Jiajie Li

Jiajie Li, Jan-Niklas Schmelzle, Yixiao Du et al.

Computational Pangenomics is an emerging field that studies genetic variation using a graph structure encompassing multiple genomes. Visualizing pangenome graphs is vital for understanding genome diversity. Yet, handling large graphs can be challenging due to the high computational demands of the graph layout process. In this work, we conduct a thorough performance characterization of a state-of-the-art pangenome graph layout algorithm, revealing significant data-level parallelism, which makes GPUs a promising option for compute acceleration. However, irregular data access and the algorithm's memory-bound nature present significant hurdles. To overcome these challenges, we develop a solution implementing three key optimizations: a cache-friendly data layout, coalesced random states, and warp merging. Additionally, we propose a quantitative metric for scalable evaluation of pangenome layout quality. Evaluated on 24 human whole-chromosome pangenomes, our GPU-based solution achieves a 57.3x speedup over the state-of-the-art multithreaded CPU baseline without layout quality loss, reducing execution time from hours to minutes.

Yuwei Hu, Jiajie Li, Zhongming Yu et al.

Graph neural networks (GNNs), which have emerged as an effective method for handling machine learning tasks on graphs, bring a new approach to building recommender systems, where the task of recommendation can be formulated as the link prediction problem on user-item bipartite graphs. Training GNN-based recommender systems (GNNRecSys) on large graphs incurs a large memory footprint, easily exceeding the DRAM capacity on a typical server. Existing solutions resort to distributed subgraph training, which is inefficient due to the high cost of dynamically constructing subgraphs and significant redundancy across subgraphs. The emerging persistent memory technologies provide a significantly larger memory capacity than DRAMs at an affordable cost, making single-machine GNNRecSys training feasible, which eliminates the inefficiencies in distributed training. One major concern of using persistent memory devices for GNNRecSys is their relatively low bandwidth compared with DRAMs. This limitation can be particularly detrimental to achieving high performance for GNNRecSys workloads since their dominant compute kernels are sparse and memory access intensive. To understand whether persistent memory is a good fit for GNNRecSys training, we perform an in-depth characterization of GNNRecSys workloads and a comprehensive analysis of their performance on a persistent memory device, namely, Intel Optane. Based on the analysis, we provide guidance on how to configure Optane for GNNRecSys workloads. Furthermore, we present techniques for large-batch training to fully realize the advantages of single-machine GNNRecSys training. Our experiment results show that with the tuned batch size and optimal system configuration, Optane-based single-machine GNNRecSys training outperforms distributed training by a large margin, especially when handling deep GNN models.

Chenhui Xu, Dancheng Liu, Yuting Hu et al.

Physics-Informed Neural Networks (PINNs) are a kind of deep-learning-based numerical solvers for partial differential equations (PDEs). Existing PINNs often suffer from failure modes of being unable to propagate patterns of initial conditions. We discover that these failure modes are caused by the simplicity bias of neural networks and the mismatch between PDE's continuity and PINN's discrete sampling. We reveal that the State Space Model (SSM) can be a continuous-discrete articulation allowing initial condition propagation, and that simplicity bias can be eliminated by aligning a sequence of moderate granularity. Accordingly, we propose PINNMamba, a novel framework that introduces sub-sequence modeling with SSM. Experimental results show that PINNMamba can reduce errors by up to 86.3\% compared with state-of-the-art architecture. Our code is available at https://github.com/miniHuiHui/PINNMamba.

Jiajie Li, Huayi Zhang, Peng Lin et al.

We present a novel framework that improves the reliability of LLM judges by selectively augmenting LLM with auxiliary evaluation dimensions. Existing LLM judges often miss crucial evaluation dimensions because they fail to recognize the implicit standards underlying human assessments. To address this challenge, we propose the Auto-Prompt Ensemble (APE), an adaptive framework that automatically learns evaluation dimensions from its failure cases. APE incorporates a confidence-based ensemble mechanism to decide when to adopt the judgments from additional evaluation dimensions through a novel confidence estimation approach called Collective Confidence. Extensive experiments demonstrate that APE improves the reliability of LLM Judge across diverse standard benchmarks. For instance, APE enhances GPT-4o agreement rate on Reward Bench from 87.2% to 90.5% in the zero-shot setting. Overall, APE provides a principled approach for LLM Judge to leverage test-time computation, and bridge the evaluation gap between human and LLM judges.