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Development of a novel approach for secondary modelling in predictive microbiology: incorporation of microbiological knowledge in black box polynomial modelling

A.H. Geeraerd a, V.P. Valdramidis a, F. Devlieghere b, H. Bernaert b, J. Debevere b, J.F. Van Impe a,*

a

BioTeC-Bioprocess Technology and Control, Department of Chemical Engineering, Katholieke Universiteit Leuven, W. de Croylaan 46, B-3001 Leuven, Belgium b Laboratory of Food Microbiology and Food Preservation, Department of Food Technology and Nutrition, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium Received 19 August 2002; received in revised form 12 February 2003; accepted 28 May 2003

Abstract This research deals with the development of a novel secondary modelling procedure within the framework of predictive microbiology. The procedure consists of three steps: (i) careful formulation of the available microbiological information, both from literature and from the experimental case study at hand, (ii) translation of these requirements in mathematical terms under the form of partial derivatives throughout the complete interpolation region of the experimental design, and (iii) determination of parameter values with suitable optimisation techniques for a flexible black box modelling approach, e.g., a polynomial model or an artificial neural network model. As a vehicle for this procedure, the description of the maximum specific growth rate of Lactobacillus sakei in modified BHI-broth as influenced by suboptimal temperature, water activity, sodium lactate and dissolved carbon dioxide concentration is under study. The procedure results in a constrained polynomial model with excellent descriptive and interpolating features in comparison with an extended Ratkowsky-type model and classical polynomial model, by combining specific properties of both model types. The developed procedure is illustrated on the description of the lag phase as well. It is stressed how the confrontation with experimental data is very important to appreciate the descriptive and interpolating capacities of new or existing models, which is nowadays not always carefully performed. Alternatively, the first two steps of the novel procedure can be used as a tool to demonstrate clearly (possible) interpolative shortcomings of an existing model with straightforward spreadsheet calculations. D 2003 Elsevier B.V. All rights reserved.

dek type models, square root models, artificial neural lehra Keywords: Predictive microbiology; Secondary modelling; Polynomial models; Be network models; Model evaluation; Constrained optimisation; Modified atmosphere packaging; Carbon dioxide; Sodium lactate; Lactobacillus sakei

1. Introduction

* Corresponding author. Fax: +32-16-32-2991. E-mail address: jan.vanimpe@cit.kuleuven.ac.be (J.F. Van Impe). 0168-1605/$ - see front matter D 2003 Elsevier B.V. All rights reserved. doi:10.1016/S0168-1605(03)00388-X

Predictive microbiology deals with the development of accurate and at the same time versatile

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mathematical models able to describe the microbial evolution in food products as function of environmental conditions, which are assumed to be known or measurable. The modelling process aims at condensing existing microbiological knowledge into mathematical models (Ross, 1999). When an appropriate model has been built and properly validated, it enables the prediction of the effect of, e.g., changing treatment conditions on the microbial evolution. A recent review on predictive microbiology concepts and new trends, including the progressive approximation of the growth/no growth interface and the increased use of probability models, can be found in McMeekin et al. (2002). In McMeekin and Ross (2002), it is extensively indicated how the systematic accumulation and storage of knowledge embodied in predictive microbiology has contributed to and facilitated the changed philosophy of managing food safety issues pro-actively rather than by retrospective end-product testing. Moreover, the possibilities to (re-)design food processing techniques by combining predictive microbiology models and knowledge of underlying physiological processes of stressed microbial cells, are dealt with. The following predictive microbiology classification scheme, which is nowadays widely used, was originally proposed by Whiting and Buchanan (1993). Primary models are dealing with the description of the microbial evolution (growth, survival, inactivation) as a function of time. Quantities may include colony forming units, biomass, absorbance measurements, as well as substrate levels or metabolic products produced (see, e.g., Whiting, 1995). Secondary models characterize parameters appearing in primary modelling approaches as function of environmental conditions like temperature, pH, water activity, etc. Tertiary models can take on several forms, starting from combined primary and secondary model types based on laboratory experiments (e.g., the Pathogen Modeling Program, designed and freely made available by the USDA); over more extended versions, including the possibility to import a temperature history in order to predict remaining shelf life with respect to Specific Spoilage Organisms, as in the Seafood Spoilage Predictor (Dalgaard et al., 2002) up to the incorporation of predictive models in the framework of

