Initializing T-SNE ... TypeError: s[e] is undefined

[charleswilmot]

Diagnostics

Diagnostics output

--- check: autoidentify
INFO: diagnose_tensorboard.py version e43767ef2b648d0d5d57c00f38ccbd38390e38da

--- check: general
INFO: sys.version_info: sys.version_info(major=3, minor=8, micro=5, releaselevel='final', serial=0)
INFO: os.name: posix
INFO: os.uname(): posix.uname_result(sysname='Linux', nodename='cx1g8', release='5.15.17-200.fc35.x86_64', version='#1 SMP Thu Jan 27 16:29:05 UTC 2022', machine='x86_64')
INFO: sys.getwindowsversion(): N/A

--- check: package_management
INFO: has conda-meta: True
INFO: $VIRTUAL_ENV: None

--- check: installed_packages
INFO: installed: tensorboard==2.8.0
INFO: installed: tensorflow==2.7.0
INFO: installed: tensorflow-estimator==2.7.0
INFO: installed: tensorboard-data-server==0.6.1

--- check: tensorboard_python_version
INFO: tensorboard.version.VERSION: '2.8.0'

--- check: tensorflow_python_version
2022-02-01 19:49:55.601843: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2022-02-01 19:49:55.601869: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
INFO: tensorflow.__version__: '2.7.0'
INFO: tensorflow.__git_version__: 'v2.7.0-rc1-69-gc256c071bb2'

--- check: tensorboard_data_server_version
INFO: data server binary: '/home/cwilmot/.conda/envs/python3.8_env/lib/python3.8/site-packages/tensorboard_data_server/bin/server'
INFO: data server binary version: b'rustboard 0.6.1'

--- check: tensorboard_binary_path
INFO: which tensorboard: b'/home/cwilmot/.conda/envs/python3.8_env/bin/tensorboard\n'

--- check: addrinfos
socket.has_ipv6 = True
socket.AF_UNSPEC = <AddressFamily.AF_UNSPEC: 0>
socket.SOCK_STREAM = <SocketKind.SOCK_STREAM: 1>
socket.AI_ADDRCONFIG = <AddressInfo.AI_ADDRCONFIG: 32>
socket.AI_PASSIVE = <AddressInfo.AI_PASSIVE: 1>
Loopback flags: <AddressInfo.AI_ADDRCONFIG: 32>
Loopback infos: [(<AddressFamily.AF_INET6: 10>, <SocketKind.SOCK_STREAM: 1>, 6, '', ('::1', 0, 0, 0)), (<AddressFamily.AF_INET: 2>, <SocketKind.SOCK_STREAM: 1>, 6, '', ('127.0.0.1', 0))]
Wildcard flags: <AddressInfo.AI_PASSIVE: 1>
Wildcard infos: [(<AddressFamily.AF_INET: 2>, <SocketKind.SOCK_STREAM: 1>, 6, '', ('0.0.0.0', 0)), (<AddressFamily.AF_INET6: 10>, <SocketKind.SOCK_STREAM: 1>, 6, '', ('::', 0, 0, 0))]

--- check: readable_fqdn
INFO: socket.getfqdn(): 'cx1g8'

--- check: stat_tensorboardinfo
INFO: directory: /tmp/.tensorboard-info
INFO: os.stat(...): os.stat_result(st_mode=16895, st_ino=238, st_dev=37, st_nlink=2, st_uid=1000, st_gid=1000, st_size=60, st_atime=1643719946, st_mtime=1643741248, st_ctime=1643741248)
INFO: mode: 0o40777

--- check: source_trees_without_genfiles
INFO: tensorboard_roots (1): ['/home/cwilmot/.conda/envs/python3.8_env/lib/python3.8/site-packages']; bad_roots (0): []

