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Error: ValueError: The parameter loc has invalid values #61

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asifajrof opened this issue Dec 13, 2022 · 1 comment
Open

Error: ValueError: The parameter loc has invalid values #61

asifajrof opened this issue Dec 13, 2022 · 1 comment

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@asifajrof
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While running on the tests data I am facing this error,

[2022-12-13 04:01:49,551] 🚨 ERROR : ValueError: The parameter loc has invalid values
              Trace Shapes:      
               Param Sites:      
          !!metagene!1!!_mu    10
          !!metagene!1!!_sd    10
mu_rate_g_condition-section  1 10
sd_rate_g_condition-section  1 10
              Sample Sites:      
        !!metagene!1!! dist 10  |
                      value 10  |
Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/trace_messenger.py", line 165, in __call__
    ret = self.fn(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/messenger.py", line 12, in _context_wrap
    return fn(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/xfuse/model/xfuse.py", line 133, in guide
    _go(self.get_experiment(experiment), x)
  File "/usr/local/lib/python3.8/dist-packages/xfuse/model/xfuse.py", line 129, in _go
    for i, y in enumerate(experiment.guide(x)):
  File "/usr/local/lib/python3.8/dist-packages/xfuse/model/experiment/st/st.py", line 647, in guide
    _sample_condition(batch_idx, slide, covariate, condition)
  File "/usr/local/lib/python3.8/dist-packages/xfuse/model/experiment/st/st.py", line 616, in _sample_condition
    Normal(mu_rate_g_condition, 1e-8 + sd_rate_g_condition),
  File "/usr/local/lib/python3.8/dist-packages/pyro/distributions/distribution.py", line 18, in __call__
    return super().__call__(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/torch/distributions/normal.py", line 50, in __init__
    super(Normal, self).__init__(batch_shape, validate_args=validate_args)
  File "/usr/local/lib/python3.8/dist-packages/torch/distributions/distribution.py", line 53, in __init__
    raise ValueError("The parameter {} has invalid values".format(param))
ValueError: The parameter loc has invalid values

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/xfuse/run.py", line 173, in run
    train(epochs)
  File "/usr/local/lib/python3.8/dist-packages/xfuse/train.py", line 62, in train
    _epoch(epoch=epoch)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/runtime.py", line 263, in _fn
    apply_stack(msg)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/runtime.py", line 198, in apply_stack
    default_process_message(msg)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/runtime.py", line 159, in default_process_message
    msg["value"] = msg["fn"](*msg["args"], **msg["kwargs"])
  File "/usr/local/lib/python3.8/dist-packages/xfuse/train.py", line 47, in _epoch
    _step(x=to_device(x))
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/runtime.py", line 263, in _fn
    apply_stack(msg)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/runtime.py", line 198, in apply_stack
    default_process_message(msg)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/runtime.py", line 159, in default_process_message
    msg["value"] = msg["fn"](*msg["args"], **msg["kwargs"])
  File "/usr/local/lib/python3.8/dist-packages/xfuse/train.py", line 35, in _step
    pyro.infer.SVI(model.model, model.guide, optim, loss).step(x)
  File "/usr/local/lib/python3.8/dist-packages/pyro/infer/svi.py", line 128, in step
    loss = self.loss_and_grads(self.model, self.guide, *args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/pyro/infer/trace_elbo.py", line 126, in loss_and_grads
    for model_trace, guide_trace in self._get_traces(model, guide, args, kwargs):
  File "/usr/local/lib/python3.8/dist-packages/pyro/infer/elbo.py", line 170, in _get_traces
    yield self._get_trace(model, guide, args, kwargs)
  File "/usr/local/lib/python3.8/dist-packages/pyro/infer/trace_elbo.py", line 52, in _get_trace
    model_trace, guide_trace = get_importance_trace(
  File "/usr/local/lib/python3.8/dist-packages/pyro/infer/enum.py", line 44, in get_importance_trace
    guide_trace = poutine.trace(guide, graph_type=graph_type).get_trace(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/trace_messenger.py", line 187, in get_trace
    self(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/trace_messenger.py", line 171, in __call__
    raise exc from e
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/trace_messenger.py", line 165, in __call__
    ret = self.fn(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/messenger.py", line 12, in _context_wrap
    return fn(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/xfuse/model/xfuse.py", line 133, in guide
    _go(self.get_experiment(experiment), x)
  File "/usr/local/lib/python3.8/dist-packages/xfuse/model/xfuse.py", line 129, in _go
    for i, y in enumerate(experiment.guide(x)):
  File "/usr/local/lib/python3.8/dist-packages/xfuse/model/experiment/st/st.py", line 647, in guide
    _sample_condition(batch_idx, slide, covariate, condition)
  File "/usr/local/lib/python3.8/dist-packages/xfuse/model/experiment/st/st.py", line 616, in _sample_condition
    Normal(mu_rate_g_condition, 1e-8 + sd_rate_g_condition),
  File "/usr/local/lib/python3.8/dist-packages/pyro/distributions/distribution.py", line 18, in __call__
    return super().__call__(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/torch/distributions/normal.py", line 50, in __init__
    super(Normal, self).__init__(batch_shape, validate_args=validate_args)
  File "/usr/local/lib/python3.8/dist-packages/torch/distributions/distribution.py", line 53, in __init__
    raise ValueError("The parameter {} has invalid values".format(param))
ValueError: The parameter loc has invalid values
              Trace Shapes:      
               Param Sites:      
          !!metagene!1!!_mu    10
          !!metagene!1!!_sd    10
mu_rate_g_condition-section  1 10
sd_rate_g_condition-section  1 10
              Sample Sites:      
        !!metagene!1!! dist 10  |
                      value 10  |