microbiological risk assessment (e.g., Salmonella enteritidis Risk Assessment (SERA), again with the USDA). This research deals specifically with secondary model types. A general overview of secondary model types can be found in McDonald and Sun (1999) and Vereecken et al. (2000). Current approaches, still receiving considerable attention and impetus for dek type models lehra new developments, are (i) Be (also referred to as Ratkowsky-type or square root models), (ii) polynomial models, (iii) cardinal values models, and (iv) artificial neural network models. Original references within predictive microbiology for each model type are, respectively, Ratkowsky et al. (1982), Gibson et al. (1988), Rosso et al. (1995) and Hajmeer et al. (1997). These secondary modelling approaches fall into two groups. On one hand, research groups around the world developing Ratkowsky-type or cardinal values models appreciate, despite the basically empirical nature of these relationships, (i) the (at least partial) biological interpretability of the parameter values, (ii) the possibility to extend towards additional or new influencing factors (based on a multi-factor model firstly presented by McMeekin et al. (1987) and formalized in the g concept approach of Zwietering et al. (1992)), (iii) their parsimony and (iv) the high quality of fit. On the other hand, people working with black box modelling approaches, like polynomial models or artificial neural networks, stress their flexible behaviour, making it possible to describe purely empirically an underlying, unknown relationship between microbial evolution parameters and environmental influences. The aim of all modelling approaches is to obtain good generalization properties. This means that a model should perform well when confronted with new data, included in the interpolation region of the original experimental design. This is related with the classical trade-off between over- and underfitting: a too rigid model will have a low Adjusted R2, but perhaps displays logical behaviour, whereas a very flexible model (like polynomial model types or artificial neural networks) will have a high Adjusted R2 but can fail when used on fresh data or even on the data used to develop the model. The issue of obtaining unrealistic curvatures is correctly appreciated by, e.g., Buchanan et al. (1997) discarding a

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third-order polynomial model for the non-thermal inactivation of Listeria monocytogenes due to an unrealistic upward trend in the time to a 4-D inactivation (t4D) for increasing values of sodium nitrite. It should be noted that some research articles in predictive microbiology (especially when developing black box artificial neural network models) announce proudly an unrealistic high R2-value (or another measure of goodness-of-fit) but do not really assess the model performance, as they limit the visualisation of results to a plot of predicted versus observed values (e.g., Hajmeer et al., 1997; Jeyamkondan et al., 2001). However, this plot is not informative with respect to the (possible) under- or overfitting of the developed model. That is where the weakness arrives: when one stops the model development at that purely fitting stage and does not take into account any microbiological properties hidden in the data set at hand or in more general microbiological literature. Resulting model types do not contribute to predictive microbiology as a confident discipline. Instead, two-dimensional lines or three-dimensional surfaces, properly displaying the identified model together with the experimental observations as a function of the independent variables, are essential to show the model interpolating behaviour (see, e.g., Geeraerd a-Gimeno et al., 2002 in the frameet al., 1998; Garc work of artificial neural network modelling). The confrontation with experimental data points (firstly, with these used for identification of the model, and, secondly, with validation data) is a step of outmost importance, without which the value of the developed model is not proven. Baranyi and Roberts (1995) illustrate this important point by making use of a set of maximum specific growth rate data as function of a range of pH values. They indicate that a better fit of the model onto the experimental data (judged by an R2 statistic, or even an F-test, taking into account the number of parameters) does not guarantee a better model. Classical second- and third-order polynomial relationships are rejected because of their unrealistic hills and valleys. Instead, a novel secondary polynomial model is proposed by taking into account the fact that it is known that the optimal pH value is around the maximum value of pH measured. Generally speaking, Baranyi

and Roberts suggest that a possible improvement of a model is to fix expected properties of the response function, e.g., expected location of extreme points, monotonicity, convexity, etc. In this research, the aim is to develop a new approach by combining the flexibility of a polynomial model with a priori knowledge of the microbial behaviour.

2. Materials and methods 2.1. Experimental data The experimental data, used as a vehicle during this research, originate from Devlieghere et al. (1999, 2000) and encompass 263 growth experiments of Lactobacillus sakei in modified BHI-broth as influenced by suboptimal temperature T [jC], dissolved carbon dioxide (CO 2 ) concentration [ppm], water activity [ ] and sodium lactate (NaL) [% (w/w)]. More specifically, the influence on the (variance stabilizing) square root of the maximum specific growth rate lmax is under study. For reasons which will be clarified further in this research, it is instructive to visualise the interpolation region of the experiments (Fig. 1). The bound-

Fig. 1. Visualisation of the four-dimensional volume enclosed by the experimental design of the case study. The volume consists of a hypercube and an additional hyperplane, the edges of which are presented and numbered in Tables 1 and 2. Data points at 4 jC are indicated with a o, at 8 jC with a and at 12 jC with a q.

