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. 2025 Apr 28;20(4):e0319159. doi: 10.1371/journal.pone.0319159

Prompt architecture induces methodological artifacts in large language models

Melanie Brucks 1,*,#, Olivier Toubia 1,#
Editor: Vijayalakshmi Kakulapati,2
PMCID: PMC12036937  PMID: 40293988

Abstract

We examine how the seemingly arbitrary way a prompt is posed, which we term “prompt architecture,” influences responses provided by large language models (LLMs). Five large-scale, full-factorial experiments performing standard (zero-shot) similarity evaluation tasks using GPT-3, GPT-4, and Llama 3.1 document how several features of prompt architecture (order, label, framing, and justification) interact to produce methodological artifacts, a form of statistical bias. We find robust evidence that these four elements unduly affect responses across all models, and although we observe differences between GPT-3 and GPT-4, the changes are not necessarily for the better. Specifically, LLMs demonstrate both response-order bias and label bias, and framing and justification moderate these biases. We then test different strategies intended to reduce methodological artifacts. Specifying to the LLM that the order and labels of items have been randomized does not alleviate either response-order or label bias, and the use of uncommon labels reduces (but does not eliminate) label bias but exacerbates response-order bias in GPT-4 (and does not reduce either bias in Llama 3.1). By contrast, aggregating across prompts generated using a full factorial design eliminates response-order and label bias. Overall, these findings highlight the inherent fallibility of any individual prompt when using LLMs, as any prompt contains characteristics that may subtly interact with a multitude of hidden associations embedded in rich language data.

Introduction

Generative artificial intelligence (AI) models and tools, in particular large language models (LLMs) such as GPT (generative pre-trained transformer), are rapidly disrupting many industries and fields of study, with many scientists and practitioners actively contemplating the use of LLMs as a substitute for humans in a wide range of tasks and occupations [1–11]. At first glance, LLMs seem particularly well-suited for some of the more tedious tasks typically performed by humans, such as combing through hordes of textual data and evaluating these data on various dimensions. LLMs have extensive memory and processing abilities, are presumably not influenced by emotions or moods, and never lack motivation.

As generative AI continues to gain traction, however, researchers are cautioning against hasty and indiscriminate use because these models tend to perpetuate pernicious social stereotypes and prejudices that may be embedded in the content on which they are trained. For example, due to co-occurrences in their corpora, LLMs may reveal gender stereotypes, such as perceiving a “nurse” more as a “woman” and a “doctor” more as a “man” [12–14]. As such, important ongoing work has begun developing tools for detecting and addressing this type of bias in the content created by LLMs [15–17].

In this article, we complement work that defines bias as “the predisposition or inclination toward a particular group (based on gender or race), often rooted in social stereotypes, that can unduly influence the representation or treatment of particular groups” [16] by focusing on methodological artifacts, or biases due to the specificities of a given task design. Methodological artifacts are a form of statistical bias, as they are systematic errors that lead to conclusions that are partly “a result of the particular research technique employed, rather than an accurate representation of the world” [18]. Using a choice architecture framework, we examine how arbitrary associations embedded in the rich language data used to train LLMs may induce statistical bias (and, therefore, errors) in output.

We propose that prompt architecture biases LLM evaluations similarly to how the context of a choice biases human judgment [19–23]. We define “prompt architecture” as the seemingly arbitrary way a prompt is posed, such as the order of options in a prompt and the framing of a prompt. For example, managers (researchers) interested in replacing their workforce (human subjects) with generative AI may ask GPT to evaluate the similarity between different sets of items. They also need to decide how to label each set in the prompts they submit to GPT, the order in which to list the sets, and how to word the exact task. For example, a user may decide to write the prompt: “Is Set B or Set C closer to Set A?” Evaluative tasks such as these, with multiple choices that are ordered and labeled, span many different LLM use cases, including diagnoses [9,11], opinion polls and surveys [2,3], and social science experiments [5,7,8].

