immuneML.reports.ml_reports package

Submodules

immuneML.reports.ml_reports.CoefficientPlottingSetting module

class immuneML.reports.ml_reports.CoefficientPlottingSetting.CoefficientPlottingSetting(value)[source]

Bases: enum.Enum

An enumeration.

ALL = 'all'
CUTOFF = 'cutoff'
NONZERO = 'nonzero'
N_LARGEST = 'n_largest'

immuneML.reports.ml_reports.CoefficientPlottingSettingList module

class immuneML.reports.ml_reports.CoefficientPlottingSettingList.CoefficientPlottingSettingList[source]

Bases: collections.abc.MutableSequence

check(v)[source]
insert(i, v)[source]

S.insert(index, value) – insert value before index

immuneML.reports.ml_reports.Coefficients module

class immuneML.reports.ml_reports.Coefficients.Coefficients(coefs_to_plot: immuneML.reports.ml_reports.CoefficientPlottingSettingList.CoefficientPlottingSettingList, cutoff: list, n_largest: list, train_dataset: Optional[immuneML.data_model.dataset.Dataset.Dataset] = None, test_dataset: Optional[immuneML.data_model.dataset.Dataset.Dataset] = None, method: Optional[immuneML.ml_methods.MLMethod.MLMethod] = None, result_path: Optional[pathlib.Path] = None, name: Optional[str] = None, hp_setting: Optional[immuneML.hyperparameter_optimization.HPSetting.HPSetting] = None)[source]

Bases: immuneML.reports.ml_reports.MLReport.MLReport

A report that plots the coefficients for a given ML method in a barplot. Can be used for LogisticRegression, SVM and RandomForestClassifier. In the case of RandomForest, the feature importances will be plotted.

When used in TrainMLModel instruction, the report can be specified under ‘models’, both on the selection and assessment levels.

Which coefficients should be plotted (for example: only nonzero, above a certain threshold, …) can be specified. Multiple options can be specified simultaneously. By default the 25 largest coefficients are plotted. The full set of coefficients will also be exported as a csv file.

Parameters

  • coefs_to_plot (list) – A list specifying which coefficients should be plotted. For options see CoefficientPlottingSetting.

  • cutoff (list) – If ‘cutoff’ is specified under ‘coefs_to_plot’, the cutoff values can be specified here. The coefficients which have an absolute value equal to or greater than the cutoff will be plotted.

  • n_largest (list) – If ‘n_largest’ is specified under ‘coefs_to_plot’, the values for n can be specified here. These should be integer values. The n largest coefficients are determined based on their absolute values.

YAML specification:

my_coef_report:
    Coefficients:
        coefs_to_plot:
            - all
            - nonzero
            - cutoff
            - n_largest
        cutoff:
            - 0.1
            - 0.01
        n_largest:
            - 5
            - 10
classmethod build_object(**kwargs)[source]

Creates the object of the subclass of the Report class from the parameters so that it can be used in the analysis. Depending on the type of the report, the parameters provided here will be provided in parsing time, while the other necessary parameters (e.g., subset of the data from which the report should be created) will be provided at runtime. For more details, see specific direct subclasses of this class, describing different types of reports.

Parameters

**kwargs – keyword arguments that will be provided by users in the specification (if immuneML is used as a command line tool) or in the dictionary when calling the method from the code, and which should be used to create the report object

Returns

the object of the appropriate report class

check_prerequisites()[source]

Checks prerequisites for the generation of the report of specific class (e.g., if the class of the MLMethod instance is the one required by the report, if the data has been encoded to make a report of encoded dataset). In the instructions in immuneML, this function is used to determine whether to call generate_report() in the specific situation. Each report subclass has its own set of prerequisites. If the report cannot be run, the information on this will be logged and the report skipped in the specific situation. No error will be raised. See subclasses of the class Instruction for more information on how the reports are executed.

Returns

boolean value True if the prerequisites are o.k., and False otherwise.

static get_documentation()[source]

immuneML.reports.ml_reports.DeepRCMotifDiscovery module

class immuneML.reports.ml_reports.DeepRCMotifDiscovery.DeepRCMotifDiscovery(n_steps, threshold, name: Optional[str] = None)[source]

Bases: immuneML.reports.ml_reports.MLReport.MLReport

This report plots the contributions of (i) input sequences and (ii) kernels to trained DeepRC model with respect to the test dataset. Contributions are computed using integrated gradients (IG). This report produces two figures:

  • inputs_integrated_gradients: Shows the contributions of the characters within the input sequences (test dataset) that was most important for immune status prediction of the repertoire. IG is only applied to sequences of positive class repertoires.

