Yaohang Li

Meng Wang, Chuqi Lei, Jianxin Wang et al.

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.

Hao Ji, Wenjian Yu, Yaohang Li

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.

Yaohang Li, Wenjian Yu

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.

Hao Ji, Seth H. Weinberg, Yaohang Li

In this paper, we revisit the generalized block power methods for approximating the eigenvector associated with $λ_1 = 1$ 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 $λ_{s+1}$ of $P$ instead of that of $λ_2$ in the power method. Therefore, the block power method with block size $s$ is particularly effective for transition matrices where $|λ_{s+1}|$ is well separated from $λ_1 = 1$ but $|λ_2|$ 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 $|λ_{s}|$ 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.

Ivan Makohon, Mohamad Najafi, Jian Wu et al.

In the past decade a surge in the amount of electronic health record (EHR) data in the United States, attributed to a favorable policy environment created by the Health Information Technology for Economic and Clinical Health (HITECH) Act of 2009 and the 21st Century Cures Act of 2016. Clinical notes for patients' assessments, diagnoses, and treatments are captured in these EHRs in free-form text by physicians, who spend a considerable amount of time entering and editing them. Manually writing clinical notes takes a considerable amount of a doctor's valuable time, increasing the patient's waiting time and possibly delaying diagnoses. Large language models (LLMs) possess the ability to generate news articles that closely resemble human-written ones. We investigate the usage of Chain-of-Thought (CoT) prompt engineering to improve the LLM's response in clinical note generation. In our prompts, we use as input International Classification of Diseases (ICD) codes and basic patient information. We investigate a strategy that combines the traditional CoT with semantic search results to improve the quality of generated clinical notes. Additionally, we infuse a knowledge graph (KG) built from clinical ontology to further enrich the domain-specific knowledge of generated clinical notes. We test our prompting technique on six clinical cases from the CodiEsp test dataset using GPT-4 and our results show that it outperformed the clinical notes generated by standard one-shot prompts.

Ali Rayat, Yaohang Li, Gia-Wei Chern

Local gauge symmetry underlies fundamental interactions and strongly correlated quantum matter, yet existing machine-learning approaches lack a general, principled framework for learning under site-dependent symmetries, particularly for intrinsically nonlocal observables. Here we introduce a gauge-equivariant graph neural network that embeds non-Abelian symmetry directly into message passing via matrix-valued, gauge-covariant features and symmetry-compatible updates, extending equivariant learning from global to fully local symmetries. In this formulation, message passing implements gauge-covariant transport across the lattice, allowing nonlocal correlations and loop-like structures to emerge naturally from local operations. We validate the approach across pure gauge, gauge-matter, and dynamical regimes, establishing gauge-equivariant message passing as a general paradigm for learning in systems governed by local symmetry.

Zirui Song, Yaohang Li, Meng Fang et al.

Large language model agents that interact with PC applications often face limitations due to their singular mode of interaction with real-world environments, leading to restricted versatility and frequent hallucinations. 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 application. 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. We evaluate MMAC-Copilot using the GAIA benchmark and our newly introduced Visual Interaction Benchmark (VIBench). MMAC-Copilot achieved exceptional performance on GAIA, with an average improvement of 6.8\% over existing leading systems. VIBench focuses on non-API-interactable applications across various domains, including 3D gaming, recreation, and office scenarios. It also demonstrated remarkable capability on VIBench. We hope this work can inspire in this field and provide a more comprehensive assessment of Autonomous agents. The anonymous Github is available at \href{https://anonymous.4open.science/r/ComputerAgentWithVision-3C12}{Anonymous Github}

Yasir Alanazi, N. Sato, Pawel Ambrozewicz et al.

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.

Yasir Alanazi, N. Sato, Tianbo Liu et al.

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.

Xu Feng, Wenjian Yu, Yaohang Li

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.

Wenjian Yu, Yu Gu, Jian Li et al.

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.