ERROR:xfuse.logging.logging:ValueError: The parameter loc has invalid values
              Trace Shapes:      
               Param Sites:      
          !!metagene!1!!_mu    10
          !!metagene!1!!_sd    10
mu_rate_g_condition-section  1 10
sd_rate_g_condition-section  1 10
              Sample Sites:      
        !!metagene!1!! dist 10  |
                      value 10  |
Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/trace_messenger.py", line 165, in __call__
    ret = self.fn(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/messenger.py", line 12, in _context_wrap
    return fn(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/xfuse/model/xfuse.py", line 133, in guide
    _go(self.get_experiment(experiment), x)
  File "/usr/local/lib/python3.8/dist-packages/xfuse/model/xfuse.py", line 129, in _go
    for i, y in enumerate(experiment.guide(x)):
  File "/usr/local/lib/python3.8/dist-packages/xfuse/model/experiment/st/st.py", line 647, in guide
    _sample_condition(batch_idx, slide, covariate, condition)
  File "/usr/local/lib/python3.8/dist-packages/xfuse/model/experiment/st/st.py", line 616, in _sample_condition
    Normal(mu_rate_g_condition, 1e-8 + sd_rate_g_condition),
  File "/usr/local/lib/python3.8/dist-packages/pyro/distributions/distribution.py", line 18, in __call__
    return super().__call__(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/torch/distributions/normal.py", line 50, in __init__
    super(Normal, self).__init__(batch_shape, validate_args=validate_args)
  File "/usr/local/lib/python3.8/dist-packages/torch/distributions/distribution.py", line 53, in __init__
    raise ValueError("The parameter {} has invalid values".format(param))
ValueError: The parameter loc has invalid values

