A Plea for Neutral Comparison Studies in Computational Sciences

by   Anne-Laure Boulesteix, et al.

In a context where most published articles are devoted to the development of "new methods", comparison studies are generally appreciated by readers but surprisingly given poor consideration by many scientific journals. In connection with recent articles on over-optimism and epistemology published in Bioinformatics, this letter stresses the importance of neutral comparison studies for the objective evaluation of existing methods and the establishment of standards by drawing parallels with clinical research.



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1 Introduction

The main goal of methodological research in computational sciences (including, e.g. bioinformatics, machine learning, or computational statistics) is the development of new methods. By development of new methods, we mean that the researchers suggest new procedures for analyzing data sets. The new procedure should be applicable to specific substantive research questions, but these substantive research questions (often) are not the primary center of interest of the methodological researcher. A methodological researcher develops new methods, in contrast to substantive researchers who apply the methods developed by others, e.g. to their e.g. genetic or transcriptomic data. New methods are expected to “make the world better” by, roughly speaking, making the results of statistical analyses closer to the truth. Surprisingly, comparison studies and reviews investigating the closeness to the truth are often considered as less exciting and less useful by many researchers or by most journal editors, and excluded from the journals’ scopes.

This is in strong contrast to clinical research. The ultimate goal in clinical research is to “make the world better” by somehow improving the health outcome of patients (or reducing the cost while maintaining the same outcome), e.g. through a specific drug, therapy or prevention strategy. Roughly speaking, the clinical analogue of a computational article suggesting a “new method” would be an article suggesting a new intervention for improving health outcome. Yet, most published medical papers do not directly suggest such a new measure. Many other types of clinical research projects are conducted, for instance large validation studies, phase IV clinical trials, or meta-analyses. Of course, crucial differences between computational science research and medical research make comparisons only partially pertinent. Research on algorithms and methods does not follow the same rules as research involving human beings with direct potentially vital consequences. The development of a new drug or new prevention strategy essentially requires more time, money, coordination and caution than the development of a new statistical method. Some principles, however, hold for both worlds. If we focus on the problem of comparison studies considered in this paper, the question is “can we imagine a world in which clinical journals accept to publish only underpowered phase I or II clinical trials evaluating new therapies but no phase III or IV trials?” The answer is of course no. In data analysis journals, however, the equivalent of phase III and IV trials, i.e. well-conducted comparison studies in our metaphor, are often considered as not deserving publication.

We claim that comparison studies in computational sciences may however be necessary to ensure that previously proposed methods work as expected in various situations and that emerging “standard practice rules” adopted by substantive researchers or statistical consultants are the result of well-designed studies performed by computational science experts. The community tends to establish standards and guidelines as time goes by. In an ideal world, these standards are the results of well-done comparative studies and consensus from independent teams. However, other factors might contribute to promote a particular method, including the reputation of the authors or the impact factor of the journals the method was published in. From the point of view of applicants (say, biologists), further criteria include the availability of well-documented and user-friendly implementations of the method or an application of this method in one of the few leading scientific journals that other scientists tend to imitate. These criteria may seem natural. After all, a method published by a renown author in an excellent journal is more likely to work well than a method published by an unknown author in a low-ranking journal. Availability of good software is of course a crucial advantage for applicants who would not be able or would not have time to implement any of the methods themselves. And a method that worked well in a previous well-published study is perhaps more likely to also work well in future studies than another method.

It is unclear, however, whether standard practice rules should be established solely on such “subjective” criteria. Would it not be better to give more importance to comparison studies? One may of course argue that comparison studies can be performed within original articles presenting new methods. Indeed, in practice new methods are usually compared to a few existing methods in order to establish their superiority. Such comparison studies are extremely important for illustrative purposes, i.e. to demonstrate that the developed method is applicable in practice and yields acceptable results, but should strictly speaking not be considered as comparison studies because they are often substantially biased and thus not “neutral”.

For example, in the context of clinical outcome prediction or diagnosis based on high-dimensional “omics data” (such as, e.g. microarray gene expression data), hundreds of articles presenting new supervised classification algorithms have been published in the bioinformatics, statistics and machine learning literature. Almost all of them claim that the new method “performs better” than existing methods. Most often these claims are based on small real data studies including a few exemplary data sets. The fact that for twelve years hundreds of authors have been claiming that their new method for classification using microarray data performs better than existing ones suggests that something goes wrong in the comparison studies performed in these articles. Similar discussions can be found in other fields of application of machine learning and computational statistics [e.g., 9]. What goes wrong? How should a proper comparison study look like? Is it possible to perform such comparison studies in the context of an original article presenting a new method?

