arXiv subjects

Cheng

Publications and source records attributed to Cheng.

9 recordsLinked to original sources

arXiv2026

TorchGWAS : GPU-accelerated GWAS for thousands of quantitative phenotypes

Motivation: Modern bioinformatics workflows, particularly in imaging and representation learning, can generate thousands to tens of thousands of quantitative phenotypes from a single cohort. In such settings, running genome-wide association analyses trait by trait rapidly becomes a computational bottleneck. While established GWAS tools are highly effective for individual traits, they are not optimized for phenotype-rich screening workflows in which the same genotype matrix is reused across a large phenotype panel. Results: We present TorchGWAS, a framework for high-throughput association testing of large phenotype panels through hardware acceleration. The current public release provides stable Python and command-line workflows for linear GWAS and multivariate phenotype screening, supports NumPy, PLINK, and BGEN genotype inputs, aligns phenotype and covariate tables by sample identifier, and performs covariate adjustment internally. In a benchmark with 8.9 million markers and 23,000 samples, fastGWA required approximately 100 second per phenotype on an AMD EPYC 7763 64-core CPU, whereas TorchGWAS completed 2,048 phenotypes in 10 minute and 20,480 phenotypes in 20 minutes on a single NVIDIA A100 GPU, corresponding to an approximately 300- to 1700-fold increase in phenotype throughput. TorchGWAS therefore makes large-scale GWAS screening practical in phenotype-rich settings where thousands of quantitative traits must be evaluated efficiently. Availability and implementation: TorchGWAS is implemented in Python and distributed as a documented source repository at https://github.com/ZhiGroup/TorchGWAS. The current release provides a command-line interface, packaged source code, tutorials, benchmark scripts, and example workflows.

cs.DC↗

arXiv2026

Generation of Multivariate Discrete Data with Generalized Poisson, Negative Binomial and Binomial Marginal Distributions

The analysis of multivariate discrete data is crucial in various scientific research areas, such as epidemiology, the social sciences, genomics, and environmental studies. As the availability of such data increases, developing robust analytical and data generation tools is necessary to understand the relationships among variables. This paper builds upon previous work on data generation frameworks for multivariate ordinal data with a prespecified correlation matrix. The proposed algorithm generates multivariate discrete data from marginal distributions that follow the generalized Poisson, negative binomial, and binomial distributions. A step-by-step algorithm is provided, and its performance is illustrated in four simulated data scenarios and three real-data scenarios. This technique has the potential to be applied in a wide range of settings involving the generation of correlated discrete data.

stat.ME↗

arXiv2025

Concept-Driven Deep Learning for Enhanced Protein-Specific Molecular Generation

In recent years, deep learning techniques have made significant strides in molecular generation for specific targets, driving advancements in drug discovery. However, existing molecular generation methods present significant limitations: those operating at the atomic level often lack synthetic feasibility, drug-likeness, and interpretability, while fragment-based approaches frequently overlook comprehensive factors that influence protein-molecule interactions. To address these challenges, we propose a novel fragment-based molecular generation framework tailored for specific proteins. Our method begins by constructing a protein subpocket and molecular arm concept-based neural network, which systematically integrates interaction force information and geometric complementarity to sample molecular arms for specific protein subpockets. Subsequently, we introduce a diffusion model to generate molecular backbones that connect these arms, ensuring structural integrity and chemical diversity. Our approach significantly improves synthetic feasibility and binding affinity, with a 4% increase in drug-likeness and a 6% improvement in synthetic feasibility. Furthermore, by integrating explicit interaction data through a concept-based model, our framework enhances interpretability, offering valuable insights into the molecular design process.

cs.LG↗

arXiv2025

Transforming Indoor Localization: Advanced Transformer Architecture for NLOS Dominated Wireless Environments with Distributed Sensors

Indoor localization in challenging non-line-of-sight (NLOS) environments often leads to poor accuracy with traditional approaches. Deep learning (DL) has been applied to tackle these challenges; however, many DL approaches overlook computational complexity, especially for floating-point operations (FLOPs), making them unsuitable for resource-limited devices. Transformer-based models have achieved remarkable success in natural language processing (NLP) and computer vision (CV) tasks, motivating their use in wireless applications. However, their use in indoor localization remains nascent, and directly applying Transformers for indoor localization can be both computationally intensive and exhibit limitations in accuracy. To address these challenges, in this work, we introduce a novel tokenization approach, referred to as Sensor Snapshot Tokenization (SST), which preserves variable-specific representations of power delay profile (PDP) and enhances attention mechanisms by effectively capturing multi-variate correlation. Complementing this, we propose a lightweight Swish-Gated Linear Unit-based Transformer (L-SwiGLU-T) model, designed to reduce computational complexity without compromising localization accuracy. Together, these contributions mitigate the computational burden and dependency on large datasets, making Transformer models more efficient and suitable for resource-constrained scenarios. Experimental results on simulated and real-world datasets demonstrate that SST and L-SwiGLU-T achieve substantial accuracy and efficiency gains, outperforming larger Transformer and CNN baselines by over 40% while using significantly fewer FLOPs and training samples.