--- check: full_pip_freeze
INFO: pip freeze --all:
absl-py @ file:///tmp/build/80754af9/absl-py_1623867230185/work
aiohttp @ file:///tmp/build/80754af9/aiohttp_1614360992924/work
argon2-cffi==21.1.0
arxiv==1.4.2
astor==0.8.1
astunparse==1.6.3
async-timeout==3.0.1
attrs @ file:///tmp/build/80754af9/attrs_1620827162558/work
backcall==0.2.0
bcrypt @ file:///tmp/build/80754af9/bcrypt_1597936221426/work
bleach==4.1.0
blinker==1.4
box2d-py==2.3.8
brotlipy==0.7.0
cachetools @ file:///tmp/build/80754af9/cachetools_1619597386817/work
certifi==2021.5.30
cffi==1.14.2
chardet @ file:///tmp/build/80754af9/chardet_1605303185383/work
charset-normalizer @ file:///tmp/build/80754af9/charset-normalizer_1630003229654/work
chex==0.0.8
click @ file:///tmp/build/80754af9/click_1621604852318/work
cloudpickle @ file:///Users/ktietz/demo/mc3/conda-bld/cloudpickle_1629142150447/work
coverage @ file:///tmp/build/80754af9/coverage_1614613670853/work
crc32c==2.2.post0
cryptography @ file:///tmp/build/80754af9/cryptography_1616769286105/work
cycler==0.10.0
Cython @ file:///tmp/build/80754af9/cython_1626256955500/work
cytoolz==0.11.0
dask @ file:///tmp/build/80754af9/dask-core_1630523592567/work
debugpy==1.4.3
decorator==4.4.2
defusedxml==0.7.1
dill @ file:///tmp/build/80754af9/dill_1623919422540/work
distrax==0.0.2
dm-haiku==0.0.5
dm-tree==0.1.6
entrypoints==0.3
feedparser==6.0.8
flatbuffers==2.0
flax==0.3.5
fsspec @ file:///tmp/build/80754af9/fsspec_1626383727127/work
future==0.18.2
gast==0.3.3
google-auth @ file:///tmp/build/80754af9/google-auth_1626320605116/work
google-auth-oauthlib @ file:///tmp/build/80754af9/google-auth-oauthlib_1617120569401/work
google-pasta @ file:///Users/ktietz/demo/mc3/conda-bld/google-pasta_1630577991354/work
googleapis-common-protos @ file:///tmp/build/80754af9/googleapis-common-protos-feedstock_1617957649450/work
grpcio @ file:///tmp/build/80754af9/grpcio_1614884175859/work
h5py @ file:///tmp/build/80754af9/h5py_1593454122442/work
idna @ file:///tmp/build/80754af9/idna_1622654382723/work
imageio @ file:///tmp/build/80754af9/imageio_1617700267927/work
importlib-metadata @ file:///tmp/build/80754af9/importlib-metadata_1617874469820/work
ipykernel==6.4.1
ipython==7.27.0
ipython-genutils==0.2.0
ipywidgets==7.6.5
jax==0.2.27
jaxlib==0.1.75
jedi==0.18.0
Jinja2==3.0.1
jmp==0.0.2
jsonschema==3.2.0
jupyter==1.0.0
jupyter-client==7.0.3
jupyter-console==6.4.0
jupyter-core==4.8.1
jupyterlab-pygments==0.1.2
jupyterlab-widgets==1.0.2
keras==2.7.0
Keras-Preprocessing @ file:///tmp/build/80754af9/keras-preprocessing_1612283640596/work
kiwisolver @ file:///tmp/build/80754af9/kiwisolver_1612282420641/work
libclang==13.0.0
locket==0.2.1
Markdown @ file:///tmp/build/80754af9/markdown_1614363528767/work
MarkupSafe==2.0.1
matplotlib @ file:///tmp/build/80754af9/matplotlib-base_1603378225747/work
matplotlib-inline==0.1.3
mistune==0.8.4
mkchromecast==0.3.9
mkl-fft==1.3.0
mkl-random @ file:///tmp/build/80754af9/mkl_random_1626186064646/work
mkl-service==2.4.0
mpld3==0.5.5
mpmath==1.1.0
msgpack==1.0.2
mujoco-py==2.0.2.10
multidict @ file:///tmp/build/80754af9/multidict_1607367757617/work
nbclient==0.5.4
nbconvert==6.1.0
nbformat==5.1.3
nest-asyncio==1.5.1
networkx @ file:///tmp/build/80754af9/networkx_1627459939258/work