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Table 1 Edges of the four-dimensional hypercube, enclosing the first part of the experimental design Temperature [jC] 4 4 4 4 4 4 4 4 8 8 8 8 8 8 8 8 12 12 12 12 12 12 12 12 Dissolved CO2 [ppm] 0 0 0 0 1968 1968 1968 1968 0 0 0 0 1796 1796 1796 1796 0 0 0 0 1624 1624 1624 1624 Water activity [] 0.9622 0.9622 0.9883 0.9883 0.9622 0.9622 0.9883 0.9883 0.9622 0.9622 0.9883 0.9883 0.9622 0.9622 0.9883 0.9883 0.9622 0.9622 0.9883 0.9883 0.9622 0.9622 0.9883 0.9883 Sodium lactate [% (w/w)] 0 3 0 3 0 3 0 3 0 3 0 3 0 3 0 3 0 3 0 3 0 3 0 3 Edge number 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24

The Mean Squared Error (MSE) equaled 7.57 10 4, while the Adjusted R2 of this model was 0.8984, indicating an acceptable quality of fit. The model visualisation is presented in Fig. 2. The second suitable modelling approach was a second-order polynomial, described as follows.

p lmax 5:46 101 7:84 101 T 1:12 102 aw 7:32 101 NaL 6:52 104 CO2 1:30 103

1 T 2 5:71 101 a2 w 8:40 10

T aw 8:56 104 T NaL 1:65 106 T CO2 7:69 101 aw NaL 6:77 104 aw CO2 2

aries of this interpolation region should be thought of as consisting of two parts: (i) a hypercube (including implicitly the temperature axis) constructed by taking the edges summarised in Table 1 and (ii) an additional hyperplane for NaL equal to zero, summarised in Table 2. 2.2. Existing modelling approaches After careful examination of four model types, Devlieghere et al. (2000) selected two suitable modp elling approaches for the description of lmax . The first one is an extended Ratkowsky-type model including the influence of suboptimal T, aw, dissolved CO2 and NaL and reads as follows.

p lmax 5:78 104 T 9:03 p aw 9:54 101 6:69 103 CO2 5:87 NaL

The MSE equals 4.01 10 4, while the Adjusted R2 equals 0.9461. It is indeed to be expected that a polynomial model is able to obtain a higher Adjusted R2 in comparison with an extended Ratkowsky-type model, due to its Universal Approximation Property. A polynomial is structurally much more flexible (as is

Table 2 Edges of the three-dimensional hyperplane, enclosing the second part of the experimental design Temperature [jC] 4 4 4 4 8 8 8 8 12 12 12 12 Dissolved CO2 [ppm] 0 49 2411 2411 0 0 2211 2236 0 0 1950 1950 Water activity [] 0.9616 0.9859 0.9616 0.9859 0.9616 0.9859 0.9616 0.9859 0.9616 0.9859 0.9616 0.9859 Sodium lactate [% (w/w)] 0 0 0 0 0 0 0 0 0 0 0 0 Edge number 25 26 27 28 29 30 31 32 33 34 35 36

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Fig. 2. Three-dimensional surfaces of the extended Ratkowsky-type model (Eq. (1)) and experimental data points under the surface (o) and above the surface (*). Upper left: aw=0.9622 and NaL=3% (w/w); upper right: CO2=0 ppm and NaL=1.5% (w/w); middle left: CO2=0 ppm and aw=0.9622; middle right: T=4 jC and NaL=3% (w/w); lower left: T=4 jC and aw=0.9722; lower right: T=8 jC and CO2=1796 ppm.

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Fig. 3. Three-dimensional surfaces of the classical polynomial model and experimental data points under the surface (o) and above the surface (*). Upper left: aw=0.9622 and NaL=3% (w/w); upper right: CO2=0 ppm and NaL=1.5% (w/w); middle left: CO2=0 ppm and aw=0.9622; middle right: T=4 jC and NaL=3% (w/w); lower left: T=4 jC and aw=0.9722; lower right: T=8 jC and CO2=1796 ppm.