2 Over-optimism and the need for neutral comparison studies

Comparison studies included in original research articles presenting new methods are often over-optimistic with respect to the superiority of the new method. Some reasons for over-optimism have been empirically assessed and discussed in the context of supervised classification using high-dimensional molecular data [1, 6]. The first and perhaps most obvious reason for over-optimism is that researchers sometimes “randomly search” for a specific data set such that their new method works better than existing approaches, yielding a so-called “data set bias” [10]

. A second source of over-optimism, which is related to the optimal choice of the data set mentioned above, is the optimal choice of a particular setting in which the superiority of the new algorithm is more pronounced. For example, researchers could report the results obtained after a particular feature filtering which favors the new algorithm compared to existing benchmark approaches. The third and probably most subtle problem is that researchers often tend to optimize their new algorithms to the data sets they consider during the development phase

[1, 6]. This mechanism essentially affects all research fields related to data analysis such as statistics, machine learning, or bioinformatics. Indeed, the trial-and-error process constitutes an important component of data analysis research. As most inventive ideas have to be improved sequentially before reaching an acceptable maturity, the development of a new method is per se an unpredictable search process. The problem is that this search process leads to an artificial optimization of the method’s characteristics to the considered data sets. Hence, the superiority of the novel method over an existing method (as measured, e.g. through the difference between the cross-validation error rates) is sometimes considerably overestimated.

Other reasons are of technical nature and related to the ability of the researchers to use the compared methods properly. For example, if an implementation problem occurs with the competing approaches and slightly worsens their results, researchers often tend to spontaneously accept these inferior results. Conversely, they would probably obstinately look for the programming error if such problems occur with their new algorithm. In the same vein, they may unintentionally set the parameters of competing methods to sub-optimal values, or choose a variant of the method that is known by experts to be sub-optimal. They may also select competing methods in a sub-optimal way, i.e. consciously or sub-consciously exclude the best methods from the comparison. Beyond the problems of technical expertise and optimization bias, interpretation and representation issues might also affect the final conclusions of a comparison study. Given the same quantitative outputs, the impression of the reader can be affected, e.g., by the choice of the vocabulary in the results section, by graphical representation, or by the choice of the main quantitative criterion used to compare the methods.

For all these reasons, most comparison studies published in the literature as part of an original paper are substantially biased. These problems stress the importance of “neutral comparison studies” that we define as follows:

  • The main focus of the article is the comparison itself. It implies that the primary goal of the article is not to introduce a new promising method.

  • The authors should be reasonably “neutral”. For example, an author who has published an article on a new method six months before is likely to be less neutral than an author who has often used several of the considered methods for statistical consulting and, say, previously investigated three of them more precisely in methodological articles.

  • The evaluation criteria, methods, and data sets should be chosen in a rational way, see Section 4 for a more extensive discussion of this problem.

Note that the comparison between the competing methods is essentially not affected by the bias discussed in the introduction. Hence, one idea could be to extract neutral comparisons from comparison studies included in original articles presenting new methods—by considering the competing methods only. However, one should keep in mind that these methods probably have not been given as much attention as in the case of a real neutral comparison study that does not involve any new method. This relative lack of attention possibly leads the underestimation of their performance.

To come to the point, in an original article on a new method, the focus is on the new method, and that is where the authors generally spend most of their energy. Consequently, comparisons between competing methods should not be over-interpreted because they may be of sub-optimal quality. On this account we make a (passionate) plea for neutral comparison studies in computational sciences.

3 Tidy neutral comparison studies

In the same way clinical research and clinical studies have to be well planned and executed (following strict guidelines), comparison studies should also follow a well-defined study design. They should be based on a sound theoretical framework, appropriate analysis methods, and carefully selected components. There is a variety of literature on the design and analysis of comparison studies available—we propagate, for example, Hothorn et al. [5] as a theoretical framework and Eugster et al. [4] as its practical implementation. However, regardless of the concrete framework, general considerations on the individual components—evaluation criteria, methods and method parameters, and data sets—can be made.