notebook==6.4.4
numpy @ file:///tmp/build/80754af9/numpy_and_numpy_base_1626271506491/work
oauthlib @ file:///tmp/build/80754af9/oauthlib_1623060228408/work
olefile @ file:///Users/ktietz/demo/mc3/conda-bld/olefile_1629805411829/work
opencv-python==4.2.0.34
opt-einsum @ file:///tmp/build/80754af9/opt_einsum_1621500238896/work
optax==0.0.9
packaging @ file:///tmp/build/80754af9/packaging_1625611678980/work
pandas==1.2.0
pandocfilters==1.5.0
paramiko @ file:///tmp/build/80754af9/paramiko_1598886428689/work
parso==0.8.2
partd @ file:///tmp/build/80754af9/partd_1618000087440/work
pexpect==4.8.0
pickleshare==0.7.5
Pillow @ file:///tmp/build/80754af9/pillow_1625655817137/work
pip==22.0.2
prometheus-client==0.11.0
promise @ file:///tmp/build/80754af9/promise_1614011636525/work
prompt-toolkit==3.0.20
protobuf==3.17.2
psutil @ file:///tmp/build/80754af9/psutil_1612298023621/work
ptyprocess==0.7.0
pyasn1 @ file:///Users/ktietz/demo/mc3/conda-bld/pyasn1_1629708007385/work
pyasn1-modules==0.2.8
pycparser @ file:///tmp/build/80754af9/pycparser_1594388511720/work
pydub==0.24.1
Pygments==2.10.0
PyJWT @ file:///tmp/build/80754af9/pyjwt_1619651636675/work
PyNaCl @ file:///tmp/build/80754af9/pynacl_1595009131182/work
pyOpenSSL @ file:///tmp/build/80754af9/pyopenssl_1608057966937/work
pyparsing @ file:///home/linux1/recipes/ci/pyparsing_1610983426697/work
PyRep @ file:///home/cwilmot/Software/PyRep
pyrsistent==0.18.0
PySocks @ file:///tmp/build/80754af9/pysocks_1605305779399/work
python-dateutil @ file:///tmp/build/80754af9/python-dateutil_1626374649649/work
pytz==2020.5
PyWavelets @ file:///tmp/build/80754af9/pywavelets_1601658317819/work
PyYAML==5.4.1
pyzmq==22.3.0
qtconsole==5.1.1
QtPy==1.11.1
requests @ file:///tmp/build/80754af9/requests_1629994808627/work
requests-oauthlib==1.3.0
rlax==0.0.4
rsa @ file:///tmp/build/80754af9/rsa_1614366226499/work
scikit-image==0.17.2
scipy @ file:///tmp/build/80754af9/scipy_1630606796110/work
selenium==3.141.0
Send2Trash==1.8.0
setuptools==52.0.0.post20210125
sgmllib3k==1.0.0
sip==4.19.13
six @ file:///tmp/build/80754af9/six_1623709665295/work
sounddevice==0.4.2
sympy==1.6.2
tabulate==0.8.9
tensorboard==2.8.0
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.6.0
tensorboardX==2.4.1
tensorflow==2.7.0
tensorflow-datasets @ file:///tmp/build/80754af9/tensorflow-datasets_1615394951098/work
tensorflow-estimator==2.7.0
tensorflow-io-gcs-filesystem==0.23.1
tensorflow-metadata==0.14.0
tensorflow-probability==0.15.0
termcolor==1.1.0
terminado==0.12.1
testpath==0.5.0
tifffile==2020.10.1
tikzplotlib==0.9.6
toolz @ file:///home/linux1/recipes/ci/toolz_1610987900194/work
tornado @ file:///tmp/build/80754af9/tornado_1606942300299/work
tqdm @ file:///tmp/build/80754af9/tqdm_1629302309755/work
traitlets==5.1.0
typing-extensions @ file:///tmp/build/80754af9/typing_extensions_1624965014186/work
urllib3 @ file:///tmp/build/80754af9/urllib3_1625084269274/work
wcwidth==0.2.5
webencodings==0.5.1
Werkzeug @ file:///home/ktietz/src/ci/werkzeug_1611932622770/work
wheel==0.37.0
widgetsnbextension==3.5.1
wrapt==1.12.1
xlrd==1.2.0
yarl @ file:///tmp/build/80754af9/yarl_1606939922162/work
zipp @ file:///tmp/build/80754af9/zipp_1625570634446/work

