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Deeply virtual exclusive scattering processes (DVES) serve as precise probes of nucleon quark and gluon distributions in coordinate space. These distributions are derived from generalized parton distributions (GPDs) via Fourier transform relative to proton momentum transfer. QCD factorization theorems enable DVES to be parameterized by Compton form factors (CFFs), which are convolutions of GPDs with perturbatively calculable kernels. Accurate extraction of CFFs from DVCS, benefiting from interference with the Bethe-Heitler (BH) process and a simpler final state structure, is essential for inferring GPDs. This paper focuses on extracting CFFs from DVCS data using a variational autoencoder inverse mapper (VAIM) and its constrained variant (C-VAIM). VAIM is shown to be consistent with Markov Chain Monte Carlo (MCMC) methods in extracting multiple CFF solutions for given kinematics, while C-VAIM effectively captures correlations among CFFs across different kinematic values, providing more constrained solutions. This study represents a crucial first step towards a comprehensive analysis pipeline towards the extraction of GPDs., Comment: 12 pages, 9 figures

In overview of the recent activity of the newly funded EXCLusives with AI and Machine learning (EXCLAIM) collaboration is presented. The main goal of the collaboration is to develop a framework to implement AI and machine learning techniques in problems emerging from the phenomenology of high energy exclusive scattering processes from nucleons and nuclei, maximizing the information that can be extracted from various sets of experimental data, while implementing theoretical constraints from lattice QCD. A specific perspective embraced by EXCLAIM is to use the methods of theoretical physics to understand the working of ML, beyond its standardized applications to physics analyses which most often rely on industrially provided tools, in an automated way., Comment: 9 pages, 3 figures

Complex networks, which are the abstractions of many real-world systems, present a persistent challenge across disciplines for people to decipher their underlying information. Recently, hyperbolic geometry of latent spaces has gained traction in network analysis, due to its ability to preserve certain local intrinsic properties of the nodes. In this study, we explore the problem from a much broader perspective: understanding the impact of nodes' global topological structures on latent space placements. Our investigations reveal a direct correlation between the topological structure of nodes and their positioning within the latent space. Building on this deep and strong connection between node distance and network topology, we propose a novel embedding framework called Topology-encoded Latent Hyperbolic Geometry (TopoLa) for analyzing complex networks. With the encoded topological information in the latent space, TopoLa is capable of enhancing both conventional and low-rank networks, using the singular value gap to clarify the mathematical principles behind this enhancement. Meanwhile, we show that the equipped TopoLa distance can also help augment pivotal deep learning models encompassing knowledge distillation and contrastive learning., Comment: 85 pages, 17 figures

We develop a new methodology for extracting Compton form factors (CFFs) in from deeply virtual exclusive reactions such as the unpolarized DVCS cross section using a specialized inverse problem solver, a variational autoencoder inverse mapper (VAIM). The VAIM-CFF framework not only allows us access to a fitted solution set possibly containing multiple solutions in the extraction of all 8 CFFs from a single cross section measurement, but also accesses the lost information contained in the forward mapping from CFFs to cross section. We investigate various assumptions and their effects on the predicted CFFs such as cross section organization, number of extracted CFFs, use of uncertainty quantification technique, and inclusion of prior physics information. We then use dimensionality reduction techniques such as principal component analysis to visualize the missing physics information tracked in the latent space of the VAIM framework. Through re-framing the extraction of CFFs as an inverse problem, we gain access to fundamental properties of the problem not comprehensible in standard fitting methodologies: exploring the limits of the information encoded in deeply virtual exclusive experiments., Comment: 17 pages, 15 figures