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clearly visible in Fig. 3). However, the polynomial model behaviour is unacceptable at certain environmental combinations (see, e.g., Fig. 3, upper and middle left plots). Devlieghere et al. (2000) already remarked an important illogical behaviour when examining the polynomial model type: at low water activities, high CO2 concentrations, and high NaL concentrations, the polynomial model predicts higher growth rates at low temperatures than at higher temperatures. Devlieghere et al. (2000) developed similar model types for the description of the (variance stabilising) square root of the lag phase k. It was indicated that a second-order polynomial model described better the experimental results, having a higher Adjusted R2 p k

(0.9564) and an MSE of 0.55. The developed polynomial model reads as follows p k 3:04 102 2:42 101 T 3:00 102 aw 2:76 101 NaL 1:36 103 CO2 3:77 102 T 2 2:04 101 NaL2 2:37 101 T aw 1:77 101 T NaL 1:70 104 T CO2 2:71 101 aw NaL 7:30 104 NaL CO2 3 while the extended Ratkowsky-type model has the following description

8:49

104 T

3. Development and implementation of a novel three-step approach for secondary modelling As a vehicle to illustrate the methodology, the experimental data as described above will be used, namely, the influence of suboptimal T, aw, dissolved p CO2 and NaL on lmax . 3.1. Microbiological information available for L. sakei The microbiological information available for L. sakei growth, considering the complete interpolation region of the experimental data as visualised in Fig. 1, can be formulated as follows. 3.1.1. Temperature Lactobacilli have an optimal growth temperature between 30 and 40 jC (Bergeys Manual, Ninth Edition). As an example, the cardinal temperature values Tmin, Topt, and Tmax for L. plantarum in MRS medium are estimated by Rosso et al. (1995) as being 5.3, 36.06 and 43.86, respectively, extracting experimental data from Zwietering et al. (1991). It is reasonable to assume that considering the range of

temperature, namely 4 to 12, and for any constant value of water activity, dissolved CO2 concentration, and sodium lactate concentration, the maximum specific growth rate of L. sakei should always be increasing for increasing values of temperature. The same holds for the (monotonous) square root transformed maximum specific growth rate. An analysis of the experimental data by simply p visualising the evolution of lmax as a function of increasing values of temperature does indeed generally confirm this. Part of this visualisation is represented by the data points in Fig. 2, upper left and right and middle left. Three exceptions at NaL 0%, 1.5% and 3% (w/w) can be found in Fig. 2, middle left. Given the experimental accuracy, these exceptions do not lead to the rejection of the first model requirement as formulated above. It can be noted that these exceptions are partly the cause of the unrealistic polynomial behaviour for these conditions (Fig. 3, middle left). 3.1.2. Water activity As with temperature, a theoretical optimal aw value exists, as microorganisms will not grow in extremely diluted solutions, having an aw close to 1. Recently,

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Le Marc (2001) proposed, based on a cardinal values model type, an aw min and aw opt for Listeria innocua ATCC 33090 of 0.907 and 0.993, respectively. Tienungoon et al. (2000) indicate an aw min and aw opt for L. monocytogenes Scott A of 0.914 and 0.995, respectively. Although no such information is, to the authors knowledge, available for Lactobacilli, it is reasonable to assume that the optimal water activity value for growth for L. sakei is above the maximum water activity value tested (0.9883), as can be seen by picturing the experimental data (e.g., Fig. 2, all right plots). An exception is displayed in the middle plot at CO2 values of 1248 and 1968 ppm. However, considering the experimental accuracy, the subsequent bending of the polynomial model (Fig. 3, middle right) must be designated as unrealistic. As such, the second model requirement is that for any constant value of T, dissolved CO2 and NaL concentration, the maximum specific growth rate of L. sakei should always be increasing for increasing values of water activity. 3.1.3. Sodium lactate In the present experimental case study, the effect of sodium lactate is studied separately from its water activity effect, as water activity is lowered by adding sodium lactate and afterwards the necessary amount of NaCl. pH is fixed at 6.1. Generally speaking, addition of sodium lactate has a negative effect on L. sakei growth (Devlieghere et al., 2000). As such, a third model re-quirement is that for any constant value of T, aw and dis-solved CO2 concentration, lmax should always be decreasing for increasing values of sodium lactate concentration. The analysis of the experimental data completely confirms this, without any exceptions (see, e.g., Fig. 2, middle left and right and lower left and right). 3.1.4. Dissolved carbon dioxide Devlieghere et al. (1999) show how the dissolved CO2 concentration negatively influences the growth of L. sakei in modified BHI-broth, in synergistic action with temperature and water activity. As such, a fourth model requirement is: for any constant value of T, aw, and NaL concentration, the maximum specific growth rate of L. sakei should always be decreasing for increasing values of dissolved CO2 concentration. An analysis of the experimental data generally confirms this (Fig. 2, upper left and lower

