real frequency axis. Our implementation supports fermionic and bosonic correlation functions on either the imaginary time or Matsubara frequency axes, and treatment of the covariance error in the input data. This paper presents an overview of the DEAC algorithm and the features implemented in the SmoQyDEAC.jl package. It also provides detailed benchmarks of the package’s output against the popular maximum entropy and stochastic analytic continuation methods. The code for this package can be downloaded from our GitHub repository at https://github.com/SmoQySuite/SmoQyDEAC.jl or installed using the Julia package manager. The online documentation, including examples, can be accessed at https://smoqysuite.github.io/SmoQyDEAC.jl/stable/.
High-throughput ion irradiation of additively manufactured compositionally complex alloys
Several advanced nuclear reactor designs promise efficiency and safety improvements over the current reactor fleet but are limited by the current set of ASME code-qualified materials. Novel alloys including high-entropy alloys (HEAs), and more broadly compositionally complex alloys (CCAs), have shown promising irradiation-tolerance. However, the vast range of alloy compositions adds to an already time-consuming alloy development process. In this study, to accelerate the development of novel alloys for nuclear applications, a high-throughput (HTP) methodology has been employed. Additive manufacturing has been used to produce a compositional array of unary, binary, ternary, and quaternary alloys, including several CCAs, which span the Cr-Fe-Mn-Ni composition space. Additionally, the compositional array was homogenized at 1000°C for 24 hours and each sample was irradiated using 4-MeV Ni2+ ions at room temperature to a peak damage of 50 dpa, as estimated using SRIM, at the University of Wisconsin Ion Beam Laboratory. A custom XY stage was built to accommodate the large compositional array and half of each sample was masked during irradiation enabling both the irradiated and unirradiated properties of each alloy to be characterized side-by-side. Each alloy was characterized using X-ray fluorescence (XRF), X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), and nanoindentation. CALPHAD simulations spanning the entire Cr-Fe-Mn-Ni composition space at 1000°C were performed to compare predicted equilibrium phases with phases identified experimentally from the unirradiated regions of each alloy. Nanoindentation measurements indicate radiation-induced hardening ranging from ~1-1.5 GPa in each of Cr-Fe-Mn-Ni CCAs, which is relatively insensitive to modest changes in alloy composition and comparable to hardening observed in neutron irradiated Cr-Fe-Mn-Ni CCAs in the literature. Overall, a substantial time savings was realized by employing HTP synthesis, irradiation, and characterization in this study compared to conventional techniques, the implications of which are discussed.