Autonomous virtual agents are often limited by their singular mode of interaction with real-world environments, restricting their versatility. To address this, we propose the Multi-Modal Agent Collaboration framework (MMAC-Copilot), a framework utilizes the collective expertise of diverse agents to enhance interaction ability with operating systems. The framework introduces a team collaboration chain, enabling each participating agent to contribute insights based on their specific domain knowledge, effectively reducing the hallucination associated with knowledge domain gaps. To evaluate the performance of MMAC-Copilot, we conducted experiments using both the GAIA benchmark and our newly introduced Visual Interaction Benchmark (VIBench). VIBench focuses on non-API-interactable applications across various domains, including 3D gaming, recreation, and office scenarios. MMAC-Copilot achieved exceptional performance on GAIA, with an average improvement of 6.8\% over existing leading systems. Furthermore, it demonstrated remarkable capability on VIBench, particularly in managing various methods of interaction within systems and applications. These results underscore MMAC-Copilot's potential in advancing the field of autonomous virtual agents through its innovative approach to agent collaboration., Comment: In processing

Human leukocyte antigen (HLA) is an important molecule family in the field of human immunity, which recognizes foreign threats and triggers immune responses by presenting peptides to T cells. In recent years, the synthesis of tumor vaccines to induce specific immune responses has become the forefront of cancer treatment. Computationally modeling the binding patterns between peptide and HLA can greatly accelerate the development of tumor vaccines. However, most of the prediction methods performance is very limited and they cannot fully take advantage of the analysis of existing biological knowledge as the basis of modeling. In this paper, we propose TripHLApan, a novel pan-specific prediction model, for HLA molecular peptide binding prediction. TripHLApan exhibits powerful prediction ability by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. The comprehensive evaluations demonstrate the effectiveness of TripHLApan in predicting HLA-I and HLA-II peptide binding in different test environments. The predictive power of HLA-I is further demonstrated in the latest data set. In addition, we show that TripHLApan has strong binding reconstitution ability in the samples of a melanoma patient. In conclusion, TripHLApan is a powerful tool for predicting the binding of HLA-I and HLA-II molecular peptides for the synthesis of tumor vaccines., Comment: 25 pages, 7 figures

We develop a framework to establish benchmarks for machine learning and deep neural networks analyses of exclusive scattering cross sections (FemtoNet). Within this framework we present an extraction of Compton form factors for deeply virtual Compton scattering from an unpolarized proton target. Critical to this effort is a study of the effects of physics constraint built into machine learning (ML) algorithms. We use the Bethe-Heitler process, which is the QED radiative background to deeply virtual Compton scattering, to test our ML models and, in particular, their ability to generalize information extracted from data. We then use these techniques on the full cross section and compare the results to analytic model calculations. We propose a quantification technique, the random targets method, to begin understanding the separation of aleatoric and epistemic uncertainties as they are manifest in exclusive scattering analyses. We propose a set of both physics driven and machine learning based benchmarks providing a stepping stone towards applying explainable machine learning techniques with controllable uncertainties in a wide range of deeply virtual exclusive processes., Comment: 16 pages, 12 figures

Event generators in high-energy nuclear and particle physics play an important role in facilitating studies of particle reactions. We survey the state-of-the-art of machine learning (ML) efforts at building physics event generators. We review ML generative models used in ML-based event generators and their specific challenges, and discuss various approaches of incorporating physics into the ML model designs to overcome these challenges. Finally, we explore some open questions related to super-resolution, fidelity, and extrapolation for physics event generation based on ML technology., Comment: 8 pages, 2 figures, paper accepted for publication in IJCAI2021

We apply generative adversarial network (GAN) technology to build an event generator that simulates particle production in electron-proton scattering that is free of theoretical assumptions about underlying particle dynamics. The difficulty of efficiently training a GAN event simulator lies in learning the complicated patterns of the distributions of the particles physical properties. We develop a GAN that selects a set of transformed features from particle momenta that can be generated easily by the generator, and uses these to produce a set of augmented features that improve the sensitivity of the discriminator. The new Feature-Augmented and Transformed GAN (FAT-GAN) is able to faithfully reproduce the distribution of final state electron momenta in inclusive electron scattering, without the need for input derived from domain-based theoretical assumptions. The developed technology can play a significant role in boosting the science of existing and future accelerator facilities, such as the Electron-Ion Collider., Comment: 7 pages, 5 figures, expanded author list, paper accepted in IJCAI21

