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feat: add script for cross-venue paper expansion in Sprint 7
- Introduced s7_extract_cross_venue.py to add papers from sibling workshops (ICLR 2025 MLGenX, NeurIPS 2025 GenAI4Health, NeurIPS 2025 AI4Science) where at least one author exists in the graph. - Implemented functionality to create new presentation nodes, author nodes, authored edges, and current_affiliation edges based on OpenReview profiles. - Added deduplication logic for papers based on titles and merged venue information. - Enhanced author and institution lookup mechanisms for better integration. - Saved new nodes and edges to staged files and merged them into the existing graph data.
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‎data/graph_data.json‎

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‎data/raw/s7_cross_venue/ai4science_papers.json‎

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‎data/raw/s7_cross_venue/genai4health_papers.json‎

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‎data/raw/s7_cross_venue/mlgenx_papers.json‎

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‎data/raw/s7_cross_venue/overlap_analysis.json‎

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[
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{
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"workshop": "mlgenx",
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"venue": "MLGenX 2025",
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"paper_id": "4YMUZ49lB3",
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"title": "Integrating Protein Language Model and Active Learning for Few-Shot Viral Variant Detection",
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"authors": [
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"Marian Huot",
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"Dianzhuo Wang",
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"Jiacheng Liu",
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"Eugene Shakhnovich"
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],
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"matches": [
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[
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"Marian Huot",
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"author_Marian_Huot1"
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],
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[
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"Dianzhuo Wang",
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"author_Dianzhuo_Wang1"
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],
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[
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"Eugene Shakhnovich",
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"author_Eugene_Shakhnovich1"
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]
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]
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},
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{
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"workshop": "mlgenx",
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"venue": "MLGenX 2025",
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"paper_id": "BZIxe22wEO",
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"title": "Spatially-Informed Sampling Enables Accurate Prediction of Large-Scale Mutational Effects",
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"authors": [
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"Maxime Basse",
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"Dianzhuo Wang",
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"Eugene Shakhnovich"
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],
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"matches": [
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[
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"Dianzhuo Wang",
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"author_Dianzhuo_Wang1"
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],
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[
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"Eugene Shakhnovich",
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"author_Eugene_Shakhnovich1"
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]
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]
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},
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{
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"workshop": "mlgenx",
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"venue": "MLGenX 2025",
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"paper_id": "lHRETQDSVu",
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"title": "Sampling Protein Language Models for Functional Protein Design",
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"authors": [
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"Jeremie Theddy Darmawan",
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"Yarin Gal",
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"Pascal Notin"
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],
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"matches": [
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[
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"Yarin Gal",
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"author_Yarin_Gal1"
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]
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]
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},
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{
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"workshop": "genai4health",
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"venue": "GenAI4Health 2025 Poster",
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"paper_id": "pSDvq2ZgPk",
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"title": "MedBrowseComp: Benchmarking Medical Deep Research and Computer Use",
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"authors": [
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"Shan Chen",
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"Pedro Jos\u00e9 Ferreira Moreira",
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"Yuxin Xiao",
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"Samuel Schmidgall",
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"Jeremy L. Warner",
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"Hugo Aerts",
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"Thomas Hartvigsen",
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"Jack Gallifant",
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"Danielle Bitterman"
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],
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"matches": [
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[
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"Thomas Hartvigsen",
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"author_Thomas_Hartvigsen1"
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]
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]
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},
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{
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"workshop": "genai4health",
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"venue": "GenAI4Health 2025 Poster",
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"paper_id": "vTIacVIpL0",
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"title": "Position: Adjacent Technologies Are the Key Enablers of Scalable and Safe Clinical MLLM Deployment",
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"authors": [
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"Azmine Toushik Wasi",
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"Md. Iqramul Hoque"
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],
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"matches": [
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"Azmine Toushik Wasi",
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"Md. Iqramul Hoque",
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"author_Md__Iqramul_Hoque1"
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]
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]
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},
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{
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"workshop": "genai4health",
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"venue": "GenAI4Health 2025 Poster",
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"paper_id": "4tnyi8RQks",
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"title": "Demo: Medbot, A Practical Tool Built by Clinicians for Clinicians to Leverage AI Agents to Enhance Clinical Practice",
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"authors": [
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"Li Lianjie Anthony",
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"Antonio Bandeira",
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"Niroj Bhandari",
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"Rahul Gorijavolu",
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"Aaron Teo Rui Kang",
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"Jasmine Xiaojin Zhang",
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"Alvin Aung Aung Hein",
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"March I-Cheng Chen"
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],
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"matches": [
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[
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"Jasmine Xiaojin Zhang",
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"author_Jasmine_Zhang1"
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]
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]
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},
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{
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"workshop": "genai4health",
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"venue": "GenAI4Health 2025 Poster",
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"paper_id": "EU3TV1Uq78",
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"title": "Natural Language Grounded Reinforcement Learning for Clinical Decision-Making in Virtual Patient Simulations",
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"authors": [
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"Niyel Hassan",
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"Benjamin Liu",
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"Jason Tsai",
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"Jeffrey K Jopling",
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"Dana Lin",
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"Edward Melcer",
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"Cara Liebert"
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],
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"matches": [
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[
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"Benjamin Liu",
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"author_Benjamin_Liu2"
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]
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]
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},
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{
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"workshop": "genai4health",
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"venue": "GenAI4Health 2025 Poster",
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"paper_id": "aOoFPWZuXY",
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"title": "Multi-Turn LLM Systems for Diagnostic Decision-Making: Considerations, Biases, and Challenges",
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"authors": [
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"Benjamin Liu",
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"Sejong Kim",
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"Drona Thoka",
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"Varun Puttagunta",
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"Kaylin Sheng",
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"Mark Li",
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"Kiran Nijjer",
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"Adnan Ahmed",
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"Thi Uyen Hanh Le",
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"Sai Chidvilas Gudiboina",
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"Ali Ugur",
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"Kevin Zhu"
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],
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"matches": [
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[