left). There are some exceptions (Fig. 2, middle right at an aw value of 0.9622 or 0.9722), but even in these cases the trend remains clear. It should be noted that all these requirements are built in a more stringent way into the structure of the extended Ratkowsky-type relationship (Eq. (1)). As an example, for any constant value T, aw and NaL, pof p lmax relates linearly with 6:69 103 CO2. However, considering the evolution of lmax as displayed in, e.g., Fig. 2, middle right, this requirement may be too stringent: lmax increases in a much more pronounced way when considering a decreasing CO2 concentration at high than at low water activity values. 3.2. Translation into mathematical modelling requirements In mathematical terms, the model requirements as described above are as follows: the partial derivative of the model with respect to T or aw should always be positive; whereas the partial derivative of the model with respect to dissolved CO2 concentration or NaL concentration should be negative. p p p B lmax B lmax B lmax > 0; < 0; > 0; BT BCO2 Baw p B lmax <0 5 BNaL These requirements should hold throughout the complete interpolation region. Calculating the partial derivatives of the extended Ratkowsky-type model (Eq. (1)), the following equations are obtained.

p B lmax 5:78 104 BT p aw 9:54 101 6:69 103 CO2 5:87 NaL p p B lmax 5:78 104 T 9:03 aw 9:54 101 5:87 NaL BCO2 1 p 2 6:69 103 CO2 p p B lmax 5:78 104 T 9:03 6:69 103 CO2 5:87 NaL Ba w 1 p 2 aw 9:54 101 p B lmax 5:78 104 T 9:03 BNaL p aw 9:54 101 6:69 103 CO2 1 p 2 5:87 NaL

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Clearly, the extended Ratkowsky-type model fulfils the mathematical model requirements as all independent variables only take on values within the interpolation region characterizing the experimental design, making all factors in the expressions above positive. The partial derivatives for the polynomial model (Eq. (2)) read as follows p B lmax 7:84 101 2:60 103 T BT 8:40 101 aw 8:56 104 NaL 1:65 106 CO2 p B lmax 6:52 104 1:65 106 T 6:77 BCO2 104 aw

p B lmax 1:12 102 1:14 102 aw B aw 8:40 101 T 7:69 101 NaL 6:77 104 CO2 p B lmax 7:32 101 8:56 104 T BNaL 7:69 101 aw 7

The sign of these partial derivatives throughout the complete interpolation region is not readily visible. In this case study, it is already known that the polynomial model is not appropriate in certain environmental combinations. Indeed, for an aw value of 0.9622 and at a NaL concentration of 3% (w/w)

Fig. 4. Evaluation of the sign of the partial derivatives (Eq. (7)) of the classical polynomial model (Eq. (2)) for experimental design, as numbered in Tables 1 and 2.

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(as visualised in Fig. 3, upper left), it can be calculated that p B lmax < 0 if T > 8:34 6:35 104 CO2 BT

as accurate as possible (as quantified by the SSE or MSE) the experimental data at hand, while still obeying the mathematical constraints formulated in Eq. (5) at all edges of the experimental design. The polynomial model structure and the 144 constraints as derived above by applying Eq. (5) at all 36 edges, constitute a Constrained Linear Least Squares problem: (i) the objective function to be minimized is the classical SSE (or MSE as its rescaled version), and (ii) the polynomial model and the constraints are linear in the parameter values. This implies that the global optimum in parameter space can always be found (if constraints are not overly stringent) by using Lagrange multipliers. We solved this problem by making use of the lsqlin function of the MatLabR Optimization Toolbox (The Mathworks, Natick, USA). Further information can be found at http://www.mathworks. com/access/helpdesk/help/toolbox/optim/optim.shtml, and an example of a suitable Matlab-coding is available upon request with the authors of the present research.