Matrix completion is a widely used technique for image inpainting and personalized recommender system, etc. In this work, we focus on accelerating the matrix completion using faster randomized singular value decomposition (rSVD). Firstly, two fast randomized algorithms (rSVD-PI and rSVD- BKI) are proposed for handling sparse matrix. They make use of an eigSVD procedure and several accelerating skills. Then, with the rSVD-BKI algorithm and a new subspace recycling technique, we accelerate the singular value thresholding (SVT) method in [1] to realize faster matrix completion. Experiments show that the proposed rSVD algorithms can be 6X faster than the basic rSVD algorithm [2] while keeping same accuracy. For image inpainting and movie-rating estimation problems, the proposed accelerated SVT algorithm consumes 15X and 8X less CPU time than the methods using svds and lansvd respectively, without loss of accuracy., Comment: 8 pages, 5 figures, ICTAI 2018 Accepted

In this article, we consider the general problem of checking the correctness of matrix multiplication. Given three $n \times n$ matrices $A$, $B$, and $C$, the goal is to verify that $A \times B=C$ without carrying out the computationally costly operations of matrix multiplication and comparing the product $A \times B$ with $C$, term by term. This is especially important when some or all of these matrices are very large, and when the computing environment is prone to soft errors. Here we extend Freivalds' algorithm to a Gaussian Variant of Freivalds' Algorithm (GVFA) by projecting the product $A \times B$ as well as $C$ onto a Gaussian random vector and then comparing the resulting vectors. The computational complexity of GVFA is consistent with that of Freivalds' algorithm, which is $O(n^{2})$. However, unlike Freivalds' algorithm, whose probability of a false positive is $2^{-k}$, where $k$ is the number of iterations. Our theoretical analysis shows that when $A \times B \neq C$, GVFA produces a false positive on set of inputs of measure zero with exact arithmetic. When we introduce round-off error and floating point arithmetic into our analysis, we can show that the larger this error, the higher the probability that GVFA avoids false positives. Moreover, by iterating GVFA $k$ times, the probability of a false positive decreases as $p^k$, where $p$ is a very small value depending on the nature of the fault on the result matrix and the arithmetic system's floating-point precision. Unlike deterministic algorithms, there do not exist any fault patterns that are completely undetectable with GVFA. Thus GVFA can be used to provide efficient fault tolerance in numerical linear algebra, and it can be efficiently implemented on modern computing architectures. In particular, GVFA can be very efficiently implemented on architectures with hardware support for fused multiply-add operations.

Principal component analysis (PCA) is a fundamental dimension reduction tool in statistics and machine learning. For large and high-dimensional data, computing the PCA (i.e., the singular vectors corresponding to a number of dominant singular values of the data matrix) becomes a challenging task. In this work, a single-pass randomized algorithm is proposed to compute PCA with only one pass over the data. It is suitable for processing extremely large and high-dimensional data stored in slow memory (hard disk) or the data generated in a streaming fashion. Experiments with synthetic and real data validate the algorithm's accuracy, which has orders of magnitude smaller error than an existing single-pass algorithm. For a set of high-dimensional data stored as a 150 GB file, the proposed algorithm is able to compute the first 50 principal components in just 24 minutes on a typical 24-core computer, with less than 1 GB memory cost., Comment: IJCAI 2017, 16 pages, 6 figures

In this paper, we present a fast implementation of the Singular Value Thresholding (SVT) algorithm for matrix completion. A rank-revealing randomized singular value decomposition (R3SVD) algorithm is used to adaptively carry out partial singular value decomposition (SVD) to fast approximate the SVT operator given a desired, fixed precision. We extend the R3SVD algorithm to a recycling rank revealing randomized singular value decomposition (R4SVD) algorithm by reusing the left singular vectors obtained from the previous iteration as the approximate basis in the current iteration, where the computational cost for partial SVD at each SVT iteration is significantly reduced. A simulated annealing style cooling mechanism is employed to adaptively adjust the low-rank approximation precision threshold as SVT progresses. Our fast SVT implementation is effective in both large and small matrices, which is demonstrated in matrix completion applications including image recovery and movie recommendation system.

