Lipeng Wan

Apu Kumar Chakroborti, Yi Ding, Lipeng Wan

As modern science becomes increasingly data-intensive, the ability to analyze and visualize large-scale, complex datasets is critical to accelerating discovery. However, many domain scientists lack the programming expertise required to develop custom data analysis workflows, creating barriers to timely and effective insight. Large language models (LLMs) offer a promising solution by generating executable code from natural language descriptions. In this paper, we investigate the trustworthiness of open-source LLMs in autonomously producing Python scripts for scientific data analysis and visualization. We construct a benchmark suite of domain-inspired prompts that reflect real-world research tasks and systematically evaluate the executability and correctness of the generated code. Our findings show that, without human intervention, the reliability of LLM-generated code is limited, with frequent failures caused by ambiguous prompts and the models' insufficient understanding of domain-specific contexts. To address these challenges, we design and assess three complementary strategies: data-aware prompt disambiguation, retrieval-augmented prompt enhancement, and iterative error repair. While these methods significantly improve execution success rates and output quality, further refinement is needed. This work highlights both the promise and current limitations of LLM-driven automation in scientific workflows and introduces actionable techniques and a reusable benchmark for building more inclusive, accessible, and trustworthy AI-assisted research tools.

Haoju Leng, Ruining Deng, Zuhayr Asad et al.

Deep-learning techniques have been used widely to alleviate the labour-intensive and time-consuming manual annotation required for pixel-level tissue characterization. Our previous study introduced an efficient single dynamic network - Omni-Seg - that achieved multi-class multi-scale pathological segmentation with less computational complexity. However, the patch-wise segmentation paradigm still applies to Omni-Seg, and the pipeline is time-consuming when providing segmentation for Whole Slide Images (WSIs). In this paper, we propose an enhanced version of the Omni-Seg pipeline in order to reduce the repetitive computing processes and utilize a GPU to accelerate the model's prediction for both better model performance and faster speed. Our proposed method's innovative contribution is two-fold: (1) a Docker is released for an end-to-end slide-wise multi-tissue segmentation for WSIs; and (2) the pipeline is deployed on a GPU to accelerate the prediction, achieving better segmentation quality in less time. The proposed accelerated implementation reduced the average processing time (at the testing stage) on a standard needle biopsy WSI from 2.3 hours to 22 minutes, using 35 WSIs from the Kidney Tissue Atlas (KPMP) Datasets. The source code and the Docker have been made publicly available at https://github.com/ddrrnn123/Omni-Seg.

Qian Gong, Jieyang Chen, Ben Whitney et al.

We describe MGARD, a software providing MultiGrid Adaptive Reduction for floating-point scientific data on structured and unstructured grids. With exceptional data compression capability and precise error control, MGARD addresses a wide range of requirements, including storage reduction, high-performance I/O, and in-situ data analysis. It features a unified application programming interface (API) that seamlessly operates across diverse computing architectures. MGARD has been optimized with highly-tuned GPU kernels and efficient memory and device management mechanisms, ensuring scalable and rapid operations.

Qian Gong, Chengzhu Zhang, Xin Liang et al.

Scientific discoveries are increasingly constrained by limited storage space and I/O capacities. For time-series simulations and experiments, their data often need to be decimated over timesteps to accommodate storage and I/O limitations. In this paper, we propose a technique that addresses storage costs while improving post-analysis accuracy through spatiotemporal adaptive, error-controlled lossy compression. We investigate the trade-off between data precision and temporal output rates, revealing that reducing data precision and increasing timestep frequency lead to more accurate analysis outcomes. Additionally, we integrate spatiotemporal feature detection with data compression and demonstrate that performing adaptive error-bounded compression in higher dimensional space enables greater compression ratios, leveraging the error propagation theory of a transformation-based compressor. To evaluate our approach, we conduct experiments using the well-known E3SM climate simulation code and apply our method to compress variables used for cyclone tracking. Our results show a significant reduction in storage size while enhancing the quality of cyclone tracking analysis, both quantitatively and qualitatively, in comparison to the prevalent timestep decimation approach. Compared to three state-of-the-art lossy compressors lacking feature preservation capabilities, our adaptive compression framework improves perfectly matched cases in TC tracking by 26.4-51.3% at medium compression ratios and by 77.3-571.1% at large compression ratios, with a merely 5-11% computational overhead.

Bingbing Li, Santosh Pandey, Haowen Fang et al.

In natural language processing (NLP), the "Transformer" architecture was proposed as the first transduction model replying entirely on self-attention mechanisms without using sequence-aligned recurrent neural networks (RNNs) or convolution, and it achieved significant improvements for sequence to sequence tasks. The introduced intensive computation and storage of these pre-trained language representations has impeded their popularity into computation and memory-constrained devices. The field-programmable gate array (FPGA) is widely used to accelerate deep learning algorithms for its high parallelism and low latency. However, the trained models are still too large to accommodate to an FPGA fabric. In this paper, we propose an efficient acceleration framework, Ftrans, for transformer-based large scale language representations. Our framework includes enhanced block-circulant matrix (BCM)-based weight representation to enable model compression on large-scale language representations at the algorithm level with few accuracy degradation, and an acceleration design at the architecture level. Experimental results show that our proposed framework significantly reduces the model size of NLP models by up to 16 times. Our FPGA design achieves 27.07x and 81x improvement in performance and energy efficiency compared to CPU, and up to 8.80x improvement in energy efficiency compared to GPU.