CellForge/CITATION.cff at main · gersteinlab/CellForge · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
cff-version: 1.2.0
title: "CellForge: Agentic Design of Virtual Cell Models"
message: "If you use CellForge, please cite both the software and the preprint below."
type: software
license: MIT
repository-code: "https://github.com/gersteinlab/CellForge"
url: "https://github.com/gersteinlab/CellForge"
version: 0.1.0
date-released: 2026-07-19
abstract: >-
  CellForge is a multi-agent framework that autonomously designs computational
  methods for single-cell omics. Given a dataset and a research question, it
  performs literature-grounded task analysis, coordinates domain-expert agents
  through a peer-review debate to converge on a model architecture, and
  generates verified, executable training code.
keywords:
  - single-cell omics
  - virtual cell models
  - perturbation prediction
  - multi-agent systems
  - large language models
  - automated machine learning
  - computational biology
authors:
  - family-names: Tang
    given-names: Xiangru
  - family-names: Yu
    given-names: Zhuoyun
  - family-names: Chen
    given-names: Jiapeng
  - family-names: Cui
    given-names: Yan
  - family-names: Shao
    given-names: Daniel
  - family-names: Wang
    given-names: Weixu
  - family-names: Wu
    given-names: Fang
  - family-names: Zhuang
    given-names: Yuchen
  - family-names: Shi
    given-names: Wenqi
  - family-names: Huang
    given-names: Zhi
  - family-names: Cohan
    given-names: Arman
  - family-names: Lin
    given-names: Xihong
  - family-names: Theis
    given-names: Fabian
  - family-names: Krishnaswamy
    given-names: Smita
  - family-names: Gerstein
    given-names: Mark
preferred-citation:
  type: article
  title: "CellForge: Agentic Design of Virtual Cell Models"
  year: 2025
  journal: "arXiv preprint arXiv:2508.02276"
  url: "https://arxiv.org/abs/2508.02276"
  identifiers:
    - type: other
      value: "arXiv:2508.02276"
      description: arXiv identifier
  authors:
    - family-names: Tang
      given-names: Xiangru
    - family-names: Yu
      given-names: Zhuoyun
    - family-names: Chen
      given-names: Jiapeng
    - family-names: Cui
      given-names: Yan
    - family-names: Shao
      given-names: Daniel
    - family-names: Wang
      given-names: Weixu
    - family-names: Wu
      given-names: Fang
    - family-names: Zhuang
      given-names: Yuchen
    - family-names: Shi
      given-names: Wenqi
    - family-names: Huang
      given-names: Zhi
    - family-names: Cohan
      given-names: Arman
    - family-names: Lin
      given-names: Xihong
    - family-names: Theis
      given-names: Fabian
    - family-names: Krishnaswamy
      given-names: Smita
    - family-names: Gerstein
      given-names: Mark