Hi, I'm Sophie Shi

Focus on Machine Learning • Expected Graduation December 2027

I am a Ph.D. candidate at Duke University in the Tim Dunn Lab, working on deep learning and machine learning. I specialize in AI/ML, computer vision, 3D pose estimation, and video-based motion analysis.

I am seeking an internship for summer/fall 2027, and full-time roles starting in January 2028.

Work Experience

DANNCE.ai logo

PhD Machine Learning Engineer Intern, DANNCE.ai

Boston, MA (remote) • May 2026 – Aug. 2026

  • Developed human motion analysis algorithms for a mobile clinical decision support application.
  • Implemented 3D motion features from monocular mobile videos, improving cadence accuracy by over 10x compared with the original 2D pipeline. Production deployment planned soon.
  • Managed and processed patient data in Google Cloud and supported patient-facing data workflows.
Honda Research Institute logo

PhD Applied Research Intern, Honda Research Institute

San Jose, CA • Jan. 2026 – Apr. 2026

  • Designed a self-supervised video representation learning framework based on contrastive learning for long videos.
  • Developed motion-aware training objectives using optical flow and pairwise motion similarity.
  • Integrated a knowledge distillation module into the pipeline to improve efficiency.

Featured Projects

A Video Pipeline for Automated Behavior Detection

Multimodal Learning • Vision Language Models • Pose Estimation • Video Processing

  • Building a multimodal system that integrates video, images, and brain signals.
  • Developing a vision language model (VLM) pipeline for automated behavior detection in clinical video data.
  • Performed supervised fine-tuning (SFT) using Sapiens (Meta) and MMPose (OpenMMLab).

Arxiv Insight: A Retrieval-Augmented Scientific Summarization Tool

LLM • RAG • Prompt Engineering

  • Built an LLM tool using Qwen-3 to extract insights from arXiv papers via single paper summarization or multi-document RAG-augmented summarization.
  • Integrated semantic chunking, BAAI/bge-small-en embeddings, FAISS search, and structured prompts for targeted summarization.

Automated Behavior Profiling Using 3D Pose Estimation and Deep Learning

Computer Vision • 3D Pose Estimation • Computational Ethology

  • Implemented a multi-camera algorithm to extract 3D pose landmarks of freely moving mice.
  • Developed an automated pipeline for quantitative behavior profiling beyond subjective manual assessments.

Quantifiable and Explainable Movement Analysis of Parkinson’s Disease

Computer Vision • 3D Pose Estimation • Hand Tracking • Gait Analysis

  • Set up a multi-camera motion capture system for specific diagnostic tasks and daily activity recording.
  • Performed hand tracking analysis (finger tapping) and gait analysis for Parkinson’s disease behavior phenotyping.

Joint Compression and Classification Network for Epilepsy Seizure Prediction

Data Compression • Deep Learning • Signal Processing

Developed joint compression-classification network using ResNet architecture for EEG seizure prediction. Implemented adaptive reconstruction module with under variable compression ratios for enhanced prediction accuracy.

Real-Time ECG Monitoring System with Cloud Server and GUI Interfaces

RESTful API • Cloud Server • Database Integration • GUI Design • Unit Test

Built virtual machine-based RESTful API server and client with persistent database integration. Developed client GUI and monitor-end GUI applications for medical record and real-time patient monitoring.

Deadline Manager: A Cross-Platform iOS/WatchOS App for Smart Deadline Tracking

SwiftUI • UIKit • iCloud • Firebase • Sakai API • Mobile App Development

Designed multi-view iOS/WatchOS mobile application for deadline management using SwiftUI and UIKit. Integrated cross-device real-time synchronization via iCloud and Firebase, with Sakai API integration for automatic course assignment deadlines.

Selected Publications

Publications & Conferences

SfN 2026

Automated Quantitative Phenotyping of Seizure Semiology Using 3D Poses Reconstructed from Routine Epilepsy Monitoring Unit Single-camera Videos

Shi Y, Agashe S, Dunn T.W.

  • Oral presentation (5% of all accepted submissions).
  • Trainee Professional Development Award recipient.
SfN Neuroscience 2026 Oral Presentation • 2026
Angiogenic therapy figure

Delivery of Angiogenic Therapy from Flowable Hyaluronic Acid Porous Scaffolds Results in Functional Improvement without Anti-Inflammatory Agents

Erning K, Wilson KL, Smith CS, Nguyen L, Joseph NI, Irengo R, Cao LY, Cumaran M, Shi Y, Lyu S, Riley L, Dunn TW, Carmichael ST, Segura T

Co-authored research on angiogenic therapy applications using hyaluronic acid scaffolds for tissue engineering applications. Contributed to the treatment effect evaluation.

Advanced Functional Materials Published • 2025

Manuscripts in Preparation

In Prep

Three-Dimensional Kinematic Phenotyping of Ictal Motor Semiology in Temporal Lobe Epilepsy

Shi Y, Harward S, Southwell D, Grant G, Dunn T*, Agashe S*

In Preparation
In Prep

DANNCE-step: a pipeline for precise, automated quantification of motor dysfunction in rodent models of stroke

Shi Y*, Lyu S*, et al.

In Preparation

Skills & Techniques

🧠AI & Machine Learning

  • Deep Learning
  • Computer Vision
  • 3D Pose Estimation
  • Self Supervised Learning

⚙️Technical Stack

  • Python, C/C++, Swift, HTML/CSS
  • Pytorch, OpenCV
  • Git
  • Emacs

🏥Biomedical Engineering

  • Neural Disorder
  • Camera Calibration
  • Medical Software Design
  • Markerless Keypoints Tracking

Get In Touch

Let's Connect

I'm always interested in new opportunities and collaborations. Whether you have a project in mind or just want to chat about research, feel free to reach out!

📧
Email
sophie.shi[at]duke.edu
📍
Location
Durham, NC / Seattle, WA
💼
Availability
Open to new opportunities

Send a Message

Have a question or want to work together? Drop me a line!

Get In Touch

Ready to collaborate or have questions about my research? I'd love to hear from you!

📧 Email Me Directly

sophie.shi[at]duke.edu