  • kernel_integrated_gradients: Shows the 1D CNN kernels with the highest contribution over all positions and amino acids.

For both inputs and kernels: Larger characters in the extracted motifs indicate higher contribution, with blue indicating positive contribution and red indicating negative contribution towards the prediction of the immune status. For kernels only: contributions to positional encoding are indicated by < (beginning of sequence), ∧ (center of sequence), and > (end of sequence).

See DeepRCMotifDiscovery for repertoire classification for a usage example.

Reference: Michael Widrich, Bernhard Schäfl, Milena Pavlović, Geir Kjetil Sandve, Sepp Hochreiter, Victor Greiff, Günter Klambauer ‘DeepRC: Immune repertoire classification with attention-based deep massive multiple instance learning’. bioRxiv preprint doi: https://doi.org/10.1101/2020.04.12.03815

Parameters

  • n_steps (int) – Number of IG steps (more steps -> better path integral -> finer contribution values). 50 is usually good enough.

  • threshold (float) – Only applies to the plotting of kernels. Contributions are normalized to range [0, 1], and only kernels with normalized contributions above threshold are plotted.

YAML specification:

my_deeprc_report:
    DeepRCMotifDiscovery:
        threshold: 0.5
        n_steps: 50
classmethod build_object(**kwargs)[source]

Creates the object of the subclass of the Report class from the parameters so that it can be used in the analysis. Depending on the type of the report, the parameters provided here will be provided in parsing time, while the other necessary parameters (e.g., subset of the data from which the report should be created) will be provided at runtime. For more details, see specific direct subclasses of this class, describing different types of reports.

Parameters

**kwargs – keyword arguments that will be provided by users in the specification (if immuneML is used as a command line tool) or in the dictionary when calling the method from the code, and which should be used to create the report object

Returns

the object of the appropriate report class

check_prerequisites()[source]

Checks prerequisites for the generation of the report of specific class (e.g., if the class of the MLMethod instance is the one required by the report, if the data has been encoded to make a report of encoded dataset). In the instructions in immuneML, this function is used to determine whether to call generate_report() in the specific situation. Each report subclass has its own set of prerequisites. If the report cannot be run, the information on this will be logged and the report skipped in the specific situation. No error will be raised. See subclasses of the class Instruction for more information on how the reports are executed.

Returns

boolean value True if the prerequisites are o.k., and False otherwise.

compute_contributions(intgrds_set_loader: torch.utils.data.dataloader.DataLoader, deeprc_model, n_steps: int = 50, threshold: float = 0.5, path_inputs: pathlib.Path = PosixPath('inputs_integrated_gradients.pdf'), path_kernels: pathlib.Path = PosixPath('kernel_integrated_gradients.pdf'))[source]

Compute and plot contributions of sequences and motifs to trained DeepRC model, given a dataset. Contribution is computed using integrated gradients (IG).

Author – Michael Widrich Created on – 2020-07-20 Contact – michael.widrich@jku.at

intgrds_set_loadertorch.utils.data.DataLoader

The dataset to compute IG for in form of a PyTorch DataLoader following the DeepRC format. E.g. one of the dataloaders returned by deeprc.deeprc_binary.predefined_datasets.cmv_dataset().

deeprc_modeldeeprc.deeprc_binary.architectures.DeepRC

DeepRC model to compute IG for. Weights of first CNN layer are accessed via deeprc_model.sequence_embedding_16bit.conv_aas.weight .

n_stepsint

Number of IG steps (more steps -> better path integral -> finer contribution values). 50 is usually good enough.

thresholdfloat

Threshold for plotting of kernels (=motifs). Contributions are normalized to range [0, 1] and then threshold is applied. 0.5 -> only kernels with normalized contributions above 0.5 are plotted.

path_inputsPath

path for inputs integrated gradients plot

path_kernelsPath

path for kernels integrated gradients plot

plot_inputs_text(chars, colorgrad, seq_lens, file_path)[source]