For browser-related issues, please additionally specify:

• Browser type and version Firefox and Chrome:

Issue description

In the PROJECTOR tab, starting a T-SNE visualization hangs while displaying Initializing T-SNE...
In the console, I see the following error:

Uncaught (in promise) TypeError: s[e] is undefined
    nearest2P http://localhost:6006/data/plugin/projector/projector_binary.js:6180
    initDataDist http://localhost:6006/data/plugin/projector/projector_binary.js:6180
    projectTSNE http://localhost:6006/data/plugin/projector/projector_binary.js:13226
    runAsyncTask http://localhost:6006/data/plugin/projector/projector_binary.js:13226
    setTimeout handler*runAsyncTask/< http://localhost:6006/data/plugin/projector/projector_binary.js:13226
    runAsyncTask http://localhost:6006/data/plugin/projector/projector_binary.js:13226
    projectTSNE http://localhost:6006/data/plugin/projector/projector_binary.js:13226
    promise callback*projectTSNE http://localhost:6006/data/plugin/projector/projector_binary.js:13226
    runTSNE http://localhost:6006/data/plugin/projector/projector_binary.js:15084
    showTSNE http://localhost:6006/data/plugin/projector/projector_binary.js:15084
    beginProjection http://localhost:6006/data/plugin/projector/projector_binary.js:15084
    showTab http://localhost:6006/data/plugin/projector/projector_binary.js:15084
    setupUIControls http://localhost:6006/data/plugin/projector/projector_binary.js:15084
    setupUIControls http://localhost:6006/data/plugin/projector/projector_binary.js:15084
    initialize http://localhost:6006/data/plugin/projector/projector_binary.js:15084
    ready http://localhost:6006/data/plugin/projector/projector_binary.js:15463
    o http://localhost:6006/data/plugin/projector/projector_binary.js:57
    promise callback*l http://localhost:6006/data/plugin/projector/projector_binary.js:57
    1 http://localhost:6006/data/plugin/projector/projector_binary.js:57
    __awaiter$1 http://localhost:6006/data/plugin/projector/projector_binary.js:57
    ready http://localhost:6006/data/plugin/projector/projector_binary.js:15463
    _enableProperties http://localhost:6006/data/plugin/projector/projector_binary.js:121
    _enableProperties http://localhost:6006/data/plugin/projector/projector_binary.js:387
    __enableOrFlushClients http://localhost:6006/data/plugin/projector/projector_binary.js:141
    _readyClients http://localhost:6006/data/plugin/projector/projector_binary.js:141
    _flushClients http://localhost:6006/data/plugin/projector/projector_binary.js:141
    _propertiesChanged http://localhost:6006/data/plugin/projector/projector_binary.js:141
    _flushProperties http://localhost:6006/data/plugin/projector/projector_binary.js:121
    ready http://localhost:6006/data/plugin/projector/projector_binary.js:141
    _enableProperties http://localhost:6006/data/plugin/projector/projector_binary.js:121
    TemplateInstanceBase http://localhost:6006/data/plugin/projector/projector_binary.js:425
    <anonymous> http://localhost:6006/data/plugin/projector/projector_binary.js:415
    i http://localhost:6006/data/plugin/projector/projector_binary.js:425
    o http://localhost:6006/data/plugin/projector/projector_binary.js:425
    __createAndInsertInstance http://localhost:6006/data/plugin/projector/projector_binary.js:472
    __ensureInstance http://localhost:6006/data/plugin/projector/projector_binary.js:472
    __render http://localhost:6006/data/plugin/projector/projector_binary.js:472
    __renderDebouncer http://localhost:6006/data/plugin/projector/projector_binary.js:472
    _timer http://localhost:6006/data/plugin/projector/projector_binary.js:283
    microtaskFlush http://localhost:6006/data/plugin/projector/projector_binary.js:121
    MutationCallback* http://localhost:6006/data/plugin/projector/projector_binary.js:121
    <anonymous> http://localhost:6006/data/plugin/projector/projector_binary.js:15597

