- Methodology article
- Open Access

# Dynamic Optimization with Particle Swarms (DOPS): a meta-heuristic for parameter estimation in biochemical models

- Adithya Sagar†
^{1}, - Rachel LeCover†
^{1}, - Christine Shoemaker
^{2}and - Jeffrey Varner
^{1}Email authorView ORCID ID profile

**Received:**29 December 2017**Accepted:**17 September 2018**Published:**12 October 2018

## Abstract

### Background

Mathematical modeling is a powerful tool to analyze, and ultimately design biochemical networks. However, the estimation of the parameters that appear in biochemical models is a significant challenge. Parameter estimation typically involves expensive function evaluations and noisy data, making it difficult to quickly obtain optimal solutions. Further, biochemical models often have many local extrema which further complicates parameter estimation. Toward these challenges, we developed Dynamic Optimization with Particle Swarms (DOPS), a novel hybrid meta-heuristic that combined multi-swarm particle swarm optimization with dynamically dimensioned search (DDS). DOPS uses a multi-swarm particle swarm optimization technique to generate candidate solution vectors, the best of which is then greedily updated using dynamically dimensioned search.

### Results

We tested DOPS using classic optimization test functions, biochemical benchmark problems and real-world biochemical models. We performed \(\mathcal {T}\) = 25 trials with \(\mathcal {N}\) = 4000 function evaluations per trial, and compared the performance of DOPS with other commonly used meta-heuristics such as differential evolution (DE), simulated annealing (SA) and dynamically dimensioned search (DDS). On average, DOPS outperformed other common meta-heuristics on the optimization test functions, benchmark problems and a real-world model of the human coagulation cascade.

### Conclusions

DOPS is a promising meta-heuristic approach for the estimation of biochemical model parameters in relatively few function evaluations. DOPS source code is available for download under a MIT license at http://www.varnerlab.org.

## Keywords

- Biochemical engineering
- Systems biology
- Modeling
- Optimization

## Background

Mathematical modeling has evolved as a powerful paradigm to analyze, and ultimately design complex biochemical networks [1–5]. Mathematical modeling of biochemical networks is often an iterative process. First, models are formulated from existing biochemical knowledge, and then model parameters are estimated using experimental data [6–8]. Parameter estimation is typically framed as a non-linear optimization problem wherein the residual (or objective function) between experimental measurements and model simulations is minimized using an optimization strategy [9]. Optimal parameter estimates are then used to predict unseen experimental data. If the validation studies fail, model construction and calibration are repeated iteratively until satisfactory results are obtained. As our biological knowledge increases, model formulation may not be as significant a challenge, but parameter estimation will likely remain difficult.

Parameter estimation is a major challenge to the development of biochemical models. Parameter estimation has been a well studied engineering problem for decades[10–13]. However, the complex dynamics of large biological systems and noisy, often incomplete experimental data sets pose a unique estimation challenge. Often optimization problems involving biological systems are non-linear and multi-modal i.e., typical models have multiple local minima or maxima [7, 9]. Non-linearity coupled with multi-modality renders local optimization techniques such as pattern search [14], Nelder-Mead simplex methods [15], steepest descent or Levenberg-Marquardt [16] incapable of reliably obtaining globally optimal solutions as these methods often terminate at local minimum. Though deterministic global optimization techniques (for example algorithms based on branch and bound) can handle non-linearity and multi-modality [17, 18], the absence of derivative information, discontinuous objective functions, non-smooth regions or the lack of knowledge about the objective function hampers these techniques.