When only one prompt is used in these evaluation tasks, the implicit assumption is that GPT operates under the normative principle of procedure invariance, revealing a stable and reliable measure of similarity between options regardless of response order, labeling, framing, or justification (i.e., asking for reasons). In support of this assumption, GPT claims “my answer will only be driven by the actual items in each set. The order or labels of the sets will not influence my answer” (S1 Fig). Contrary to this claim, we find that the arbitrary architecture of the prompt (i.e., order, label, framing, and justification) systematically and significantly biases the output of LLMs, rendering the results from LLMs prone to methodological artifacts [18]. In other words, without taking this form of bias into account, a user may erroneously conclude that set A is closer to set B, candidate 1 is more qualified than candidate 2, or diagnosis I is more likely than diagnosis II, simply because of the architecture of the prompt.

Contemporaneous work in computer science and medicine offers preliminary support of our proposition that the architecture of the prompt may affect LLM responses. For example, research finds that the order of options in multiple-choice questions affects LLMs’ answers [24–27] and that this bias can be exacerbated when the task becomes more difficult [24]. Research also finds that the responses provided by LLMs are subject to the labels given to multiple-choice options [28–30]. Moreover, nascent work documents that prompt wording can influence LLM judgment. For example, Arroyo et al. [31] find that the performance of LLMs on tasks such as mortality prediction vary based on slight differences in the wording of the instructions.

We present a unifying theory of prompt architecture that can explain this work and expand on it, by framing it within a broader type of methodological artifacts to which LLMs are vulnerable. To test this, we design a full factorial experiment to systematically examine and disentangle the impact of multiple elements of prompt architecture. Specifically, in addition to order and labeling [32], we test two other classic choice architectural elements demonstrated in psychology—framing [33] and justification [34,35]—and examine how these elements interact with order and label bias within the same prompt. Mirroring findings in choice architecture, we find robust evidence that order, label, framing, and justification affect LLM responses. In particular, we uncover response-order and label bias and demonstrate how framing and justification affect these biases. We also test strategies to mitigate the methodological artifacts elicited by prompt architecture. We find that the use of uncommon labels reduces (but does not eliminate) label bias but exacerbates response-order bias for GPT-4 (it does not reduce either bias in Llama 3.1) and that specifying to the LLM that the order and labels of the items have been randomized does not alleviate either response-order or label bias in GPT-4 or Llama 3.1. By contrast, aggregating across prompt architectures generated using a full factorial design eliminates response-order and label bias. Although developing a full factorial design each time a user prompts a LLM may be impractical, the benefits likely outweigh the costs for decisions where bias is particularly harmful, such as in hiring or diagnoses. In addition, such factorial design may be implemented automatically (and potentially in a way that is transparent to the end user) by developing simple applications that generate the design and run it on the API.

By demonstrating the effect of different prompt architecture elements on LLM output, we hope to reorganize the emerging literature which has narrowly focused on the effect of specific elements of order or labeling under the umbrella of prompt architecture. Specifically, choice architecture argues that “there is no such thing as a neutral design” [19]. Similarly, there is no such thing as a neutral prompt: inherent in any individual prompt is an arbitrary architecture that includes order, labeling, framing, and a host of other characteristics that may subtly impact LLM output. As a result, “prompt engineering,” which typically attempts to identify one optimal prompt for a given task, may be a futile exercise. We suggest that rather than attempting to remove bias, users aggregate across different prompts, canceling out random and unpredictable noise due to the architecture of any individual prompt [36].

Study 1

Materials and methods

Our main test uses the application programming interface (API) of GPT-4 to perform a large number of evaluations. For replicability and because the behavior of GPT-4 keeps evolving [37], we pinned GPT-4 to its 06/13/2023 version (accessed 02/12/2024; the 06/13 version was the latest pinned version that was not in “preview” mode as of January 2024). We set temperature to 0 to obtain GPT-4’s most probable answer to each prompt. Borrowing from a standard psychology task [38], we show GPT-4 three sets of items (e.g., three sets of five countries) and ask whether the second or third set is closer to the first. This type of task is described as zero-shot because we do not provide any training example in the prompt. For a given triplet {Set1, Set2, Set3}, our experimental design has 32 conditions, in a 2^5 full factorial design (Table 1 for a summary of the conditions, Fig 1 for an example of the task, and S1 File for more detail).

Fig 1. Example prompt generated in the category of countries.

Fig 1

In this example sets are described using letters, ordered as A, B, C, and we ask for the closer set without an explanation.