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/xfuse/run.py", line 173, in run
    train(epochs)
  File "/usr/local/lib/python3.8/dist-packages/xfuse/train.py", line 62, in train
    _epoch(epoch=epoch)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/runtime.py", line 263, in _fn
    apply_stack(msg)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/runtime.py", line 198, in apply_stack
    default_process_message(msg)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/runtime.py", line 159, in default_process_message
    msg["value"] = msg["fn"](*msg["args"], **msg["kwargs"])
  File "/usr/local/lib/python3.8/dist-packages/xfuse/train.py", line 47, in _epoch
    _step(x=to_device(x))
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/runtime.py", line 263, in _fn
    apply_stack(msg)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/runtime.py", line 198, in apply_stack
    default_process_message(msg)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/runtime.py", line 159, in default_process_message
    msg["value"] = msg["fn"](*msg["args"], **msg["kwargs"])
  File "/usr/local/lib/python3.8/dist-packages/xfuse/train.py", line 35, in _step
    pyro.infer.SVI(model.model, model.guide, optim, loss).step(x)
  File "/usr/local/lib/python3.8/dist-packages/pyro/infer/svi.py", line 128, in step
    loss = self.loss_and_grads(self.model, self.guide, *args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/pyro/infer/trace_elbo.py", line 126, in loss_and_grads
    for model_trace, guide_trace in self._get_traces(model, guide, args, kwargs):
  File "/usr/local/lib/python3.8/dist-packages/pyro/infer/elbo.py", line 170, in _get_traces
    yield self._get_trace(model, guide, args, kwargs)
  File "/usr/local/lib/python3.8/dist-packages/pyro/infer/trace_elbo.py", line 52, in _get_trace
    model_trace, guide_trace = get_importance_trace(
  File "/usr/local/lib/python3.8/dist-packages/pyro/infer/enum.py", line 44, in get_importance_trace
    guide_trace = poutine.trace(guide, graph_type=graph_type).get_trace(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/trace_messenger.py", line 187, in get_trace
    self(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/trace_messenger.py", line 171, in __call__
    raise exc from e
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/trace_messenger.py", line 165, in __call__
    ret = self.fn(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/pyro/poutine/messenger.py", line 12, in _context_wrap
    return fn(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/xfuse/model/xfuse.py", line 133, in guide
    _go(self.get_experiment(experiment), x)
  File "/usr/local/lib/python3.8/dist-packages/xfuse/model/xfuse.py", line 129, in _go
    for i, y in enumerate(experiment.guide(x)):
  File "/usr/local/lib/python3.8/dist-packages/xfuse/model/experiment/st/st.py", line 647, in guide
    _sample_condition(batch_idx, slide, covariate, condition)
  File "/usr/local/lib/python3.8/dist-packages/xfuse/model/experiment/st/st.py", line 616, in _sample_condition
    Normal(mu_rate_g_condition, 1e-8 + sd_rate_g_condition),
  File "/usr/local/lib/python3.8/dist-packages/pyro/distributions/distribution.py", line 18, in __call__
    return super().__call__(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/torch/distributions/normal.py", line 50, in __init__
    super(Normal, self).__init__(batch_shape, validate_args=validate_args)
  File "/usr/local/lib/python3.8/dist-packages/torch/distributions/distribution.py", line 53, in __init__
    raise ValueError("The parameter {} has invalid values".format(param))
ValueError: The parameter loc has invalid values
              Trace Shapes:      
               Param Sites:      
          !!metagene!1!!_mu    10
          !!metagene!1!!_sd    10
mu_rate_g_condition-section  1 10
sd_rate_g_condition-section  1 10
              Sample Sites:      
        !!metagene!1!! dist 10  |
                      value 10  |

[2022-12-13 04:01:49,552] ℹ : Saving session to exception.session
INFO:xfuse.logging.logging:Saving session to exception.session

the error is not consistent, that is, it goes away sometimes if I run it from scratch again. what could be the reason behind this error?

changes i made:
in the xfuse/_config.py file: at 155 line -> ("epochs", Item(value=200)),
cause, higher epoch value was giving me memory error.
@ludvb
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ludvb commented Mar 30, 2023

Thank you for this report and sorry for my late reply! Can you provide the config.toml file you used for this analysis?

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@ludvb @asifajrof