Meta-heuristics like Genetic Algorithms (GAs) [19], Simulated Annealing (SA) [20], Evolutionary Programming [21] and Differential Evolution (DE) [22–25] have all shown promise on non-linear multi-modal problems [26]. These techniques do not make any assumptions nor do they require, *a priori* information about the structure of the objective function. Meta-heuristics are often very effective at finding globally optimal or near optimal solutions. For example, Mendes et al. used SA to estimate rate constants for the inhibition of HIV proteinase [27], while Modchang et al. used a GA to estimate parameters for a model of G-protein-coupled receptor (GPCR) activity [28]. Parameter estimates obtained using the GA stratified the effectiveness of two G-protein agonists, N6-cyclopentyladenosine (CPA) and 5’-N-ethylcarboxamidoadenosine (NECA). Tashkova et al. compared different meta-heuristics for parameter estimation on a dynamic model of endocytosis; DE was the most effective of the approaches tested [29]. Banga and co-workers have also successfully applied scatter-search to estimate model parameters [30–32]. Hybrid approaches, which combine meta-heuristics with local optimization techniques, have also become popular. For example, Egea et al. developed the enhanced scatter search (eSS) method [32], which combined scatter and local search methods, for parameter estimation in biological models [33]. However, despite these successes, a major drawback of most meta-heuristics remains the large number of function evaluations required to explore parameter space. Performing numerous potentially expensive function evaluations is not desirable (and perhaps not feasible) for many types of biochemical models. Alternatively, Tolson and Shoemaker found, using high-dimensional watershed models, that perturbing only a subset of parameters was an effective strategy for estimating parameters in expensive models [34]. Their approach, called Dynamically Dimensioned Search (DDS), is a simple stochastic single-solution heuristic that estimates nearly optimal solutions within a specified maximum number of function (or model) evaluations. Thus, while meta-heuristics are often effective at estimating globally optimal or nearly optimal solutions, they require a large number of function evaluations to converge to a solution.

In this study, we developed Dynamic Optimization with Particle Swarms (DOPS), a novel hybrid meta-heuristic that combines the global search capability of multi-swarm particle swarm optimization with the greedy refinement of dynamically dimensioned search (DDS). The objective of DOPS is to obtain near optimal parameter estimates for large biochemical models within a relatively few function evaluations. DOPS uses multi-swarm particle swarm optimization to generate nearly optimal candidate solutions, which are then greedily updated using dynamically dimensioned search. While particle swarm techniques are effective, they have the tendency to become stuck in small local regions and lose swarm diversity, so we combined multi-swarm particle optimization with DDS to escape these local regions and continue towards better solutions [35]. We tested DOPS using a combination of classic optimization test functions, biochemical benchmark problems and real-world biochemical models. First, we tested the performance of DOPS on the Ackley and Rosenbrock functions, and published biochemical benchmark problems. Next, we used DOPS to estimate the parameters of a model of the human coagulation cascade. On average, DOPS outperformed other common meta-heuristics like differential evolution, a genetic algorithm, CMA-ES (Covariance Matrix Adaptation Evolution Strategy), simulated annealing, single-swarm particle swarm optimization, and dynamically dimensioned search on the optimization test functions, benchmark problems and the coagulation model. For example, DOPS recovered the nominal parameters for the benchmark problems using an order of magnitude fewer function evaluations than eSS in all cases. It also produced parameter estimates for the coagulation model that predicted unseen coagulation data sets. Thus, DOPS is a promising hybrid meta-heuristic for the estimation of biochemical model parameters in relatively few function evaluations. However, the relative performance of DOPS should be evaluated cautiously; only naive implementations of the other approaches were tested. Thus, it is possible that other optimized meta-heuristics could outperform DOPS on both test and real-world problems.

## Results

### DOPS explores parameter space using a combination of global methods.

### DOPS minimized benchmark problems using fewer function evaluations.

Villaverde and co-workers published a set of benchmark biochemical problems to evaluate parameter estimation methods [33]. They ranked the example problems by computational cost from most to least expensive. We evaluated the performance of DOPS on problems from the least and most expensive categories. The least expensive problem was a metabolic model of Chinese Hamster Ovary (CHO) with 35 metabolites, 32 reactions and 117 parameters [37]. The biochemical reactions were modeled using modular rate laws and generalized Michaelis–Menten kinetics. On the other hand, the expensive problem was a genome scale kinetic model of *Saccharomyces cerevisiae* with 261 reactions, 262 variables and 1759 parameters [38]. In both cases, synthetic time series data generated with known parameter values, was used as training data to estimate the model parameters. For the *Saccharomyces cerevisiae* model, the time series data consisted of 44 observables, while for the CHO metabolism problem the data corresponded to 13 different metabolite measurement sets. The number of function evaluations was fixed at \(\mathcal {N} = 4000\), and we trained both models against the synthetic experimental data. DOPS produced good fits to the synthetic data (Additional file 1: Figure S1 and Additional file 2: Figure S2), and recapitulated the nominal parameter values using only \(\mathcal {N}\leq ~4000\) function evaluations (Additional file 3: Figure S3). On the other hand, the enhanced scatter search (eSS) with a local optimizer method, took on order 10^{5} function evaluations for the same problems. DOPS required a comprable amount of time (Additional file 4: Figure S4), faster convergence (Additional file 5: Figure S5 and Additional file 6: Figure S6), and also had lower variability in the best value obtained (Additional file 7: Figure S7) across multiple runs when compared to other meta-heuristics. Thus, DOPS estimated the parameters in benchmark biochemical models, and recovered the original parameters from the synthetic data, using fewer function evaluations. Next, we compared the performance of DOPS with four other meta-heuristics for a model of the human coagulation cascade.