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"Benjamin Liu",
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"author_Benjamin_Liu2"
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],
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[
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"Kevin Zhu",
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"author_Kevin_Zhu3"
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]
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]
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},
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{
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"workshop": "genai4health",
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"venue": "GenAI4Health 2025 Poster",
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"paper_id": "sjEuoLSvqS",
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"title": "Examining the Vulnerability of Multi-Agent Medical Systems to Human Interventions for Clinical Reasoning",
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"authors": [
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"Benjamin Liu",
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"Dillon Mehta",
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"Rishi Malhotra",
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"Adam Zobian",
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"Yong Ying Tan",
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"Samir Chopra",
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"Daniella Rand",
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"Natalie Pang",
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"Abhiram Gudimella",
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"Raghav Thallapragada",
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"Derek Jiu",
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"Prisha Shah",
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"Kevin Zhu"
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],
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"matches": [
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[
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"Benjamin Liu",
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"author_Benjamin_Liu2"
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],
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[
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"Kevin Zhu",
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"author_Kevin_Zhu3"
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]
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]
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},
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{
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"workshop": "genai4health",
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"venue": "GenAI4Health 2025 Poster",
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"paper_id": "cxffbxltME",
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"title": "Explaining Temporal Effects in Sepsis Prediction",
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"authors": [
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"Chaehyeon Kim",
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"Eric Wong"
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],
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"matches": [
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[
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"Eric Wong",
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"author_Eric_Wong1"
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]
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]
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},
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{
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"workshop": "genai4health",
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"venue": "GenAI4Health 2025 Oral",
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"paper_id": "9Nhrk0Cuk0",
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"title": "Position: Restricted Release of Advanced Biological Models Safeguards Biosecurity",
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"authors": [
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"Jonathan Feldman",
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"Tal Feldman"
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],
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"matches": [
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[
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"Jonathan Feldman",
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"author_Jonathan_Feldman1"
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],
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[
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"Tal Feldman",
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"author_Tal_Feldman1"
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]
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]
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},
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{
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"workshop": "ai4science",
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"venue": "NeurIPS2025-AI4Science Poster",
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"paper_id": "cRhbNNv2kA",
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"title": "Differentiable Predictive Control for Precise Oxygen Level Maintenance for Critical Patients",
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"authors": [
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"Azmine Toushik Wasi",
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"Md Manjurul Ahsan"
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],
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"matches": [
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[
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"Azmine Toushik Wasi",
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]
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]
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},
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{
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"workshop": "ai4science",
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"venue": "NeurIPS2025-AI4Science Poster",
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"paper_id": "FGmV1Ssqfa",
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"title": "Closing the Omics Gap: A Benchmark for Unified Evaluation of Biomolecular Foundation Models",
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"authors": [
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"Joseph G. Wakim",
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"Vinayak Gupta",
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"Jose Manuel Marti",
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"Jonathan E Allen",
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"Brian R. Bartoldson",
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"Bhavya Kailkhura"
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],
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"matches": [
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[
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"Bhavya Kailkhura",
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"author_Bhavya_Kailkhura1"
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]
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]
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},
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{
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"workshop": "ai4science",
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"venue": "NeurIPS2025-AI4Science Poster",
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"paper_id": "v1cxKcwPFP",
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"title": "Improving RNA Secondary Structure Prediction Through Expanded Training Data",
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"authors": [
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"Conner J. Langeberg",
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"Taehan Kim",
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"Roma Nagle",
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"Charlotte Meredith",
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"Dimple Amitha Garuadapuri",
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"Jennifer Doudna",
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"Jamie H. D. Cate"
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],
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"matches": [
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[
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"Jennifer Doudna",
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"author_jennifer_doudna"
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]
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]
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},
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{
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"workshop": "ai4science",
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"venue": "NeurIPS2025-AI4Science Poster",
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"paper_id": "DvnxwBA067",
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"title": "Without Safeguards, AI-Biology Integration Risks Accelerating Future Pandemics",
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"authors": [
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"Dianzhuo Wang",
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"Marian Huot",
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"Zechen Zhang",
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"Kaiyi Jiang",
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"Eugene Shakhnovich",
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"Kevin M. Esvelt"
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],
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"matches": [
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[
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"Dianzhuo Wang",
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"author_Dianzhuo_Wang1"
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],
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[
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"Marian Huot",
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"author_Marian_Huot1"
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],
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[
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"Zechen Zhang",
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"author_Zechen_Zhang2"
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],
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[
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"Kaiyi Jiang",
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"author_Kaiyi_Jiang1"
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],
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[
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"Eugene Shakhnovich",
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"author_Eugene_Shakhnovich1"
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],
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[
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"Kevin M. Esvelt",
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"author_Kevin_M__Esvelt1"
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]
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]
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},
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{
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"workshop": "ai4science",
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"venue": "NeurIPS2025-AI4Science Poster",
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"paper_id": "ub5OzaE03M",
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"title": "Explaining Temporal Effects in Sepsis Prediction",
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"authors": [
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"Chaehyeon Kim",
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"Eric Wong"
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],
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"matches": [
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[
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"Eric Wong",
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"author_Eric_Wong1"
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]
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]
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}
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]

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