Author – Michael Widrich Created on – 2020-07-20 Contact – michael.widrich@jku.at

plot_kernels_text(kernels, charset, file_path)[source]

Author – Michael Widrich Created on – 2020-07-20 Contact – michael.widrich@jku.at

immuneML.reports.ml_reports.MLReport module

class immuneML.reports.ml_reports.MLReport.MLReport(train_dataset: Optional[immuneML.data_model.dataset.Dataset.Dataset] = None, test_dataset: Optional[immuneML.data_model.dataset.Dataset.Dataset] = None, method: Optional[immuneML.ml_methods.MLMethod.MLMethod] = None, result_path: Optional[pathlib.Path] = None, name: Optional[str] = None, hp_setting: Optional[immuneML.hyperparameter_optimization.HPSetting.HPSetting] = None, label=None)[source]

Bases: immuneML.reports.Report.Report

ML model reports show some type of features or statistics about one trained ML model.

In the TrainMLModel instruction, ML model reports can be specified inside the ‘selection’ or ‘assessment’ specification under the key ‘reports:models’.

When using the reports with TrainMLModel instruction, the arguments defined below are set at runtime by the instruction. Concrete classes inheriting MLReport may include additional parameters that will be set by the user in the form of input arguments.

Parameters

  • train_dataset (Dataset) – a dataset object (repertoire, receptor or sequence dataset) with encoded_data attribute set to an EncodedData object that was used for training the ML method

  • test_dataset (Dataset) – same as train_dataset, except it is not used for training and then maybe be used for testing the method

  • method (MLMethod) – a trained instance of a concrete subclass of MLMethod object

  • result_path (Path) – location where the report results will be stored

  • hp_setting (HPSetting) – a HPSetting object describing the ML method, encoding and preprocessing used

  • label (str) – name of the label for which the model was trained

  • name (str) – user-defined name of the report used in the HTML overview automatically generated by the platform

static get_title()[source]

immuneML.reports.ml_reports.MotifSeedRecovery module

class immuneML.reports.ml_reports.MotifSeedRecovery.MotifSeedRecovery(implanted_motifs_per_label, train_dataset: Optional[immuneML.data_model.dataset.Dataset.Dataset] = None, test_dataset: Optional[immuneML.data_model.dataset.Dataset.Dataset] = None, method: Optional[immuneML.ml_methods.MLMethod.MLMethod] = None, result_path: Optional[pathlib.Path] = None, name: Optional[str] = None)[source]

Bases: immuneML.reports.ml_reports.MLReport.MLReport

This report can be used to show how well implanted motifs (for example, through the Simulation instruction) can be recovered by various machine learning methods using the k-mer encoding. This report creates a boxplot, where the x axis (box grouping) represents the maximum possible overlap between an implanted motif seed and a kmer feature (measured in number of positions), and the y axis shows the coefficient size of the respective kmer feature. If the machine learning method has learned the implanted motif seeds, the coefficient size is expected to be largest for the kmer features with high overlap to the motif seeds.

Note that to use this report, the following criteria must be met: - KmerFrequencyEncoder must be used. - One of the following classifiers must be used: RandomForestClassifier, LogisticRegression, SVM - For each label, the implanted motif seeds relevant to that label must be specified

To find the overlap score between kmer features and implanted motif seeds, the two sequences are compared in a sliding window approach, and the maximum overlap is calculated.

Overlap scores between kmer features and implanted motifs are calculated differently based on the Hamming distance that was allowed during implanting.

Without hamming distance:
Seed:     AAA  -> score = 3
Feature: xAAAx
          ^^^

Seed:     AAA  -> score = 0
Feature: xAAxx

With hamming distance:
Seed:     AAA  -> score = 3
Feature: xAAAx
          ^^^

Seed:     AAA  -> score = 2
Feature: xAAxx
          ^^

Furthermore, gap positions in the motif seed are ignored:
Seed:     A/AA  -> score = 3
Feature: xAxAAx
          ^/^^

See Recovering simulated immune signals for more details and an example plot.