In this paper, we revisit the generalized block power methods for approximating the eigenvector associated with $\lambda_1 = 1$ of a Markov chain transition matrix. Our analysis of the block power method shows that when $s$ linearly independent probability vectors are used as the initial block, the convergence of the block power method to the stationary distribution depends on the magnitude of the $(s+1)$th dominant eigenvalue $\lambda_{s+1}$ of $P$ instead of that of $\lambda_2$ in the power method. Therefore, the block power method with block size $s$ is particularly effective for transition matrices where $|\lambda_{s+1}|$ is well separated from $\lambda_1 = 1$ but $|\lambda_2|$ is not. This approach is particularly useful when visiting the elements of a large transition matrix is the main computational bottleneck over matrix--vector multiplications, where the block power method can effectively reduce the total number of times to pass over the matrix. To further reduce the overall computational cost, we combine the block power method with a sliding window scheme, taking advantage of the subsequent vectors of the latest $s$ iterations to assemble the block matrix. The sliding window scheme correlates vectors in the sliding window to quickly remove the influences from the eigenvalues whose magnitudes are smaller than $|\lambda_{s}|$ to reduce the overall number of matrix--vector multiplications to reach convergence. Finally, we compare the effectiveness of these methods in a Markov chain model representing a stochastic luminal calcium release site.

Randomized algorithms for low-rank matrix approximation are investigated, with the emphasis on the fixed-precision problem and computational efficiency for handling large matrices. The algorithms are based on the so-called QB factorization, where Q is an orthonormal matrix. Firstly, a mechanism for calculating the approximation error in Frobenius norm is proposed, which enables efficient adaptive rank determination for large and/or sparse matrix. It can be combined with any QB-form factorization algorithm in which B's rows are incrementally generated. Based on the blocked randQB algorithm by P.-G. Martinsson and S. Voronin, this results in an algorithm called randQB EI. Then, we further revise the algorithm to obtain a pass-efficient algorithm, randQB FP, which is mathematically equivalent to the existing randQB algorithms and also suitable for the fixed-precision problem. Especially, randQB FP can serve as a single-pass algorithm for calculating leading singular values, under certain condition. With large and/or sparse test matrices, we have empirically validated the merits of the proposed techniques, which exhibit remarkable speedup and memory saving over the blocked randQB algorithm. We have also demonstrated that the single-pass algorithm derived by randQB FP is much more accurate than an existing single-pass algorithm. And with data from a scenic image and an information retrieval application, we have shown the advantages of the proposed algorithms over the adaptive range finder algorithm for solving the fixed-precision problem., Comment: 21 pages, 10 figures

In this paper, we present a Rank Revealing Randomized Singular Value Decomposition (R3SVD) algorithm to incrementally construct a low-rank approximation of a potentially large matrix while adaptively estimating the appropriate rank that can capture most of the actions of the matrix. Starting from a low-rank approximation with an initial guessed rank, R3SVD adopts an orthogonal Gaussian sampling approach to obtain the dominant subspace within the leftover space, which is used to add up to the existing low-rank approximation. Orthogonal Gaussian sampling is repeated until an appropriate low-rank approximation with satisfactory accuracy, measured by the overall energy percentage of the original matrix, is obtained. While being a fast algorithm, R3SVD is also a memory-aware algorithm where the computational process can be decomposed into a series of sampling tasks that use constant amount of memory. Numerical examples in image compression and matrix completion are used to demonstrate the effectiveness of R3SVD in low-rank approximation.

In this work we present an efficient implementation of Canonical Monte Carlo simulation for Coulomb many body systems on graphics processing units (GPU). Our method takes advantage of the GPU Single Instruction, Multiple Data (SIMD) architectures. It adopts the sequential updating scheme of Metropolis algorithm, and makes no approximation in the computation of energy. It reaches a remarkable 440-fold speedup, compared with the serial implementation on CPU. We use this method to simulate primitive model electrolytes. We measure very precisely all ion-ion pair correlation functions at high concentrations, and extract renormalized Debye length, renormalized valences of constituent ions, and renormalized dielectric constants. These results demonstrate unequivocally physics beyond the classical Poisson-Boltzmann theory.