Theoretically speaking, calculation of all four partial derivatives should be performed throughout the complete interpolation region in order to evaluate carefully where this polynomial model fails to obey the implied mathematical constraints as derived from microbiological knowledge. However, calculations like the one presented above can be simplified. As the derived mathematical constraints, presented in Eq. (7), are linear in the independent variables, it is sufficient that the constraints are obeyed at all 36 edges of the experimental design (as listed in Tables 1 and 2) in order to ensure that they are also fulfilled throughout the interpolation region, as required. The evaluation of all four partial derivatives (Eq. (7)) at all edges is visualised in Fig. 4. The partial derivative with respect to temperature becomes negative at edges number 14, 17, 18, 21, 22, 31, 33 and 35 (indicating, e.g., at combinations of high temperature and low water activity values, for the whole range of CO2 and NaL values). The partial derivatives with respect to CO2 or NaL are always negative, as required, whereas the partial derivative with respect to water activity is negative at edge number 8. Observe how this procedure indicates limiting edges of problematic combinations, without having to visualise all possible combinations in threedimensional polynomial surfaces (as partially done in Fig. 3). 3.3. Implementation of the mathematical modelling requirements Combining all observations of the previous sections, the specific objective of the present research with respect to the case study chosen can be formulated. As the second-order polynomial equation (Eq. (2)) is clearly flexible enough for the data set at hand, it was decided to retain its structure. Find parameter values for the second-order polynomial equation (Eq. (2)), able to describe

4. Results 4.1. Implementation of the developed procedure on p the description of lmax Application of the above-derived procedure leads to the following polynomial model structure. p lmax 3:27 101 6:88 101 T 6:60 101 aw 6:69 101 NaL 6:13 104 CO2 3:62 104 T 2

1 3:31 a2 T aw w 7:26 10

1:86 104 T NaL 3:72 107 T CO2 7:11 101 aw NaL 6:46 aw CO2 9

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Fig. 5. Three-dimensional surfaces of the constrained polynomial model (Eq. (9)) and experimental data points under the surface (o) and above the surface (*). Upper left: aw=0.9622 and NaL=3% (w/w); upper right: CO2=0 ppm and NaL=1.5% (w/w); middle left: CO2=0 ppm and aw=0.9622; middle right: T=4 jC and NaL=3% (w/w); lower left: T=4 jC and aw=0.9722; lower right: T=8 jC and CO2=1796 ppm.

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The MSE equals 4.84 10 4 and the Adjusted R2 equals 0.9351. Self-evidently, the MSE-value is higher than the one which can be obtained with the original, non-constrained polynomial model. As the MSE-value is lower than the one of the Ratkowsky-type model, an overall better quality of fit is indicated. The Adjusted R2 is lower than the one obtained by the original polynomial model, but higher than the extended Ratkowsky-type model. Observe that the parameter values remain in the same order of magnitude in comparison with the original polynomial model, which means that only a limited shift in parameter space is induced by the application of the constraints. The suitable description of this polynomial model, fulfilling all formulated parameter constraints, is visualised in Fig. 5. 4.2. Implementation pof the developed procedure on the description of k Next to the case study, used in Section 3 to illustrate the development and properties of the three-step modelling approach, the procedure is also applied to test the appropriateness of the second-order p polynomial model for k (Eq. (3)). Based on the microbiological analysis presented in Section 3.1, the following mathematical model requirements can be formulated p p p p B k B k B k B k < 0; >0 > 0; < 0; BT BCO2 Baw BNaL

Fig. 6. Two-dimensional representation of the experimental data p points of k at 12 jC and no NaL added. Four different water activity values are pictured: 0.9616 (o), 0.9738 (5), 0.9798 (+), 0.9859 (). The extended Ratkowsky-type model (Eq. (4)) is indicated with the dotted lines (....), the original polynomial model (Eq. (3)) with the full lines (-) and the constrained polynomial model (Eq. (11)) with the dashed line (- -). For each model type, the upper line belongs to aw = 0.9616.

10

An analysis of the pexperimental data by visualising the evolution of k as function of one independent variable, keeping the other three variables constant, generally these statements (not shown). As pconfirms p usual, k values are more variable than lmax values, and, as such, more exceptions to Eq. (10) can be found within the data p in comparison with Eq. (5). However, for Bp k =BT there are no exceptions, and also for B k=BNaL the trendpis very clear. Most exceptions can be found for B k =BCO2, as visualised partially by the data points in Fig. 6. Especially the data at the lower aw values indicate a lowering instead of the expected raising

