arXiv subjects

Wencheng Li

Publications and source records attributed to Wencheng Li.

6 recordsLinked to original sources

arXiv2026

ZhuLong: Execution-Grounded LLM Agent for EDA Scripting with Offline API Self-Exploration

EDA scripting with tool-specific, often undocumented APIs remains a long-tail bottleneck that existing LLMs fail to address. This paper presents ZhuLong, an execution-grounded LLM coding agent for PyAether and SKILL that combines API retrieval, documentation inspection, and sandbox execution via unified MCP tools, augmented by an offline API self-exploration mechanism that infers undocumented API behaviors through counterfactual experimentation. We evaluate ZhuLong on EDA-Eval-PyAether, a benchmark of 158 real-world tasks with assertion-based execution, where the complete system achieves 78.5% Pass@1 in the commercial Empyrean Aether environment, substantially outperforming a pure LLM baseline (23.6%). Ablation studies identify sandbox execution as the dominant performance driver (41.2 pp drop when removed), with the self-exploration mechanism contributing an additional 3.2 pp accuracy gain and a 22.1% reduction in per-task tool calls. On 20 interactive tasks involving unsaved layouts and schematics, ZhuLong achieves 60.0% Pass@1 for PyAether and 50.0% for SKILL.

cs.AI↗

arXiv2026

Adoption and Use of LLMs at an Academic Medical Center

While large language models (LLMs) can support clinical documentation needs, standalone tools struggle with "workflow friction" from manual data entry. We developed ChatEHR, a system that enables the use of LLMs with the entire patient timeline spanning several years. ChatEHR enables automations - which are static combinations of prompts and data that perform a fixed task - and interactive use in the electronic health record (EHR) via a user interface (UI). The resulting ability to sift through patient medical records for diverse use-cases such as pre-visit chart review, screening for transfer eligibility, monitoring for surgical site infections, and chart abstraction, redefines LLM use as an institutional capability. This system, accessible after user-training, enables continuous monitoring and evaluation of LLM use. In 1.5 years, we built 7 automations and 1075 users have trained to become routine users of the UI, engaging in 23,000 sessions in the first 3 months of launch. For automations, being model-agnostic and accessing multiple types of data was essential for matching specific clinical or administrative tasks with the most appropriate LLM. Benchmark-based evaluations proved insufficient for monitoring and evaluation of the UI, requiring new methods to monitor performance. Generation of summaries was the most frequent task in the UI, with an estimated 0.73 hallucinations and 1.60 inaccuracies per generation. The resulting mix of cost savings, time savings, and revenue growth required a value assessment framework to prioritize work as well as quantify the impact of using LLMs. Initial estimates are $6M savings in the first year of use, without quantifying the benefit of the better care offered. Such a "build-from-within" strategy provides an opportunity for health systems to maintain agency via a vendor-agnostic, internally governed LLM platform.

cs.CY↗

arXiv2025

Learning the Language of Histopathology Images reveals Prognostic Subgroups in Invasive Lung Adenocarcinoma Patients

Recurrence remains a major clinical challenge in surgically resected invasive lung adenocarcinoma, where existing grading and staging systems fail to capture the cellular complexity that underlies tumor aggressiveness. We present PathRosetta, a novel AI model that conceptualizes histopathology as a language, where cells serve as words, spatial neighborhoods form syntactic structures, and tissue architecture composes sentences. By learning this language of histopathology, PathRosetta predicts five-year recurrence directly from hematoxylin-and-eosin (H&E) slides, treating them as documents representing the state of the disease. In a multi-cohort dataset of 289 patients (600 slides), PathRosetta achieved an area under the curve (AUC) of 0.78 +- 0.04 on the internal cohort, significantly outperforming IASLC grading (AUC:0.71), AJCC staging (AUC:0.64), and other state-of-the-art AI models (AUC:0.62-0.67). It yielded a hazard ratio of 9.54 and a concordance index of 0.70, generalized robustly to external TCGA (AUC:0.75) and CPTAC (AUC:0.76) cohorts, and performed consistently across demographic and clinical subgroups. Beyond whole-slide prediction, PathRosetta uncovered prognostic subgroups within individual cell types, revealing that even within benign epithelial, stromal, or other cells, distinct morpho-spatial phenotypes correspond to divergent outcomes. Moreover, because the model explicitly understands what it is looking at, including cell types, cellular neighborhoods, and higher-order tissue morphology, it is inherently interpretable and can articulate the rationale behind its predictions. These findings establish that representing histopathology as a language enables interpretable and generalizable prognostication from routine histology.