Parameters

implanted_motifs_per_label (dict) –

a nested dictionary that specifies the motif seeds that were implanted in the given dataset. The first level of keys in this dictionary represents the different labels. In the inner dictionary there should be two keys: “seeds” and “hamming_distance”

seeds: a list of motif seeds. The seeds may contain gaps, specified by a ‘/’ symbol. hamming_distance: A boolean value that specifies whether hamming distance was allowed when implanting the

motif seeds for a given label. Note that this applies to all seeds for this label.

gap_sizes: a list of all the possible gap sizes that were used when implanting a gapped motif seed.

When no gapped seeds are used, this value has no effect.

YAML specification:

my_motif_report:
    MotifSeedRecovery:
        implanted_motifs_per_label:
            CD:
                seeds:
                - AA/A
                - AAA
                hamming_distance: False
                gap_sizes:
                - 0
                - 1
                - 2
            T1D
                seeds:
                - CC/C
                - CCC
                hamming_distance: True
                gap_sizes:
                - 2
classmethod build_object(**kwargs)[source]

Creates the object of the subclass of the Report class from the parameters so that it can be used in the analysis. Depending on the type of the report, the parameters provided here will be provided in parsing time, while the other necessary parameters (e.g., subset of the data from which the report should be created) will be provided at runtime. For more details, see specific direct subclasses of this class, describing different types of reports.

Parameters

**kwargs – keyword arguments that will be provided by users in the specification (if immuneML is used as a command line tool) or in the dictionary when calling the method from the code, and which should be used to create the report object

Returns

the object of the appropriate report class

calculate_seed_overlap(motif_seeds, features, overlap_fn)[source]
check_prerequisites()[source]

Checks prerequisites for the generation of the report of specific class (e.g., if the class of the MLMethod instance is the one required by the report, if the data has been encoded to make a report of encoded dataset). In the instructions in immuneML, this function is used to determine whether to call generate_report() in the specific situation. Each report subclass has its own set of prerequisites. If the report cannot be run, the information on this will be logged and the report skipped in the specific situation. No error will be raised. See subclasses of the class Instruction for more information on how the reports are executed.

Returns

boolean value True if the prerequisites are o.k., and False otherwise.

hamming_overlap(seed, feature)[source]
identical_overlap(seed, feature)[source]
max_overlap_sliding(seed, feature, overlap_fn)[source]

immuneML.reports.ml_reports.ROCCurve module

class immuneML.reports.ml_reports.ROCCurve.ROCCurve(name: Optional[str] = None)[source]

Bases: immuneML.reports.ml_reports.MLReport.MLReport

A report that plots the ROC curve for a binary classifier.

YAML specification:

reports:
  my_roc_report: ROCCurve
classmethod build_object(**kwargs)[source]

Creates the object of the subclass of the Report class from the parameters so that it can be used in the analysis. Depending on the type of the report, the parameters provided here will be provided in parsing time, while the other necessary parameters (e.g., subset of the data from which the report should be created) will be provided at runtime. For more details, see specific direct subclasses of this class, describing different types of reports.

Parameters

**kwargs – keyword arguments that will be provided by users in the specification (if immuneML is used as a command line tool) or in the dictionary when calling the method from the code, and which should be used to create the report object

Returns

the object of the appropriate report class

check_prerequisites()[source]

Checks prerequisites for the generation of the report of specific class (e.g., if the class of the MLMethod instance is the one required by the report, if the data has been encoded to make a report of encoded dataset). In the instructions in immuneML, this function is used to determine whether to call generate_report() in the specific situation. Each report subclass has its own set of prerequisites. If the report cannot be run, the information on this will be logged and the report skipped in the specific situation. No error will be raised. See subclasses of the class Instruction for more information on how the reports are executed.

Returns

boolean value True if the prerequisites are o.k., and False otherwise.

immuneML.reports.ml_reports.SequenceAssociationLikelihood module

class immuneML.reports.ml_reports.SequenceAssociationLikelihood.SequenceAssociationLikelihood(method: Optional[immuneML.ml_methods.MLMethod.MLMethod] = None, result_path: Optional[pathlib.Path] = None, name: Optional[str] = None, **kwargs)[source]

Bases: immuneML.reports.ml_reports.MLReport.MLReport

Plots the beta distribution used as a prior for class assignment in ProbabilisticBinaryClassifier. The distribution plotted shows the probability that a sequence is associated with a given class for a label.

Attributes: the report does not take in any arguments.