First, we vary whether the prompt describes the sets using letters (A, B, C) or symbols (#, %, *). We examined both letter and symbol labels to test whether letters produce additional label bias, as they (i) possess an inherent order (i.e., the alphabet) and (ii) could be more frequently present in the training set in ways that might create extraneous associations given that letter labeling is a common practice. Second, we independently vary order by swapping the second and third labels (A, B, C vs. A, C, B or #, %, * vs. #, *, %) and the second and third sets (123 or 132). For example, the same triplet labeled with letters would be presented in four different ways (A. Set 1, B. Set 2, C. Set 3; A. Set 1, C. Set 2, B. Set 3; A. Set 1, B. Set 3, C. Set 2; A. Set 1, C. Set 3, B. Set 2). This is a full factorial design in which each set has one instance of each order and label combination, which allows us to test for statistical bias because we experimentally manipulate order and label independent of the actual content of the set. As a result, any impact of order and/or label is definitionally biased and does not reflect a real difference between sets. Third, to examine other elements of the prompt architecture, we vary the framing by asking GPT-4 either which set is closer to the first set or which set is farther away [33]. Finally, following work on justification [34,35], we vary whether we ask GPT-4 to justify its answer.

Table 1. Summary of conditions.

Element Manipulation
Label Type Letters (A, B, C) vs. Symbols (#, %, *)
Label Order A, B, C vs. A, C, B or #, %, * vs #, *, %
Set Order Set 1, Set 2, Set 3 vs. Set 1, Set 3, Set 2
Framing Which of the two sets is… “closer” vs. “farther”?
Justification Please give me a precise answer… “don’t explain it” vs “with an explanation”

We employ stimuli sampling and generate stimuli across six different categories (e.g., countries) borrowed from prior research [16], with 30 different triplets {Set1, Set2, Set3} in each category (S2 File for more detail on the stimuli generation). In sum, our experimental design generates 5,760 observations: 6 categories × 30 triplets per category × 32 prompts per triplet. All data and code used to analyze the data are available at OSF (https://osf.io/2pzh9, https://doi.org/10.17605/OSF.IO/2PZH9).

Results

Of the 5,760 observations, GPT-4 failed to complete the task 313 times (5.43% failure rate). We removed these observations to obtain our final dataset of 5,447 observations.

Response-order and label bias.

Given full randomization, an unbiased responder should select the first option 50% of the time and any specific label 50% of the time. Instead, we find evidence that GPT-4 is prone to response-order and label bias. On average, across all observations, GPT-4 selected the first option in 63.21% of the cases (p <.001) and selected B over C in 74.27% of the cases (p <.001). Fig 2a and 2b break down these biases by condition. Across condition, we consistently find response-order bias and lettered-label bias. In contrast with labeling with letters, we find that label bias is reduced, but not completely eliminated, when using symbols: the symbol % is chosen over the symbol * in 54.16% of the cases (vs. 63.21% of “B” for letters, p <.01; Fig 2c). This finding is consistent with the explanation that label bias is due to LLMs favoring more common tokens (e.g., B over C), as this bias is reduced when using labels that are uncommon for the task at hand. LLMs’ favoring of common tokens mirrors psychological work that finds that exposure frequency positively affects people’s liking [39].

Fig 2. Methodological bias as a result of prompt architecture.

Fig 2

A. Frequency of first response selection across conditions. B. Frequency of selecting the set labeled as B, among observations in which sets are labeled using letters. C. Frequency of selecting the set labeled as %, among observations in which sets are labeled using symbols. All figures show 95% confidence intervals (CIs) estimated using a random effects linear model (lmer in R), which included random intercept for triplet.

Interaction of architectural elements.

Because we systematically and jointly manipulate multiple elements of prompt architecture, we can also examine how these architectural elements interact to produce bias. First, we examine how response-order and label bias interact with each other. We find that the former is much stronger when using symbols (which are uncommon labels) than when using letters (which are common labels). GPT-4 selected the first option in 53.55% of the cases that were labeled with letters and 73.35% of the cases that were labeled with symbols. This is consistent with contemporaneous work with GPT that finds that order bias is more pronounced when options are labeled using less common letters, such as N, R, S, rather than more common letters, such as A, B, C [28]. That is, when the labels of the various options are weaker cues, GPT-4 seems to rely more heavily on other cues (i.e., the ordering of the options), suggesting that simply removing the bias from one element (e.g., labeling) will not necessarily improve LLM performance given the multifaceted nature of prompt architecture; potential bias lurks in every semantic corner of a prompt, and reducing one form of bias may simply open the opportunity for another bias to dominate.

