GeneLab_benchmark/CITATION.cff at main · jang1563/GeneLab_benchmark · 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
cff-version: 1.2.0
message: "If you use this benchmark in your research, please cite as below."
type: software

title: "SpaceBio-Bench / GeneLab Benchmark: Mission-Held-Out Spaceflight Transcriptomics Benchmark"
version: "7.1.2"
date-released: "2026-06-05"

abstract: >
  SpaceBio-Bench / GeneLab Benchmark is a comprehensive benchmark for evaluating
  AI and machine learning models on NASA OSDR (Open Science Data Repository)
  mouse spaceflight transcriptomics data. It provides standardized
  Leave-One-Mission-Out (LOMO) cross-validation splits, multi-method evaluation
  (8 classifiers x 4 feature types), foundation model comparisons (Geneformer,
  scGPT, UCE, scFoundation), and an evaluation framework for multi-tissue
  spaceflight detection across 8 tissues (liver, gastrocnemius, kidney, thymus,
  skin, eye, lung, colon), cross-mission transfer, cross-tissue transfer,
  multi-species analysis (mouse, Drosophila), spatial transcriptomics (Visium),
  and single-cell RNA-seq (RRRM-1, RRRM-2). The v7 release also includes
  unified scPRINT2 and graph neural network benchmarking, plus cross-method
  synthesis across classical, foundation-model, and graph-based approaches. The
  v7.1.2 release is a documentation, public-card, and metadata patch; it does
  not introduce new benchmark result generation.

authors:
  - family-names: "Kim"
    given-names: "JangKeun"
    affiliation: "Weill Cornell Medicine"

repository-code: "https://github.com/jang1563/GeneLab_benchmark"
url: "https://github.com/jang1563/GeneLab_benchmark"

keywords:
  - spaceflight
  - transcriptomics
  - RNA-seq
  - benchmark
  - machine learning
  - NASA OSDR
  - GeneLab
  - SpaceBio-Bench
  - LOMO
  - cross-mission transfer
  - foundation model
  - Geneformer
  - scGPT
  - UCE
  - scFoundation
  - pathway analysis
  - single-cell
  - spatial transcriptomics
  - multi-species
  - mouse
  - Drosophila

license: MIT

references:
  - type: dataset
    title: "NASA Open Science Data Repository (OSDR)"
    url: "https://osdr.nasa.gov"
    notes: >
      Source data: 24+ OSD accessions across 8 tissues (liver, gastrocnemius, kidney,
      thymus, skin, eye, lung, colon) from ISS missions RR-1 through RR-9, MHU-1, MHU-2.
      Additional data: OSD-352 (brain Visium spatial), RRRM-1/RRRM-2 scRNA-seq,
      Drosophila spaceflight studies for cross-species analysis.

preferred-citation:
  type: article
  title: "SpaceBio-Bench / GeneLab Benchmark: Mission-Held-Out Spaceflight Transcriptomics Benchmark"
  authors:
    - family-names: "Kim"
      given-names: "JangKeun"
      affiliation: "Weill Cornell Medicine"
  status: "in-preparation"
  year: 2026
  notes: "Manuscript in preparation; v7.1.2 documentation, public-card, and metadata patch."