likelihood_function

Calculates cross-validated likelihood for a set of parameters by:<ol>
<li>Splitting data into training/validation sets</li>
<li>Fitting model on training data</li>
<li>Evaluating likelihood on validation set</li>
<li>Repeating across folds
To calculate one NLL per set of parameters, the function uses a pooled errors approach which combines
all validation errors into one set, then calculate a single NLL. This approach has two main advantages:
1- It treats all validation errors equally, respecting the underlying error distribution assumption
2- It properly accounts for the total number of validation points</li>
</ol>

internal

An implementation of the TopoLow algorithm, a novel, physics-inspired method for
antigenic cartography. TopoLow addresses significant challenges in mapping antigenic relationships,
especially from sparse and noisy experimental data. The package transforms cross-reactivity and
binding affinity measurements into accurate spatial representations in a phenotype space.
Key features include:
* Robust Mapping from Sparse Data: Effectively creates complete and consistent maps even with high
proportions of missing data (e.g., >95%).
* Physics-Inspired Optimization: Models antigens as particles connected by springs (for measured
interactions) and subject to repulsive forces (for missing interactions), reducing the need for
complex gradient computations.
* Automatic Dimensionality Detection: Employs a likelihood-based approach to determine the optimal
number of dimensions for the antigenic map, avoiding distortions common in methods with fixed low dimensions.
* Noise and Bias Reduction: Naturally mitigates experimental noise and bias through its network-based,
error-dampening mechanism.
* Antigenic Velocity Calculation: Introduces and quantifies "antigenic velocity," a vector that describes
the rate and direction of antigenic drift for each pathogen isolate. This can help identify cluster
transitions and potential lineage replacements.
* Broad Applicability: Analyzes data from various pathogens, including influenza, HIV, and Dengue viruses.
It can be applied to any continuous and relational phenotype under directional selection pressure.
Methods are described in Arhami and Rohani (2025) <doi:10.1093/bioinformatics/btaf372>.

Omid Arhami

topolow

Antigenic Mapping and Antigenic Velocity Algorithm

likelihood_function function

<dl><dt>distance_matrix</dt>
<dd>Distance matrix to fit</dd>
<dt>mapping_max_iter</dt>
<dd>Maximum map optimization iterations</dd>
<dt>relative_epsilon</dt>
<dd>Convergence threshold</dd>
<dt>N</dt>
<dd>Number of dimensions</dd>
<dt>k0</dt>
<dd>Initial spring constant</dd>
<dt>cooling_rate</dt>
<dd>Spring constant decay rate</dd>
<dt>c_repulsion</dt>
<dd>Repulsion constant</dd>
<dt>folds</dt>
<dd>Number of CV folds</dd>
<dt>num_cores</dt>
<dd>Number of cores for parallel processing</dd></dl>

Arguments

Evaluate Likelihood with Cross-Validation — likelihood_function

<dl>

<dt>distance_matrix</dt>
<dd>Distance matrix to fit</dd>


<dt>mapping_max_iter</dt>
<dd>Maximum map optimization iterations</dd>


<dt>relative_epsilon</dt>
<dd>Convergence threshold</dd>


<dt>N</dt>
<dd>Number of dimensions</dd>


<dt>k0</dt>
<dd>Initial spring constant</dd>


<dt>cooling_rate</dt>
<dd>Spring constant decay rate</dd>


<dt>c_repulsion</dt>
<dd>Repulsion constant</dd>


<dt>folds</dt>
<dd>Number of CV folds</dd>


<dt>num_cores</dt>
<dd>Number of cores for parallel processing</dd>

</dl>

likelihood_function: Evaluate Likelihood with Cross-Validation

Description

Usage

Value

Arguments