Second, we examine the two additional architectural elements of (i) framing and (ii) justification and test whether they impact response-order or lettered-label bias. We find that asking GPT-4 for justification reduces but does not eliminate response-order bias (from the first option being selected in 67.87% of cases to 58.28% of cases) and lettered-label bias (from “B” being selected in 78.76% of cases to 69.50% of cases). This is consistent with prior work in choice architecture that finds that when people feel accountable for their decisions, they are less likely to rely on contextual cues in their decision making [35]. However, research also finds that justification can bias human decision makers in other ways. For example, asking for justification leads people to select options that contain features that are easier to articulate, even if these options are less preferred (e.g., a humorous poster vs. an abstract, aesthetic one) [34]. Although LLMs do not experience emotions or motivation, structural patterns in the training set could lead to similar results. For example, perhaps asking an LLM to justify its selection of a job candidate or image could bias it toward decisions that are easier to articulate, such as the candidate with a higher GPA or an image with more discernible components. Again, as choice architecture dictates, there is no neutral prompt. Asking for justification might bypass one type of bias but unwittingly invite another.

We also find that framing interacts with both response-order and label bias. Specifically, we find that both response-order and letter-label biases are stronger when GPT-4 is asked which set is closer to a given stimulus than when it is asked which set is farther from it (from the first option being selected in 70.36% of cases with closer framing to 56.37% of cases with farther framing, and from option “B” being selected in 79.68% of cases with closer framing to 68.60% of cases with farther framing; ps <.001). Response-order and label bias are probably multiply determined, and a “closer” framing may exacerbate bias in our similarity paradigm for several reasons. One possibility could be that order and label are part of the stimuli evaluated by GPT (e.g., the content of the set is “bundled” with its letter and position, and the bundle is evaluated holistically). If this is the case, the answer could be influenced by the fact that A is closer to B than C and the first response is physically closer to the reference stimuli than the second response. Another possibility is that the “closer” framing is a more common question. The effect could then be interpreted in the context of work in psychology showing that people are more likely to rely on heuristic processing when stimuli are familiar and/or easy to process [40]. Future research could test whether a less familiar framing leads LLMs to process in a way that appears more thorough, similarly to a request for justification.

Although we do not have answers as to why an individual element of prompt architecture affects GPT evaluations, we provide robust evidence for the widespread and intricate effect of prompt architecture. Our results show that subtle differences in the context of choices that affect human decision making are also affecting GPT-4 evaluations. Not only did all four classic elements of choice architecture that we manipulated impact GPT-4 evaluations, but these elements interacted with each other to form a complex web of different biases. In our particular setup, the prompt that yielded the most bias was when sets were labeled A, B, C and GPT-4 was asked which set was closer (the likely default framing for many users). In this case, GPT-4 selected B (which also happens to be the first response) in a remarkable 91.67% of the cases.

We replicate these results using Llama 3.1 (S3 File) and GPT-3 (S4 File). Similar to GPT-4, Llama 3.1 exhibits response-order bias (Llama 3.1 selected the first response in 58.14% of cases) and label bias (Llama 3.1 selected B for 76.70% of the cases and % for 76.73% of the cases), and these biases are moderated by label type, framing, and justification, though not always in the same way as in GPT-4. For example, the prompt that yields the most bias is when sets are labeled #, %, * and Llama 3.1 is asked which set is closer. In this setup, Llama 3.1 selected % (which also happens to be the first response) in a remarkable 99.44% of the cases. GPT-3 also exhibits response-order bias and label bias. However, relative to GPT-4, the response-order bias was reduced (GPT-3 selected the first response in 53.16% of cases) and the label bias increased (GPT-3 selected B for 64.10% of the cases and % for 77.15% of the cases). As with GPT-4, these biases are moderated by label type, framing, and justification, though again, not always in the same way. For example, first response bias was exacerbated when GPT-3 was asked for justification (whereas it was reduced with GPT-4). These findings imply that identifying the “least biased” prompt or avoiding the “most biased” prompt may be futile, as different LLMs and different versions may react to prompt architecture differently. We examine the implications of these results further in the General Discussion.