### DOPS estimated the parameters of a human coagulation model.

Table with optimization settings and results for the coagulation problem, the benchmarks and test functions using DOPS

Coagulation | B1 | B4 | Ackley | Rastrigin | |
---|---|---|---|---|---|

Evaluations | 4000 | 4000 | 4000 | 4000 | 4000 |

Lower Bound | 0.001.pnom | 0.2.pnom | 0.2.pnom | -15 | -5.12 |

Upper Bound | 1000.pnom | 5.pnom | 5.pnom | 30 | 5.12 |

CPU Time | 10.1 hrs | 38.3 hrs | 6.2 min | 2.8 s | 2.6 s |

Scaled initial error | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |

Scaled final error | < 0.01 | < 0.01 | < 0.01 | < 0.01 | < 0.01 |

Scaled nominal error | 0.42 | 0.1 | < 0.01 | 0 | 0 |

Error analysis for the human coagulation model

TF/FVIIa concentration | Normalized S.E. | Category |
---|---|---|

5 nM | 0.1336 | Training |

500 pM | 0.2242 | Prediction |

50 pM | 0.3109 | Prediction |

10 pM | 0.2023 | Prediction |

5 pM | 0.1170 | Training |

### Phase switching was critical to DOPS performance.

## Discussion

In this study, we developed dynamic optimization with particle swarms (DOPS), a novel meta-heuristic for parameter estimation. DOPS combined multi-swarm particle swarm optimization, a global search approach, with the greedy strategy of dynamically dimensioned search to estimate optimal or nearly optimal solutions in a fixed number of function evaluations. We tested the performance of DOPS and seven widely used meta-heuristics on the Ackley and Rastrigin test functions, a set of biochemical benchmark problems and a model of the human coagulation cascade. We also compared the performance of DOPS to enhanced Scatter Search (eSS), another widely used meta-heuristic approach. As the number of parameters increased, DOPS outperformed the other meta-heuristics, generating optimal or nearly optimal solutions using significantly fewer function evaluations compared with the other methods. We tested the solutions generated by DOPS by comparing the estimated and true parameters in the benchmark studies, and by using the coagulation model to predict unseen experimental data. For both benchmark problems, DOPS retrieved the true parameters in significantly fewer function evaluations than other meta-heuristics. For the coagulation model, we used experimental coagulation measurements under two different conditions to estimate optimal or nearly optimal parameters. These parameters were then used to predict unseen coagulation data; the coagulation model parameters estimated by DOPS predicted the correct thrombin dynamics following TF/FVIIa induced coagulation without anticoagulants. Lastly, we showed the average performance of DOPS improved when combined with dynamically dimensioned search phase, compared to an identical multi-swarm approach alone, and that multiple mode switches could improve performance for some classes of problems. Taken together, DOPS is a promising meta-heuristic for the estimation of parameters in large biochemical models.

