Crispy13

According to "https://www.med.upenn.edu/sbia/brats2018/tasks.html": > The TC describes the bulk of the tumor, which is what is typically resected. The TC entails the ET, as well as the necrotic (fluid-filled) and...

AttributeError: 'Functional' object has no attribute 'loss_weights'

6

**The code i used:** ``` model = P['model'](P['backbone'], encoder_weights='imagenet', encoder_freeze = True)#, gn_groups = P['gn_groups']) if P['use_reg']: model = set_regularization(model, kernel_regularizer=P['reg_class'](P['reg_lambda']), bias_regularizer = P['reg_class'](P['reg_lambda']) ) dice = DiceCoefficient() if P['mixed_precision']:...

InaccessibleTensorError: The tensor 'Tensor("mul:0", shape=(), dtype=float32)' cannot be accessed here

2

In Chapter 12, ``` class ReconstructingRegressor(keras.models.Model): def __init__(self, output_dim, **kwargs): super().__init__(**kwargs) self.hidden = [keras.layers.Dense(30, activation="selu", kernel_initializer="lecun_normal") for _ in range(5)] self.out = keras.layers.Dense(output_dim) # TODO: check https://github.com/tensorflow/tensorflow/issues/26260 #self.reconstruction_mean = keras.metrics.Mean(name="reconstruction_error")...

[core] ray.init raises Error when giving _temp_dir argument

5

### What happened + What you expected to happen Jupyter Server python 3.10.6 ``` ray.init(num_cpus = 32) ``` works But ``` ray.init(num_cpus=32, _temp_dir =".tmp/ray") ``` raised: ``` Traceback (most recent...

sklearn.base.clone failed with Catboostclassifier in a Pipeline

3

Problem: ``` from catboost import CatBoostClassifier from sklearn.base import clone from sklearn.pipeline import Pipeline pp = Pipeline( [ ('ML', CatBoostClassifier(learning_rate=None)), ] ) pp.set_params(**{'ML__learning_rate':None}) pp.get_params() pp_clone = clone(pp) ``` **raised:** ```...

Is there `--offline` mode?

1

'Cargo run' has `--offline` mode which disables internet usage. It seems that `cargo flamegraph --offline` does not work. Can I disable internet usage when run flamegraph?

``` from nucleus.protos import reads_pb2 from nucleus.io import sam read_requirements = reads_pb2.ReadRequirements() sam_reader = sam.SamReader( input_path="NA12878_sliced.bam", read_requirements=read_requirements) for r in sam_reader: print(r) ``` ``` RuntimeError: PythonNext() argument read is not...

An option to limit cluster submission by total threads

6

As far as I know, we can limit job submission of snakemake with `--jobs`. But is there an option to limit job submissions by total threads usage? For example, if...

Multiple runs show different unique read count. `vec` is sorted differently a bit per run. Some `Match`s have the same `read_break` and `seq.length()`. This was found with hg19.fa, druggable.hg18.csv, test...

In indexer.cpp:347 ```cpp ... // or smaller positive if contig is the same if(left.startGP.contig == right.startGP.contig && abs(left.startGP.position) < abs(left.startGP.position)) return true; else return false; ... ``` Your intention was...