  • Choice of evaluation criteria:

    In the case of supervised learning algorithms, simple evaluation criteria are, e.g., the error rate or preferably the area under curve that is based on the predicted class probabilities. Such criteria are natural and objective. However, many other criteria have an impact on the usefulness of a method in practice for applications. From a pedagogical point of view, one should not forget that the method is destined to be used by experts or non-expert users. Therefore, all other things being equal, simplicity of a method constitutes an important advantage, similarly to the clinical context where the simplicity of a therapy protocol should be seen as a major advantage. From a technical point of view, particular attention may be devoted to computational aspects such as computation time and storage requirements (similarly to the costs in the clinical context), the influence on initial values in an iterative algorithm, or more generally the dependence on a random generator (similarly to the robustness of the therapy’s effect against e.g. technical problems or human errors).

  • Choice of methods and method parameters: The choice of methods is a very subjective one. At any rate, the concrete choice should be clearly motivated and personal preferences and similar influences should be clearly acknowledged. Researchers are inevitably conducted by personal preferences, past experiences and own technical competence. However, the choice should also be guided by objective arguments. Possible criteria are i) the popularity of the methods in practice (for instance: restrict to methods that have been used in at least three concrete studies), ii) results available from the literature (e.g. from a previous comparison study) to pre-filter good candidates, or iii) specific pre-defined criteria specifying the nature of the method, for example “only statistical regression-based methods”. None of these criteria should be considered as mandatory for a neutral comparison study. But we claim that, the set of criteria being defined, the methods should be more or less randomly sampled within the range of available methods.

    As far as method parameters like hyperparameters are concerned, they should be chosen based on “standard practice rules”.

  • Choice of data sets:

    Researchers performing comparison studies also choose data sets. Considering the high variability of relative performance across data sets, a comparison study based on different data sets (all other things being equal) may obviously yield different results. Variability arises both because error estimation with standard resampling-based estimators is highly variable for a given underlying joint distribution of predictors and response

    [3] and because different data sets also have different underlying distributions. Therefore, it is important to make an “as representative as possible” selection of data sets to cover the domain of interest. At best, the data sets are chosen from a set of data sets representing the domain of interest using standard sampling methodology.

In summary, many choices have to be met when performing a comparison study, for example, in the case of supervised learning with high-dimensional data: the included methods (e.g. penalized regression, tree ensembles, support vector machines, partial least squares dimension reduction, etc), the considered variants (which kernel for SVM, which fitting algorithm for penalized regression, which optimality criterion for PLS, which splitting criterion for tree ensembles, etc), the data domain (which type of data sets), the parameter tuning procedure (which resampling scheme, which candidate values). With this in mind, it is clear that the topic of interest cannot be handled completely by a single comparison study. Different comparison studies with similar scope may yield different conclusions. This can be seen as a limitation of each single comparison study – or as an argument to perform more such comparison studies. Going one step further in the comparison with clinical research, one could also imagine a concept of meta-analysis for comparison studies in computational sciences. In the clinical context, meta-analyses provide a synthesis over different populations, different variants of the investigated therapies, different technical conditions, different medical teams, etc. Similarly, meta-analyses for computational studies in computational sciences would provide syntheses over different data domains, different variants of the considered methods, different software environments, different teams with their own areas of expertise, etc.

4 Negative results

Comparison studies can be a good vehicle for negative research findings. Publication biases and the necessity to ”accentuate the negative” [8] are well-documented in the context of medical and pharmaceutical research. In applied statistics and data analysis research, however, this issue receives very poor attention [1], even if the publication of negative results may be extremely useful in many cases.

The systematic exclusion of negative results from publication might in some cases be misleading. For example, imagine that ten teams around the world working on the same specific research question have a similar promising idea that in fact does not work properly for any reason. Eight of the ten teams obtain disappointing results. The ninth team sees a false positive in the sense that they observe significant superiority of the new promising method over existing approaches although it is in fact not better. The tenth team optimizes the method’s characteristics [6] and thus also observes significant superiority. The two latter teams report the superiority of the promising idea in their papers, while the eight other studies with negative results remain unpublished: a typical case of publication bias. This scenario is certainly caricatural, but similar things are likely to happen in practice although in a milder form. Note that it is very difficult to give concrete examples at this stage, since such stories essentially remain unpublished.