cs.LG↗

arXiv2024

Reinforcement Learning for LLM Post-Training: A Survey

Large language models (LLMs) trained via pretraining and supervised fine-tuning (SFT) can still produce harmful and misaligned outputs, or struggle in domains like math and coding. Reinforcement learning (RL)-based post-training methods, including Reinforcement Learning from Human Feedback (RLHF) methods like Direct Preference Optimization (DPO) and Reinforcement Learning with Verifiable Rewards (RLVR) approaches like PPO and GRPO, have made remarkable gains to alleviate these issues. Yet, no existing work offers a technically detailed comparison of the various methods driving this progress. In order to fill this gap, we present a timely survey that connects foundational components with latest advancements. We derive a single policy gradient framework that unifies pretraining, SFT, RLHF, and RLVR as special cases while also organizing the more recent techniques therein. The main contributions of our survey are as follows: (1) a self-contained introduction to MLE, RLHF, and RLVR foundations and the unified policy gradient framework; (2) detailed technical analysis of PPO- and GRPO-based methods alongside offline and iterative DPO approaches, decomposed along prompt sampling, response sampling, and gradient coefficient axes; (3) standardized notation enabling direct cross-method comparison; and (4) comprehensive comparison of implementation details and empirical results of each method in the appendix. We aim to serve as a technically grounded reference for researchers and practitioners working on LLM post-training.

cs.CL↗

arXiv2024

PAFT: A Parallel Training Paradigm for Effective LLM Fine-Tuning

Large language models (LLMs) have shown remarkable abilities in diverse natural language processing (NLP) tasks. The LLMs generally undergo supervised fine-tuning (SFT) followed by preference alignment to be usable in downstream applications. However, this sequential training pipeline leads to alignment tax that degrades the LLM performance. This paper introduces PAFT, a new PArallel training paradigm for effective LLM Fine-Tuning, which independently performs SFT and preference alignment (e.g., DPO and ORPO, etc.) with the same pre-trained model on respective datasets. The model produced by SFT and the model from preference alignment are then merged into a final model by parameter fusing for use in downstream applications. This work reveals important findings that preference alignment like DPO naturally results in a sparse model while SFT leads to a natural dense model which needs to be sparsified for effective model merging. This paper introduces an effective interference resolution which reduces the redundancy by sparsifying the delta parameters. The LLM resulted from the new training paradigm achieved Rank #1 on the HuggingFace Open LLM Leaderboard. Comprehensive evaluation shows the effectiveness of the parallel training paradigm.

cs.CL↗

arXiv2019

One-Shot Imitation Filming of Human Motion Videos

Imitation learning has been applied to mimic the operation of a human cameraman in several autonomous cinematography systems. To imitate different filming styles, existing methods train multiple models, where each model handles a particular style and requires a significant number of training samples. As a result, existing methods can hardly generalize to unseen styles. In this paper, we propose a framework, which can imitate a filming style by "seeing" only a single demonstration video of the same style, i.e., one-shot imitation filming. This is done by two key enabling techniques: 1) feature extraction of the filming style from the demo video, and 2) filming style transfer from the demo video to the new situation. We implement the approach with deep neural network and deploy it to a 6 degrees of freedom (DOF) real drone cinematography system by first predicting the future camera motions, and then converting them to the drone's control commands via an odometer. Our experimental results on extensive datasets and showcases exhibit significant improvements in our approach over conventional baselines and our approach can successfully mimic the footage with an unseen style.

cs.CV↗

arXiv2017

REDBEE: A Visual-Inertial Drone System for Real-Time Moving Object Detection

Aerial surveillance and monitoring demand both real-time and robust motion detection from a moving camera. Most existing techniques for drones involve sending a video data streams back to a ground station with a high-end desktop computer or server. These methods share one major drawback: data transmission is subjected to considerable delay and possible corruption. Onboard computation can not only overcome the data corruption problem but also increase the range of motion. Unfortunately, due to limited weight-bearing capacity, equipping drones with computing hardware of high processing capability is not feasible. Therefore, developing a motion detection system with real-time performance and high accuracy for drones with limited computing power is highly desirable. In this paper, we propose a visual-inertial drone system for real-time motion detection, namely REDBEE, that helps overcome challenges in shooting scenes with strong parallax and dynamic background. REDBEE, which can run on the state-of-the-art commercial low-power application processor (e.g. Snapdragon Flight board used for our prototype drone), achieves real-time performance with high detection accuracy. The REDBEE system overcomes obstacles in shooting scenes with strong parallax through an inertial-aided dual-plane homography estimation; it solves the issues in shooting scenes with dynamic background by distinguishing the moving targets through a probabilistic model based on spatial, temporal, and entropy consistency. The experiments are presented which demonstrate that our system obtains greater accuracy when detecting moving targets in outdoor environments than the state-of-the-art real-time onboard detection systems.

cs.RO↗

arXiv2017

Local Feature Descriptor Learning with Adaptive Siamese Network

Although the recent progress in the deep neural network has led to the development of learnable local feature descriptors, there is no explicit answer for estimation of the necessary size of a neural network. Specifically, the local feature is represented in a low dimensional space, so the neural network should have more compact structure. The small networks required for local feature descriptor learning may be sensitive to initial conditions and learning parameters and more likely to become trapped in local minima. In order to address the above problem, we introduce an adaptive pruning Siamese Architecture based on neuron activation to learn local feature descriptors, making the network more computationally efficient with an improved recognition rate over more complex networks. Our experiments demonstrate that our learned local feature descriptors outperform the state-of-art methods in patch matching.

cs.LG↗