YAML specification:

my_sequence_assoc_report: SequenceAssociationLikelihood
DISTRIBUTION_PERCENTAGE_TO_SHOW = 0.999
STEP = 400
classmethod build_object(**kwargs)[source]

Creates the object of the subclass of the Report class from the parameters so that it can be used in the analysis. Depending on the type of the report, the parameters provided here will be provided in parsing time, while the other necessary parameters (e.g., subset of the data from which the report should be created) will be provided at runtime. For more details, see specific direct subclasses of this class, describing different types of reports.

Parameters

**kwargs – keyword arguments that will be provided by users in the specification (if immuneML is used as a command line tool) or in the dictionary when calling the method from the code, and which should be used to create the report object

Returns

the object of the appropriate report class

check_prerequisites()[source]

Checks prerequisites for the generation of the report of specific class (e.g., if the class of the MLMethod instance is the one required by the report, if the data has been encoded to make a report of encoded dataset). In the instructions in immuneML, this function is used to determine whether to call generate_report() in the specific situation. Each report subclass has its own set of prerequisites. If the report cannot be run, the information on this will be logged and the report skipped in the specific situation. No error will be raised. See subclasses of the class Instruction for more information on how the reports are executed.

Returns

boolean value True if the prerequisites are o.k., and False otherwise.

get_distribution_limits() → Tuple[float, float][source]

immuneML.reports.ml_reports.TCRdistMotifDiscovery module

class immuneML.reports.ml_reports.TCRdistMotifDiscovery.TCRdistMotifDiscovery(train_dataset: Optional[immuneML.data_model.dataset.ReceptorDataset.ReceptorDataset] = None, test_dataset: Optional[immuneML.data_model.dataset.ReceptorDataset.ReceptorDataset] = None, method: Optional[immuneML.ml_methods.MLMethod.MLMethod] = None, result_path: Optional[pathlib.Path] = None, name: Optional[str] = None, cores: Optional[int] = None, context: Optional[dict] = None, positive_class_name=None, min_cluster_size: Optional[int] = None, use_reference_sequences: Optional[bool] = None)[source]

Bases: immuneML.reports.ml_reports.MLReport.MLReport

The report for discovering motifs in paired immune receptor data of given specificity based on TCRdist3. The receptors are hierarchically clustered based on the tcrdist distance and then motifs are discovered for each cluster. The report outputs logo plots for the motifs along with the raw data used for plotting in csv format.

For the implementation, TCRdist3 library was used (source code available here). More details on the functionality used for this report are available here.

Original publications:

Dash P, Fiore-Gartland AJ, Hertz T, et al. Quantifiable predictive features define epitope-specific T cell receptor repertoires. Nature. 2017; 547(7661):89-93. doi:10.1038/nature22383

Mayer-Blackwell K, Schattgen S, Cohen-Lavi L, et al. TCR meta-clonotypes for biomarker discovery with tcrdist3: quantification of public, HLA-restricted TCR biomarkers of SARS-CoV-2 infection. bioRxiv. Published online December 26, 2020:2020.12.24.424260. doi:10.1101/2020.12.24.424260

Parameters

  • positive_class_name (str) – the class value (e.g., epitope) used to select only the receptors that are specific to the given epitope so that

  • those sequences are used to infer motifs; the reference receptors as required by TCRdist will be the ones from the dataset that have (only) –

  • or no epitope specified in their metadata; if the labels are available only on the epitope level (e.g. (different) –

  • is "AVFDRKSDAK" and (label) –

  • are True and False) (classes) –

  • here it should be specified that only the receptors with value "True" for label "AVFDRKSDAK" should be used; (then) –

  • is no default value for this argument (there) –

  • cores (int) – number of processes to use for the computation of the distance and motifs

  • min_cluster_size (int) – the minimum size of the cluster to discover the motifs for

  • use_reference_sequences (bool) – when showing motifs, this parameter defines if reference sequences should be provided as well as a background

YAML specification:

my_tcr_dist_report: # user-defined name
    TCRdistMotifDiscovery:
        positive_class_name: True # class name, could also be epitope name, depending on how it's defined in the dataset
        cores: 4
        min_cluster_size: 30
        use_reference_sequences: False
classmethod build_object(**kwargs)[source]

Creates the object of the subclass of the Report class from the parameters so that it can be used in the analysis. Depending on the type of the report, the parameters provided here will be provided in parsing time, while the other necessary parameters (e.g., subset of the data from which the report should be created) will be provided at runtime. For more details, see specific direct subclasses of this class, describing different types of reports.