Meta-heuristics can be effective tools to estimate optimal or nearly optimal solutions for complex, multi-modal functions. However, meta-heuristics typically require a large number of function evaluations to converge to a solution compared with techniques that use derivative information. DOPS is a combination of particle swarm optimization, which is a global search method, and dynamically dimensioned search, which is a greedy evolutionary technique. Particle swarm optimization uses collective information shared amongst swarms of computational particles to search for global extrema. Several particle swarm variants have been proposed to improve the search ability and rate of convergence. These variations involve different neighborhood structures, multi-swarms or adaptive parameters. Multi-swarm particle swarm optimization with small particle neighborhoods has been shown to be better in searching on complex multi-modal solutions [36]. Multi-swarm methods generate diverse solutions, and avoid rapid convergence to local optima. However, at least for the coagulation problem used in this study, multi-swarm methods stagnated after approximately 25% of the available function evaluations; only the introduction of dynamically dimensioned search improved the rate of error convergence. Dynamically dimensioned search, which greedily perturbs only a subset of parameter dimensions in high dimensional parameter spaces, refined the globally best particle and produced significantly lower error on average when compared to multi-swarm particle swarm optimization alone. However, dynamically dimensioned search, starting from a initial random parameter guess, was not as effective on average as DOPS. The initial solutions generated by the multi swarm search had a higher propensity to produce good parameter estimates when refined by dynamically dimensioned search. Thus, our hybrid combination of two meta-heuristics produced better results than either constituent approach, and better results than other meta-heuristic approaches on average. This was true of not only the convergence rate on the coagulation problem, but also the biochemical benchmark problems; DOPS required two-orders of magnitude fewer function evaluations compared with enhanced Scatter Search (eSS) to estimate the biochemical benchmark model parameters. What remains to be explored is the performance of DOPS compared to techniques that utilize derivative information, either on their own or in combination with other meta-heuristics, and the performance of DOPS in real-world applications compared with other meta-heuristics such as hybrid genetic algorithms e.g., see [52]. Gradient methods perform well on smooth convex problems which have either a closed form of the gradient of the function being minimized, or a form that can be inexpensively estimated numerically. While the biological problems DOPS is intended for often do not have this form, perhaps the solutions could be further improved by following (or potentially replacing) the DDS phase with a gradient based technique when applicable. Taken together, the combination of particle swarm optimization and dynamically dimensioned search performed better than either of these constituent approaches alone, and required fewer function evaluations compared with other common meta-heuristics.

## Conclusions

DOPS performed well on many different systems with no pre-optimization of algorithm parameters, however there are many research questions that should be pursued further. DOPS comfortably outperformed existing, widely used meta-heuristics for high dimensional global optimization functions, biochemical benchmark models and a model of the human coagulation system. However, it is possible that highly optimized versions of common meta-heuristics could surpass DOPS; we should compare the performance of DOPS with optimized versions of the other common meta-heuristics on both test and real-world problems to determine if a performance advantage exists in practice. Next, DOPS has a hybrid architecture, thus the particle swarm phase could be combined with other search strategies such as local derivative based approaches to improve convergence rates. We could also consider multiple phases beyond particle swarm and dynamically dimensioned search, for example switching to a gradient based search following the dynamically dimensioned search phase. Lastly, we should update DOPS to treat multi-objective problems. The identification of large biochemical models sometimes requires training using qualitative, conflicting or even contradictory data sets. One strategy to address this challenge is to estimate experimentally constrained model ensembles using multiobjective optimization. Previously, we developed Pareto Optimal Ensemble Techniques (POETs) which integrates simulated annealing with Pareto optimality to identify models near the optimal tradeoff surface between competing training objectives [53]. Since DOPS consistently outperformed simulated annealing on both test and real-world problems, we expect a multi-objective form of DOPS would more quickly estimate solutions which lie along high dimensional trade-off surfaces.

## Methods

### Optimization problem formulation.

*K*(

**p**) (typically the Euclidean norm of the difference between simulations and measurements) subject to problem and parameter constraints:

*K*(

**p**) denotes the objective function (sum of squared error), t denotes time,

*g*

_{i}(

*t*

_{i},

**x**

**,**

**p**

**,**

**u**) is the model output for experiment

*i*, while

*y*

_{i}denotes the measured value for experiment

*i*. The quantity

**x**(

*t*,

**p**) denotes the state variable vector with an initial state

**x**

_{0},

**u**(

*t*) is a model input vector,

**f**(

*t*,

**x**(

*t*,

**p**),

**u**(

*t*),

**p**) is the system of model equations (e.g., differential equations or algebraic constraints) and

**p**denotes the model parameter vector (quantity to be estimated). The parameter search (or model simulations) can be subject to

**c**(

*t*,

**x**

**,**

**p**

**,**

**u**) linear or non-linear constraints, and parameter bound constraints where

**p**

^{L}and

**p**

^{U}denote the lower and upper parameter bounds, respectively. Optimal model parameters are then given by:

In this study, we considered only parameter bound constraints, and did not include the **c**(*t*,**x****,****p****,****u**) linear or non-linear problem constraints. However, additional these constraints can be handled, without changing the approach, using a penalty function method.