[japie1235813]

I cannot reproduce the issue on tensorboard 2.8 using projector demo data. (located at tensorboard/plugins/projector/projector_demo.py)
It might be data specific bug. We cannot debug without the data you use. Please provide a script generating the data or a file path we can get access to.

In the meanwhile, you can see if you get the same error using the demo data.

1. bazel run tensorboard/plugins/projector:projector_demo should generate demo data in /tmp/projector_demo.py
2. tensorboard --logdir /tmp/projector_demo
3. access localhost:6006/#projector

[charleswilmot]

Thanks for your help,

I compiled tensorboard from source (v2.9.0) and ran it on my data, as well as on the projector_demo data.

The problem occurs on my data only, however I noticed that there is no problem when using the sphereize data option.

My data seem completely fine to me, there should not be an issue (see tensors.zip)

content of tensor.tsv :

0.41261935234069824	-0.30933845043182373	0.751000702381134	-0.6602575778961182	0.26799091696739197	-0.605022668838501	-0.40298160910606384
0.6585190296173096	0.043644074350595474	-0.3256230652332306	0.538148045539856	-0.8753103613853455	0.453938752412796	-0.07665182650089264
0.2773173451423645	-0.512788712978363	0.48738646507263184	-0.6247603297233582	-0.1932700276374817	-0.28596973419189453	-0.679033100605011
0.8333990573883057	0.3049888610839844	-0.4623134136199951	0.6774163842201233	-0.5180268287658691	-0.18519626557826996	0.7377837896347046
0.4817347228527069	-0.6345074772834778	0.15676507353782654	0.16463136672973633	-0.6295274496078491	0.35932156443595886	-0.14367364346981049
0.13213635981082916	0.26796332001686096	-0.062249861657619476	0.4746905267238617	-0.4472222328186035	-0.2612312138080597	0.12044423073530197
0.333714097738266	-0.5431245565414429	0.6923206448554993	-0.4834308326244354	-0.2934952974319458	0.29740390181541443	-0.4244072437286377
0.5357987284660339	-0.5883268713951111	0.06502329558134079	0.20051398873329163	-0.6870564222335815	-0.40181389451026917	-0.34142911434173584
0.47534018754959106	-0.6636059284210205	-0.2301163375377655	0.315655380487442	-0.6055193543434143	-0.16207623481750488	-0.23333695530891418
0.2952864170074463	-0.2280627340078354	0.2480943351984024	-0.15922397375106812	-0.2946184277534485	-0.14825209975242615	-0.22396112978458405
0.33015620708465576	-0.3459835350513458	0.2971732020378113	-0.2728993594646454	-0.6524147391319275	-0.44049203395843506	-0.11959771066904068
0.6441382765769958	-0.5825163125991821	0.21314644813537598	-0.578417181968689	-0.5481680035591125	-0.40366166830062866	-0.6208031177520752
0.47128528356552124	-0.536465585231781	0.5929620862007141	-0.26959314942359924	-0.7817497849464417	-0.021026642993092537	-0.7585403323173523
0.6326906681060791	-0.37740951776504517	0.6549848914146423	-0.1349419802427292	-0.5948198437690735	0.1556691974401474	-0.0696152001619339
0.8458236455917358	-0.47488731145858765	0.4259035885334015	0.31686681509017944	-0.7687863111495972	-0.018100261688232422	-0.7692713737487793
0.42964428663253784	0.5434109568595886	0.10773809254169464	0.4290538430213928	-0.13124626874923706	-0.506121814250946	0.2924951910972595
0.7975246906280518	-0.6590331792831421	-0.042071714997291565	0.22654739022254944	-0.6824729442596436	-0.21425096690654755	-0.4618348479270935
-0.148405060172081	-0.2579922676086426	0.4741310179233551	-0.040385231375694275	-0.8070585131645203	-0.5802115797996521	-0.29312875866889954
0.45750343799591064	-0.21344634890556335	-0.15280862152576447	-0.21006518602371216	-0.25632768869400024	0.3951415419578552	-0.27734851837158203
0.7272177934646606	-0.6832552552223206	0.4296260178089142	-0.5849362015724182	-0.6350590586662292	-0.24157863855361938	-0.4252912998199463
0.7962886691093445	-0.4267905056476593	-0.5654287934303284	0.6892534494400024	-0.5332249402999878	-0.563567578792572	-0.17114628851413727
0.3931999206542969	-0.17789587378501892	0.17210441827774048	-0.13622964918613434	0.20058494806289673	-0.5564549565315247	-0.15853093564510345