cs.CV↗

arXiv2024

CausalCellSegmenter: Causal Inference inspired Diversified Aggregation Convolution for Pathology Image Segmentation

Deep learning models have shown promising performance for cell nucleus segmentation in the field of pathology image analysis. However, training a robust model from multiple domains remains a great challenge for cell nucleus segmentation. Additionally, the shortcomings of background noise, highly overlapping between cell nucleus, and blurred edges often lead to poor performance. To address these challenges, we propose a novel framework termed CausalCellSegmenter, which combines Causal Inference Module (CIM) with Diversified Aggregation Convolution (DAC) techniques. The DAC module is designed which incorporates diverse downsampling features through a simple, parameter-free attention module (SimAM), aiming to overcome the problems of false-positive identification and edge blurring. Furthermore, we introduce CIM to leverage sample weighting by directly removing the spurious correlations between features for every input sample and concentrating more on the correlation between features and labels. Extensive experiments on the MoNuSeg-2018 dataset achieves promising results, outperforming other state-of-the-art methods, where the mIoU and DSC scores growing by 3.6% and 2.65%.

eess.IV↗

arXiv2021

PF-Net: Personalized Filter for Speaker Recognition from Raw Waveform

Speaker recognition using i-vector has been replaced by speaker recognition using deep learning. Speaker recognition based on Convolutional Neural Networks (CNNs) has been widely used in recent years, which learn low-level speech representations from raw waveforms. On this basis, a CNN architecture called SincNet proposes a kind of unique convolutional layer, which has achieved band-pass filters. Compared with standard CNNs, SincNet learns the low and high cut-off frequencies of each filter. This paper proposes an improved CNNs architecture called PF-Net, which encourages the first convolutional layer to implement more personalized filters than SincNet. PF-Net parameterizes the frequency domain shape and can realize band-pass filters by learning some deformation points in frequency domain. Compared with standard CNN, PF-Net can learn the characteristics of each filter. Compared with SincNet, PF-Net can learn more characteristic parameters, instead of only low and high cut-off frequencies. This provides a personalized filter bank for different tasks. As a result, our experiments show that the PF-Net converges faster than standard CNN and performs better than SincNet. Our code is available at github.com/TAN-OpenLab/PF-NET.

eess.AS↗

arXiv2020

A new paradigm for accelerating clinical data science at Stanford Medicine

Stanford Medicine is building a new data platform for our academic research community to do better clinical data science. Hospitals have a large amount of patient data and researchers have demonstrated the ability to reuse that data and AI approaches to derive novel insights, support patient care, and improve care quality. However, the traditional data warehouse and Honest Broker approaches that are in current use, are not scalable. We are establishing a new secure Big Data platform that aims to reduce time to access and analyze data. In this platform, data is anonymized to preserve patient data privacy and made available preparatory to Institutional Review Board (IRB) submission. Furthermore, the data is standardized such that analysis done at Stanford can be replicated elsewhere using the same analytical code and clinical concepts. Finally, the analytics data warehouse integrates with a secure data science computational facility to support large scale data analytics. The ecosystem is designed to bring the modern data science community to highly sensitive clinical data in a secure and collaborative big data analytics environment with a goal to enable bigger, better and faster science.

cs.CY↗