### Dynamic optimization with particle swarms (DOPS).

DOPS combines multi-swarm particle swarm optimization with dynamically dimensioned search (Fig. 1) and (Algorithm 1). The goal of DOPS is to estimate optimal or near optimal parameter vectors for high-dimensional biological models within a specified number of function evaluations. Toward this objective, DOPS begins by using a particle swarm search and then dynamically switches, using an adaptive switching criteria, to a DDS search phase.

#### Phase 1: Particle swarm phase.

*z*

_{i}), wherein each particle corresponded to a \(\mathcal {K}\)-dimensional parameter vector. After initialization, particles were randomly partitioned into

*k*equally sized sub-swarms \(\mathcal {S}_{1},\hdots,\mathcal {S}_{k}\). Particles within each sub-swarm \(\mathcal {S}_{k}\) were updated according to the rule:

*θ*

_{1},

*θ*

_{2},

*θ*

_{3}) were adjustable parameters, \(\mathcal {L}_{i}\) denotes the best solution found by particle

*i*within sub-swarm \(\mathcal {S}_{k}\) for function evaluation 1→

*j*−1, and \(\mathcal {G}_{k}\) denotes the best solution found over all particles within sub-swarm \(\mathcal {S}_{k}\). The quantities

*r*

_{1}and

*r*

_{2}denote uniform random vectors with the same dimension as the number of unknown model parameters (\(\mathcal {K}\times {1}\)). Equation 3 is similar to the general particle swarm update rule, however, it does not contain velocity terms. In DOPS, the parameter

*θ*

_{1,j−1}is similar to the inertia weight parameter for the velocity term described by Shi and Eberhart [56]; Shi and Eberhart proposed a linearly decreasing inertia weight to improve convergence properties of particle swarm optimization. Our implementation of

*θ*

_{1,j−1}is inspired by this and the decreasing perturbation probability proposed by Tolson and Shoemaker [34]. It is an analogous equivalent to inertia weight on velocity. However

*θ*

_{1,j−1}places inertia on the position rather than velocity and uses the same rule described by Shi and Eberhart to adaptively change with the number of function evaluations:

where \(\mathcal {N}\) represents the total number of function evaluations, *w*_{max} and *w*_{min} are the maximum and minimum inertia weights, respectively. In this study, we used *w*_{max}= 0.9 and *w*_{min}= 0.4, however, these values are user configurable and could be changed depending upon the problem being explored. Similarly, *θ*_{2} and *θ*_{3} were treated as constants, where *θ*_{2} = *θ*_{3}= 1.5; the values of *θ*_{2} and *θ*_{3} control how heavily the particle swarm weighs the previous solutions it has found when generating a new candidate solution. If *θ*_{2}≫*θ*_{3} the new parameter solution will resemble the best *local* solution found by particle *i* (\(\mathcal {L}_{i}\)), while *θ*_{3}≫*θ*_{2} suggests the new parameter solution will resemble the best *global* solution found so far. While updating the particles, parameter bounds were enforced using reflection boundary conditions (Algorithm 2).

The quantity NP denotes the total number of particles in the swarm, \(\mathcal {N}\) denotes the total possible number of function evaluations, while the counter *j* denotes the number of successful particle swarm iterations (each costing NP function evaluations). If the simulation error stagnated e.g., did not change by more than 1% for a specified number of evaluations (default value of 4), the swarm phase was terminated and DOPS switched to exploring parameter space using the DDS approach using the remaining \(\left (1-\mathcal {F}\right)\mathcal {N}\) function evaluations.