Parameters

**kwargs – keyword arguments that will be provided by users in the specification (if immuneML is used as a command line tool) or in the dictionary when calling the method from the code, and which should be used to create the report object

Returns

the object of the appropriate report class

check_prerequisites()[source]

Checks prerequisites for the generation of the report of specific class (e.g., if the class of the MLMethod instance is the one required by the report, if the data has been encoded to make a report of encoded dataset). In the instructions in immuneML, this function is used to determine whether to call generate_report() in the specific situation. Each report subclass has its own set of prerequisites. If the report cannot be run, the information on this will be logged and the report skipped in the specific situation. No error will be raised. See subclasses of the class Instruction for more information on how the reports are executed.

Returns

boolean value True if the prerequisites are o.k., and False otherwise.

set_context(context: dict)[source]

Context is a dictionary with information that is accessible from the level of instruction and can be used to precompute certain values that can be later reused to speed up the generation of the subsequent reports of the same time. For instance, if one should compute the distance between all repertoires based on the sequence content, it is possible to store the full dataset in the context, compute the distances on the full dataset and then only extract the distances need for the current dataset in the later calls (e.g., when training dataset is passed as input). Only some reports will need this functionality.

Warning: It is very important to be careful when using the context to avoid leaking the information between training and test datasets.

Parameters

context (dict) – a dictionary where the values are variables that are typically only available on the top-level of the instruction, and which are used to precompute results in order to speed up subsequent generation of the same report on subsets of those values.

Returns

self - so that it can be chained with the other function calls

immuneML.reports.ml_reports.TrainingPerformance module

class immuneML.reports.ml_reports.TrainingPerformance.TrainingPerformance(metrics: set, train_dataset: immuneML.data_model.dataset.Dataset.Dataset = None, test_dataset: immuneML.data_model.dataset.Dataset.Dataset = None, method: immuneML.ml_methods.MLMethod.MLMethod = None, result_path: pathlib.Path = None, name: str = None, hp_setting: <module 'immuneML.hyperparameter_optimization.HPSetting' from '/Users/milenpa/PycharmProjects/BMIImmuneML/immuneML/hyperparameter_optimization/HPSetting.py'> = None)[source]

Bases: immuneML.reports.ml_reports.MLReport.MLReport

A report that plots the evaluation metrics for the performance given machine learning model and training dataset. The available metrics are accuracy, balanced_accuracy, confusion_matrix, f1_micro, f1_macro, f1_weighted, precision, recall, auc and log_loss (see immuneML.environment.Metric.Metric).

Parameters

metrics (list) – A list of metrics used to evaluate training performance. See immuneML.environment.Metric.Metric for available options.

YAML specification:

my_performance_report:
    TrainingPerformance:
        metrics:
            - accuracy
            - balanced_accuracy
            - confusion_matrix
            - f1_micro
            - f1_macro
            - f1_weighted
            - precision
            - recall
            - auc
            - log_loss
classmethod build_object(**kwargs)[source]

Creates the object of the subclass of the Report class from the parameters so that it can be used in the analysis. Depending on the type of the report, the parameters provided here will be provided in parsing time, while the other necessary parameters (e.g., subset of the data from which the report should be created) will be provided at runtime. For more details, see specific direct subclasses of this class, describing different types of reports.

Parameters

**kwargs – keyword arguments that will be provided by users in the specification (if immuneML is used as a command line tool) or in the dictionary when calling the method from the code, and which should be used to create the report object

Returns

the object of the appropriate report class

check_prerequisites() → bool[source]

Checks prerequisites for the generation of the report of specific class (e.g., if the class of the MLMethod instance is the one required by the report, if the data has been encoded to make a report of encoded dataset). In the instructions in immuneML, this function is used to determine whether to call generate_report() in the specific situation. Each report subclass has its own set of prerequisites. If the report cannot be run, the information on this will be logged and the report skipped in the specific situation. No error will be raised. See subclasses of the class Instruction for more information on how the reports are executed.

Returns

boolean value True if the prerequisites are o.k., and False otherwise.

Module contents