0.37487876415252686	-0.30409345030784607	-0.2475462555885315	0.05212647095322609	-0.6525878310203552	0.0717334970831871	0.26766011118888855
0.4448974132537842	-0.6488282680511475	0.03342601656913757	-0.4423765242099762	-0.5515333414077759	-0.4594171941280365	0.01024293340742588
0.5188003182411194	-0.29964447021484375	-0.05104481801390648	0.2591145932674408	-0.8005467057228088	-0.11691851913928986	-0.6269388198852539
0.35196101665496826	-0.3155381977558136	0.0795987918972969	0.18270696699619293	-0.529849648475647	-0.23710116744041443	-0.3905792534351349
0.3557889461517334	-0.5773909687995911	0.3515767455101013	-0.33512380719184875	-0.7901892066001892	-0.4049224853515625	-0.6401242613792419
0.34932807087898254	-0.49587321281433105	0.06906239688396454	-0.1958797425031662	-0.655144989490509	-0.23660080134868622	0.22102618217468262
0.5799153447151184	-0.6667081713676453	0.1411367952823639	-0.09799714386463165	-0.6723695993423462	0.019006073474884033	0.5814189314842224
0.401383638381958	-0.3841375708580017	-0.02125827595591545	-0.386139452457428	-0.41876420378685	-0.4384351670742035	0.06850621849298477
0.4032065272331238	-0.265353262424469	0.5387586355209351	-0.4858088195323944	-0.3007432520389557	-0.17323674261569977	-0.6917352676391602
0.6747868657112122	-0.08395448327064514	0.37104588747024536	-0.18843869864940643	-0.047626469284296036	-0.026271553710103035	-0.2600330412387848
0.4509996771812439	-0.27213147282600403	0.2742778956890106	-0.38338369131088257	-0.20523180067539215	-0.027020616456866264	0.3782220184803009
0.6094363331794739	-0.31812387704849243	-0.35825100541114807	0.23014004528522491	-0.6553797721862793	-0.027957014739513397	-0.03995659202337265
0.5508537292480469	-0.4567246735095978	-0.23126640915870667	-0.49492147564888	-0.5980444550514221	-0.18642856180667877	-0.02648032270371914
0.36935120820999146	-0.49257463216781616	-0.2601390480995178	0.49696654081344604	-0.8507259488105774	-0.21090862154960632	-0.34347638487815857
0.7493250370025635	-0.8383593559265137	-0.00713611114770174	-0.3969101309776306	-0.7778359055519104	0.2518765330314636	-0.4741354286670685
0.7399752736091614	-0.6550410985946655	0.5752899050712585	-0.5481942296028137	-0.36637353897094727	0.048813048750162125	-0.13648870587348938
0.33041349053382874	-0.1301327645778656	0.6927703022956848	-0.6606253385543823	-0.4263150990009308	0.1811126172542572	-0.4928678572177887
0.8457213640213013	-0.4819096326828003	0.378982812166214	-0.6493110656738281	-0.23972082138061523	-0.3908083438873291	-0.47456035017967224
0.39102593064308167	-0.7619760036468506	-0.253330260515213	-0.6983211636543274	-0.7757083773612976	-0.1964697688817978	-0.0028384397737681866
-0.0184350423514843	-0.0015192708233371377	0.4620024263858795	-0.4649481177330017	-0.08823603391647339	-0.17063046991825104	0.24492111802101135
0.5715298056602478	-0.264204204082489	-0.12471212446689606	0.6828669309616089	-0.9217164516448975	-0.3724055886268616	-0.32439976930618286
0.4992314279079437	-0.15657241642475128	-0.12467595189809799	0.1825639307498932	-0.6844205856323242	-0.23257820308208466	-0.22492866218090057
0.7308486104011536	-0.47906795144081116	-0.1587889939546585	0.38055485486984253	-0.40138429403305054	-0.07556025683879852	-0.36126673221588135
0.38808491826057434	0.12153726816177368	-0.25495216250419617	0.4636315405368805	-0.5586026310920715	-0.26795417070388794	0.4080509841442108
0.7001973986625671	-0.5225085020065308	-0.008574629202485085	-0.43982523679733276	0.09750426560640335	-0.5609787702560425	-0.1989474892616272
0.14878854155540466	-0.497171014547348	0.5285943150520325	-0.4777604043483734	-0.3623255491256714	0.16964948177337646	-0.17532356083393097
0.6289509534835815	-0.6687101125717163	0.7187771797180176	0.44262564182281494	-0.6036470532417297	0.15489450097084045	-0.8178285956382751
0.4608602225780487	-0.4202639162540436	0.5478454828262329	-0.7915196418762207	-0.18103908002376556	-0.20767171680927277	-0.48970353603363037