trend as a function of CO2. Assuming that exceptions are acceptable given the inherent variability of lag phase estimation, it is concluded that the mathematical model requirements as formulated in Eq. (10) should hold for a suitable model structure. Again, the constraints (Eq. (10)) are linear in the independent variables. The evaluation of the constraints (Eq. (10)) for the polynomial model (Eq. (3)) at all edges of the experimental interpolation region (listed in Tables 1 and 2) is pictured in Fig. 7. Asp can be seen, model requirements are violated p for B k=BT at edges number 19 and 34, for B k =BCO2 atp edges number 17, 19, 21, 23 and 33 36, and for B k=BNaL at edges number 11, 17, 19, 20, 23, 30, 33 and 34. It can be concluded that the polynomial model description gives unrealistic predictions at combinations of high temperatures (mostly 12 jC) and low NaL [mostly 0% (w/w)], for the complete range of CO2 and aw, as illustrated already in Fig. 6. p As with the lmax case study, a new parameter set is estimated by taking into account 144 constraints derived by applying Eq. (10) at all 36 edges of the

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Fig. 7. Evaluation of the sign of the partial derivatives of the classical polynomial model (Eq. (3)) for as numbered in Tables 1 and 2.

experimental design. This results in the following polynomial model description. p k 3:17 102 2:40 101 T 3:12 102 aw 1:24 101 NaL 1:20 103 CO2 3:90 102 T 2 2:33 101 T aw 1:35 101 T NaL 1:00 104 T CO2 1:10 101 aw NaL 4:48 104 NaL CO2 11

which is in between the values of the Ratkowsky-type model (0.9118) and the original polynomial model (0.9564). MSE equals 0.76, again in between the values of the Ratkowsky-type model (1.11) and the original polynomial model (0.55). The comparison of the three available models on a subset of the data points is presented in Fig. 6. It is clear that the original polynomial model is highly influenced by the experimental trend in these exceptional data and displays an illogical lowering trend. On the contrary, the extended Ratkowsky-type model (Eq. (4)) structurally imposes a raising trend. The new polynomial model shows only a very limited, but still positive trend, as forced by the trade-off between minimizing the MSE and SSE while obeying the implied constraints.

Note that the parameter values have the same order of magnitude in comparison with Eq. (3), except for the term in NaL2, which became negligibly small and was eliminated. The resulting Adjusted R2 equals 0.9396,

5. Discussion Ratkowsky-type or cardinal values type models have a model structure incorporating a priori microbi-

242

ological knowledge (as in Section 3.1), while parameter values are identified on the data set at hand, having the possibility to extract good starting values from literature. Black box modelling approaches like artificial neural networks or polynomial equations focus completely on the experimental data, and, as such, carry with them the danger of overfitting if used as purely fitting tools. The newly developed procedure aims at combining specific properties of these two approaches: the flexibility of a black box approach, and the incorporation of a priori microbiological knowledge during the parameter estimation step. Observe that, as noted previously, constraints are interpreted in a less stringent way in comparison with the way they are incorporated in Ratkowsky or cardinal values model types. This is the reason for the more suitable data description (Fig. 5) in comparison with the extended Ratkowsky-type model (Fig. 3), or, otherwise stated, the lower MSE and p higher Adjusted p R2 values, both for the lmax as the k data set. Le Marc et al. (2002) developed an extended version of the usual multiplicative g approach, describing the growth rate of L. innocua ATCC 33090 in a modified BHI broth as influenced by temperature, pH and organic acid concentration by means of a cardinal values model. The authors included an extra term in the multiplicative approach in order to deal with the synergistic effect of environmental factors appearing only at very stringent conditions for growth. As such, their results are comparable with the present research: at stringent conditions, the secondary model should be able to display a different behaviour in comparison with more favourable conditions. Considering artificial neural network (ANN) modelling, some different approaches are currently in use for assessing the model behaviour. In Geeraerd et al. (1998), the performance of the low complexity ANN models are illustrated on threedimensional surface, enabling the reader to appreciate the suitable, non-overfitting behaviour. Jeyamkondan et al. (2001) use an appropriate value for the smoothing factor: a low (or no) smoothing factor leads to overfitting, a too high smoothing factor could lead to under-fitting. The authors stress the importance of graphic plots and display the predicted versus observed values for both the data sets used for identification (training) and for testing (validation). However, it is difficult to appreciate the results of this

