arXiv subjects

John Hsu

Publications and source records attributed to John Hsu.

5 recordsLinked to original sources

arXiv2025

RAPID-Graph: Recursive All-Pairs Shortest Paths Using Processing-in-Memory for Dynamic Programming on Graphs

All-pairs shortest paths (APSP) remains a major bottleneck for large-scale graph analytics, as data movement with cubic complexity overwhelms the bandwidth of conventional memory hierarchies. In this work, we propose RAPID-Graph to address this challenge through a co-designed processing-in-memory (PIM) system that integrates algorithm, architecture, and device-level optimizations. At the algorithm level, we introduce a recursion-aware partitioner that enables an exact APSP computation by decomposing graphs into vertex tiles to reduce data dependency, such that both Floyd-Warshall and Min-Plus kernels execute fully in-place within digital PIM arrays. At the architecture and device levels, we design a 2.5D PIM stack integrating two phase-change memory compute dies, a logic die, and high-bandwidth scratchpad memory within a unified advanced package. An external non-volatile storage stack stores large APSP results persistently. The design achieves both tile-level and unit-level parallel processing to sustain high throughput. On the 2.45M-node OGBN-Products dataset, RAPID-Graph is 5.8x faster and 1,186x more energy efficient than state-of-the-art GPU clusters, while exceeding prior PIM accelerators by 8.3x in speed and 104x in efficiency. It further delivers up to 42.8x speedup and 392x energy savings over an NVIDIA H100 GPU.

cs.AR↗

arXiv2022

NeuraHealth: An Automated Screening Pipeline to Detect Undiagnosed Cognitive Impairment in Electronic Health Records with Deep Learning and Natural Language Processing

Dementia related cognitive impairment (CI) is a neurodegenerative disorder, affecting over 55 million people worldwide and growing rapidly at the rate of one new case every 3 seconds. 75% cases go undiagnosed globally with up to 90% in low-and-middle-income countries, leading to an estimated annual worldwide cost of USD 1.3 trillion, forecasted to reach 2.8 trillion by 2030. With no cure, a recurring failure of clinical trials, and a lack of early diagnosis, the mortality rate is 100%. Information in electronic health records (EHR) can provide vital clues for early detection of CI, but a manual review by experts is tedious and error prone. Several computational methods have been proposed, however, they lack an enhanced understanding of the linguistic context in complex language structures of EHR. Therefore, I propose a novel and more accurate framework, NeuraHealth, to identify patients who had no earlier diagnosis. In NeuraHealth, using patient EHR from Mass General Brigham BioBank, I fine-tuned a bi-directional attention-based deep learning natural language processing model to classify sequences. The sequence predictions were used to generate structured features as input for a patient level regularized logistic regression model. This two-step framework creates high dimensionality, outperforming all existing state-of-the-art computational methods as well as clinical methods. Further, I integrate the models into a real-world product, a web app, to create an automated EHR screening pipeline for scalable and high-speed discovery of undetected CI in EHR, making early diagnosis viable in medical facilities and in regions with scarce health services.

cs.CL↗

arXiv2021

Using Deep Learning to Identify Patients with Cognitive Impairment in Electronic Health Records

Dementia is a neurodegenerative disorder that causes cognitive decline and affects more than 50 million people worldwide. Dementia is under-diagnosed by healthcare professionals - only one in four people who suffer from dementia are diagnosed. Even when a diagnosis is made, it may not be entered as a structured International Classification of Diseases (ICD) diagnosis code in a patient's charts. Information relevant to cognitive impairment (CI) is often found within electronic health records (EHR), but manual review of clinician notes by experts is both time consuming and often prone to errors. Automated mining of these notes presents an opportunity to label patients with cognitive impairment in EHR data. We developed natural language processing (NLP) tools to identify patients with cognitive impairment and demonstrate that linguistic context enhances performance for the cognitive impairment classification task. We fine-tuned our attention based deep learning model, which can learn from complex language structures, and substantially improved accuracy (0.93) relative to a baseline NLP model (0.84). Further, we show that deep learning NLP can successfully identify dementia patients without dementia-related ICD codes or medications.

cs.CL↗

arXiv2020

Natural Language Processing to Detect Cognitive Concerns in Electronic Health Records Using Deep Learning

Dementia is under-recognized in the community, under-diagnosed by healthcare professionals, and under-coded in claims data. Information on cognitive dysfunction, however, is often found in unstructured clinician notes within medical records but manual review by experts is time consuming and often prone to errors. Automated mining of these notes presents a potential opportunity to label patients with cognitive concerns who could benefit from an evaluation or be referred to specialist care. In order to identify patients with cognitive concerns in electronic medical records, we applied natural language processing (NLP) algorithms and compared model performance to a baseline model that used structured diagnosis codes and medication data only. An attention-based deep learning model outperformed the baseline model and other simpler models.

cs.CL↗

arXiv2019

Data science is science's second chance to get causal inference right: A classification of data science tasks

Causal inference from observational data is the goal of many data analyses in the health and social sciences. However, academic statistics has often frowned upon data analyses with a causal objective. The introduction of the term "data science" provides a historic opportunity to redefine data analysis in such a way that it naturally accommodates causal inference from observational data. Like others before, we organize the scientific contributions of data science into three classes of tasks: Description, prediction, and counterfactual prediction (which includes causal inference). An explicit classification of data science tasks is necessary to discuss the data, assumptions, and analytics required to successfully accomplish each task. We argue that a failure to adequately describe the role of subject-matter expert knowledge in data analysis is a source of widespread misunderstandings about data science. Specifically, causal analyses typically require not only good data and algorithms, but also domain expert knowledge. We discuss the implications for the use of data science to guide decision-making in the real world and to train data scientists.

stat.ML↗