Thanks for the code.
I cannot reproduce the error using this command and your repository:
python -m graphsage.model
0 1.9449124336242676
1 1.9262391328811646
2 1.9075403213500977
3 1.869475245475769
4 1.8472117185592651
5 1.8181393146514893
6 1.8005340099334717
7 1.746289849281311
8 1.6870187520980835
9 1.6369025707244873
10 1.5767720937728882
11 1.4736994504928589
12 1.4498679637908936
13 1.4377225637435913
14 1.4284756183624268
15 1.3335570096969604
16 1.2711284160614014
17 1.1341012716293335
18 1.1241765022277832
19 1.0289225578308105
20 0.9355937242507935
21 0.9255473613739014
22 0.8900326490402222
23 0.806100606918335
24 0.8072971701622009
25 0.8284955620765686
26 0.6966670751571655
27 0.6289700269699097
28 0.6647626757621765
29 0.8228136897087097
30 0.747298538684845
31 0.714832067489624
32 0.5909189581871033
33 0.5408354997634888
34 0.5010537505149841
35 0.5862414836883545
36 0.5422082543373108
37 0.4259440004825592
38 0.44785746932029724
39 0.48034438490867615
40 0.43961235880851746
41 0.4774445593357086
42 0.41150081157684326
43 0.36814427375793457
44 0.35858404636383057
45 0.3964439332485199
46 0.3785482347011566
47 0.45746365189552307
48 0.6183907985687256
49 0.7749939560890198
50 0.9017699956893921
51 0.4618622958660126
52 0.37373557686805725
53 0.34176552295684814
54 0.3155927062034607
55 0.35520535707473755
56 0.3165806531906128
57 0.31519120931625366
58 0.32234856486320496
59 0.2658422887325287
60 0.2659823000431061
61 0.3343285620212555
62 0.25045305490493774
63 0.2747704088687897
64 0.22687111794948578
65 0.3643914461135864
66 0.263433039188385
67 0.26506614685058594
68 0.25543108582496643
69 0.2547190189361572
70 0.2573583424091339
71 0.21613654494285583
72 0.273402601480484
73 0.1756642758846283
74 0.21497443318367004
75 0.31738513708114624
76 0.2398620843887329
77 0.22140288352966309
78 0.22747889161109924
79 0.26642531156539917
80 0.2145370990037918
81 0.21441781520843506
82 0.16217008233070374
83 0.19470077753067017
84 0.1829792857170105
85 0.24118557572364807
86 0.21673281490802765
87 0.1997360736131668
88 0.20058968663215637
89 0.1757909208536148
90 0.21877747774124146
91 0.20824533700942993
92 0.17878247797489166
93 0.21536171436309814
94 0.22572994232177734
95 0.17374852299690247
96 0.2164204865694046
97 0.20531226694583893
98 0.24563446640968323
99 0.19727684557437897
Validation F1: 0.858
Test F1: 0.857
Average batch time: 0.036545968055725096

Which PyTorch and CUDA version and which GPU are you using?