#### Phase 2: DDS phase.

Dynamically Dimensioned Search (DDS) is a single solution based search algorithm. DDS is used to obtain good solutions to high-dimensional search problems within a fixed number of function evaluations. DDS starts as a global search algorithm by perturbing all the dimensions. Later the number of dimensions that are perturbed is decreased with a certain probability. The probability that a certain dimension is perturbed reduces (a minimum of one dimension is always perturbed) as the iterations increase. This causes the algorithm to behave as a local search algorithm as the number of iterations increase. The perturbation magnitude of each dimension is from normal distribution with zero mean. The standard deviation that was used in the original DDS paper and the current study is 0.2. DDS performs a greedy search where the solution is updated only if it is better than the previous solution. The combination of perturbing a subset of dimensions along with greedy search indirectly relies on model sensitivity to a specific parameter combination. The reader is requested to refer to the original paper by Tolson and Shoemaker for further detail [34].

**J**is a vector representing the subset of dimensions that are being perturbed,

**r**

_{normal}denotes a normal random vector of the same dimensions as \(\mathcal {G}\), and

*σ*denotes the perturbation amplitude:

*R*is the scalar perturbation size parameter,

**p**

^{U}and

**p**

^{L}are (\(\mathcal {K}\times {1}\)) vectors that represent the maximum and minimum bounds on each dimension. The set

**J**was constructed using a probability function \(\mathcal {P}_{i}\) that represents a threshold for determining whether a specific dimension

*j*was perturbed or not; \(\mathcal {P}_{i}\) is monotonically decreasing function of function evaluations:

where *i* is the current iteration. After \(\mathcal {P}_{i}\) is determined, we drew \(\mathcal {P}_{j}\) from a uniform distribution for each dimension *j*. If \(\mathcal {P}_{j}<\mathcal {P}_{i}\) was included in **J**. Thus, the probability that a dimension *j* was perturbed was inversely proportional to the number of function evaluations. DDS updates are greedy; \(\mathcal {G}_{new}\) becomes the new solution vector only if it is better than \(\mathcal {G}\).

### Multiswitch DOPS

We investigated whether switching search methods more than once would result in better performance; this DOPS variant is referred to as multiswitch DOPS or msDOPS. msDOPS begins with the PSO phase and uses the same criteria as DOPS to switch to the DDS phase. However, msDOPS can switch back to a PSO search when the DDS phase has reduced the functional value to 90% of its initial value. Should the DDS phase fail to improve the functional value sufficiently, this version is identical to DOPS. When the switch from DDS to PSO occurs, we use the best solution from DDS to seed the particle swarm. DOPS and msDOPS source code is available for download under a MIT license at http://www.varnerlab.org.

### Comparison techniques

The implementations of particle swarm optimization, simulated annealing, and genetic algorithms are the ones given in Matlab R2017A (particleswarm, simulannealbnd and ga). The implementation of DE used was developed by R.Storn and available at http://www1.icsi.berkeley.edu/~storn/code.html. The version of eSS used was Release 2014B - AMIGO2014bench VERSION WITH eSS MAY-2014-BUGS FIXED - JRB, released by the Process Engineering Group IIM-CSIC. The genetic algorithm, particle swarm, and differential evolution algorithms were run with a 40 particles to be directly comparable to the number of particles used in the PSO phase of DOPS. For comparison, the version of CM-AES used was cmaes.m, Version 3.61.beta from http://cma.gforge.inria.fr/cmaes_sourcecode_page.html. The scripts used to run the comparison methods are also available at http://www.varnerlab.org.

## Notes

## Declarations

### Funding

This study was supported by an award from the US Army and Systems Biology of Trauma Induced Coagulopathy (W911NF-10-1-0376).

### Availability of data and materials

DOPS is open source, available under an MIT software license from http://www.varnerlab.org. All scripts used in this study are included in the utilities directory. The optimization problems used are located in the CoagulationFiles and testFunctions directories.

### Authors’ contributions

AS developed original DOPS algorithm. RL developed msDOPS and generated figures in the manuscript. CS developed the dynamic dimensional search approach, and assisted in editing the manuscript. JV directed the study, prepared and edited the manuscript. All authors read and approved the final manuscript.

### Ethics approval and consent to participate

Not applicable.

### Consent for publication

Not applicable.

### Competing interests

The authors declare that they have no competing interests.

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## Authors’ Affiliations

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