Nevertheless, the publication of negative results might entail substantial problems. Most researchers (including ourselves!) probably have more ideas that turn out to be disappointing than ideas that work fine. Try-and-error is an essential component of research. It would thus be impossible (and uninteresting anyway) to publish all negative results. But then, what was promising and what was not promising? What is likely to interest readers and what was just a bad idea that nobody else would have thought of? Obviously this decision that would have to be taken by reviewers and editors is a subjective one. Assessing whether a new method with negative results deserves publication in a separate paper is anything but trivial. With this in mind, we believe that the publication of negative findings within large well-designed comparison studies would be a sensible compromise in order to diffuse negative findings without congesting the literature with negative papers.

Journals would not have to fear for their impact, since good comparison studies are usually highly accessed and cited. Authors would not be urged to make something out of their promising idea on which they have spent a lot of time: a large comparison study would be an alternative to publish important results and share their vast experience on the topic without fishing for significance. And "fishing for significance" would lose part of its attractiveness. Most importantly, readers would be informed about important research activities they would not have heard of otherwise.

Note that “standard practice rules” in computational sciences (e.g., regarding the choice of method parameters) are often implicitly the result of comparison studies. For instance, a “standard parameter value” becomes standard because it yields better results than another value. In other words, negative results are often hidden behind standard practice rules - most of them remaining unpublished. Our point is that this process could be made more transparent and more informative for the readers if these negative results were published within extensive comparison studies.

Drawing the comparison with clinical research from the introduction even further, we also think that it may be interesting to publish articles on “pitfalls”. By “pitfall” we mean the inconveniences of a data analysis method such as, e.g., a non-negligible bias, a particularly high variability, or non-convergence of an algorithm in specific cases that may lead to misleading results. By “negative result” we mean a disappointing result of a new method that had been considered as promising problem solver for a specific case. In computational literature such research results are often hidden in the middle of articles that are actually devoted to something else. This is in contrast to clinical research, where pitfalls of existing methods (e.g. an adverse effect of a drug) may be the main object of an article, even if no alternative solution is proposed (for example in form of an alternative drug).

5 Limitations

Neutral comparison studies are in our opinion crucial to make the establishment of standards more objective and to give a chance to methods that are at first view unspectacular and would otherwise be pigeonholed. However, comparison studies and their impact should not be over-interpreted. Firstly, one should not forget that no method is expected to work well with all data sets (the well-known “no free lunch theorem”). Hence, a method that scores well in many comparison studies may do poorly in a specific data set. Comparison studies are not expected to yield an absolute truth applicable to all situations. They are solely useful to determine general trends that may be useful to the community to select a set of standard methods that often perform well.

Secondly, comparison studies are essentially limited because they rely on the specific and sometimes arbitrary choices regarding the study design: the choice of simplifying evaluation criteria that probably do not reflect the complexity of concrete data analysis situations, the choice of method parameters that may substantially impact the relative performance of the considered methods, and last but not least the choice of specific example data sets.

Thirdly, comparison studies are often underpowered in the sense that the number of included data sets is insufficient considering the high variability of performance across data sets. With a few exceptions (see [2] for a comparison of machine learning algorithms based on 65 gene expression data sets), comparison studies often include up to 10-15 data sets, which is probably not enough. This issue may be further investigated in future research.

Fourthly, comparison studies essentially ignore the substantive context of the data sets they consider. Data sets are sometimes preprocessed without much knowledge of the signification of the variables. All methods are applied in the same standardized way to all data sets. The analysis is thus intentionally over-simplified. An important aspect of the data analysis approach is neglected, which does not reflect the complexity and subtleties of the data analyst’s work [7]. A method that does not work well if applied in a standard way without knowledge of the substantive context might perform better in concrete situations, hence reducing the relevance of comparison studies.

6 Conclusion

Neutral comparison studies are often considered as less exciting than project on new methods by both researchers and journal editors – but not by readers. They can neither be expected to always give the best answer to the question “which method should I use to analyze my data set” nor reflect a real data analysis approach that takes the substantive context into account. However, we believe that they may play a crucial role to make the evaluation of existing methods more rational and to establish standards on a scientific basis. They certainly deserve more consideration than is currently the case in the literature.


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