[charleswilmot]

I can replicate the issue on projector.tensorflow.org
With the following data:

0.1	0.2	0.3	0.4
0.5	0.6	0.7	0.8
0.9	0.1	0.2	0.3
0.4	0.5	0.6	0.7

The error in the console is different tho:

TypeError: x[L] is undefined

Again, Sphereizing the data prior to computing the T-SNE works, although I don't want to sphereize my data...

[japie1235813]

Re-running with your data now I saw a TSNE init error

Will file a bug on this.

[japie1235813]

I think the error comes from the nearest returned from knnComputation is undefined.
https://github.com/tensorflow/tensorboard/blob/master/tensorboard/plugins/projector/vz_projector/data.ts#L362

While we're prioritizing this bug, you can have a second look on the data and might find some insight? (I'm not a TSNE export so I don't have much to say here)

Might not be directly related to the bug but could you also provide the metadats.tsv you are using?

[japie1235813]

update: The nearest returned from knnComputation does not have the same number of neighbors for each data point , for example, with your second data it is [Array(3), Array(3), Array(2), Array(2)]
https://github.com/tensorflow/tensorboard/blob/master/tensorboard/plugins/projector/vz_projector/data.ts#L365

which cause the tsne implementation tried to index out of the neighbor
https://github.com/tensorflow/tensorboard/blob/master/tensorboard/plugins/projector/vz_projector/bh_tsne.ts#L180%28
(with your data the length of pRow is 3 which neighbors length is 2)

[AtharvaKalsekar]

Hello all,
I also am facing a similar error while visualizing t-SNE without spherizing it.

any suggestions?