smoothing factor because no figures are shown of the model prediction and the data versus independent variables, and because final model structures are not presented. a-Gimeno et al. (2002) also warn against an Garc overtrained ANN model, leading to worse generalization capacity. The authors present three-dimensional figures, illustrating their suitable ANN modelling approaches obtained after the use of genetic and pruning algorithms. The resulting ANN models, carefully presented, are comparable with the low complexity ANN models we obtained to describe the maximum specific growth rate and lag phase as function of temperature, pH and % NaCl (Geeraerd et al., 1998). The approaches proposed by Jeyamkondan et al. a-Gimeno et al. (2002) are different (2001) and Garc from the one presented in this research in the following aspect: while in this research, the focus to prevent overfitting is placed with the microbiological information, in the former researches the overfitting preventing measures are more general and purely data-driven. Otherwise said, in the present research, the black box polynomial model is forced to learn a certain behaviour as based on a priori microbiological knowledge, while the approaches in Jeyamkondan et al. (2001) and a-Gimeno et al. (2002) are more flexible and Garc could learn unexpected or unknown phenomena (for example, if for certain conditions, the maximum specific growth rate would not follow the trends as presented in Section 3.1). On the other hand, these flexible approaches, even by making use of the overfitting preventing measures, cannot be guaranteed to follow any trend. It is up to the model developer to decide on the level and certainty of microbiological information available for a specific case study.

6. Conclusions and further perspectives The newly proposed procedure for secondary model development, combining the flexibility of a black box approach and the incorporation of a priori microbiological knowledge during the parameter estimation step, can be summarised as follows. (1) Formulate carefully available microbiological information, both from literature and from the experimental case study at hand.

243

(2) Translate these requirements in mathematical terms under the form of partial derivatives throughout the complete interpolation region of the experimental design. (3) Determine parameter values with suitable optimisation techniques for a flexible modelling approach, e.g., a polynomial model or an artificial neural network model. Observe that the application of the first two steps only enables the careful analysis of any existing secondary model. By delimiting carefully the interpolation region, as visualised for this case study in Fig. 1 and Tables 1 and 2, and calculating partial derivatives throughout the interpolation region, it is possible to demonstrate clearly (possible) shortcomings of an existing polynomial or artificial neural network model with straightforward spreadsheet calculations [as in Eq. (8)]. The simplification of only calculating the partial derivative at the edges of the interpolation region (as in Figs. 4 and 7) is possible for all second-order polynomial case studies. A possible extension of the results in this research is the application in non-monotonous environmental conditions, e.g., when trying to describe the maximum specific growth rate as function of a complete temperature range (in combinations with other environmental factors). For a case study like that one, appropriate regions where the partial derivative should be negative/positive need to be defined. In a small region around the optimal growth temperature Topt, it will probably be advisable to not define the sign of the partial derivative. Subsequent calculations do not need to be more complicated than in the present research, e.g., parameters of a second-order polynomial model can probably still be determined by assessing the edges only. Next to the MatLab environment we used, it would also be possible to solve the Constrained Linear Least Squares problem in Step 3 using PROC NLP of the SAS/ORR software (SAS Institute, Cary, NC, USA). In any case, the global optimum in parameter space will, if feasible given the constraints, always be found and convergence can be guaranteed. If the user selects an artificial neural network model instead of a linear polynomial model, the resulting problem will be of a Constrained Nonlinear Least Squares type, which is more difficult to solve than the one presented in this

research. The PROC NLP of SAS/OR or the sequential quadratic programming routine E04UCF of the NAGR Library (Numerical Algorithms Group, Oxford, UK) could be used. It is anticipated that the proposed methodology could exemplify the statement of Tom Ross (1999, Chapter 1) (). . .In practice, even if they were available, completely mechanistic models may be too complex to use. Nonetheless, if empirical models are used it is a reasonable aim to adopt or develop models that both match our knowledge of the effects of environmental factors on bacterial population change and which are constructed with the aim of describing the qualitative feature of those responses (e.g., cardinal values, optimal values, monotonic behaviour) not solely with the aim of improving the fit to the data available.

Acknowledgements Author A.H. Geeraerd is a Postdoctoral Fellow with the Fund for Scientific Research-Flanders (Belgium) (FWO-Vlaanderen). This research is supported by the Research Council of the Katholieke Universiteit Leuven as part of projects OT/99/24 and IDO/00/ 008, the Institute for the Promotion of Innovation by Science and Technology in Flanders as part of project STWW 980366, the Fund for Scientific ResearchFlanders (FWO-Vlaanderen) as part of project G.0213.02, the Belgian Program on Interuniversity Poles of Attraction and the Second Multi-annual Scientific Support Plan for a Sustainable Development Policy, initiated by the Belgian State, Prime Ministers Office for Science, Technology and Culture, and the European Commission as part of project QLK1-CT2001-01415. The scientific responsibility is assumed by its authors.

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