Study 2

Study 2 had two goals: to investigate the effect of response-order and label bias using one single-word item per set, in which evaluations are arguably much easier, and to test an intervention identified by contemporaneous research to reduce bias. Specifically, Gui and Toubia [41] find that manipulating prompt content can confound experiments due to associations in LLM training data. For example, manipulating the price in a prompt affects the kind of consumer information the LLM draws from when responding. Importantly, this work finds that specifying to the LLM that the price is randomly determined may help mitigate this confound. If the biases we observe here are due to confounding factors that correlate with the choice of order and label (e.g., more important or prominent items listed first in the training set), perhaps instructing LLM that order and label were determined randomly would similarly reduce the effect. If, however, prompt architecture effects are driven by intrinsic or idiosyncratic tendencies in favor of certain prompt characteristics, we may not observe an attenuation. We test these competing predictions in Study 2.

Materials and methods

We again use the API of GPT-4 pinned on 06/13/203 and a temperature of 0. We employ a similar experimental design to that in our main experiment, with two modifications. First, we use sets with single items that are all single words (unigrams). Second, from the design in Study 1, we include the four conditions that orthogonally vary the order of the items and the order of the labels (A-B-C vs. A-C-B), but we only use letters as labels, only ask GPT-4 which item was closer to item A, and never ask for justification. This replicates the conditions that produced the highest level of bias in Study 1.

A crucial difference in this study is the introduction of our intervention factor in the experimental design. In the first condition (Control), we simply ask GPT-4 which of the two items is closer. In the second condition (Randomized), we add the following statement at the end of the prompt: “I have randomized the order and labels of these two items.” In the third condition (Chosen), we add: “I have chosen the order and labels of these two items.” If the order and label biases are due to confounding factors that correlate with the choice of order and labels, the bias may be attenuated in the Randomized condition and potentially exacerbated in the Chosen condition compared with the Control condition.

Combining these experimental factors in a 2 (item ordering) × 2 (label ordering) × 3 (Control vs. Randomized vs. Chosen) full factorial design, we have 12 prompts per triplet. We use the same six categories as in Study 1 but this time increase the number of replications to 900 per category. Therefore, our experimental design generates 64,800 observations. All data and code used to analyze the data are available at OSF (https://osf.io/2pzh9/?view_only=aa6d1b2759134b7a8408d7ccc38f1922).

Results

Of the 64,800 observations, GPT-4 failed to complete the task 489 times (.75% failure rate). We removed these observations to obtain our final dataset of 64,311 observations.

Response-order and label bias.

On average, across all observations, we replicate both response-order and label bias among these simpler, single-word items. GPT-4 selected the first option in 64.29% of the cases (p <.001) and selected response “B” in 66.72% of the cases (p <.001).

Intervention.

As Fig 3a shows, order bias is consistent across the Control, Chosen, and Randomized conditions, varying only between 63.82% in the Randomized condition to 65.00% in the Chosen condition. We again find evidence of bias in favor of the label B over C, which is again consistent across conditions, as shown in Fig 3b. The frequency of the B selection varies only between 65.95% in the Randomized condition and 67.30% in the Control condition.

Fig 3. Methodological bias as a result of prompt architecture (Study 2).

Fig 3

A. Frequency of first response selection for GPT-4 across conditions. B. Frequency of selecting the set labeled as B for GPT-4 among observations in which sets are labeled using letters. Both figures show 95% CIs estimated using a random effects linear model (lmer in R), which included random intercept for triplet.

In summary, although in the context of using LLMs to simulate human response to price variations research finds that confounding may be reduced by informing the LLM of the source of random variation across stimuli [41], in our context, in which we ask LLMs to evaluate similarity, informing the LLM that the ordering and labeling of items have been randomized has only negligible effects and does not appear as a viable solution to the problem. Our results instead are more consistent with those of Zheng et al. [29], who find that a similar intervention does not mitigate label bias in the context of multiple-choice questions with objectively correct answers.

As in Study 1, we replicate this study design using Llama 3.1 (S5 File) and again find no evidence that the intervention worked. Instead, indicating that the order and labels were “chosen” or “randomized” flipped and exacerbated the response-order effect (among those prompts, Llama 3.1 was significantly more likely to select the second item). This further underscores that although the presence of prompt architecture effects is predictable, the specific impacts are unpredictable.

Discussion

The arbitrary architecture of a prompt induces statistical bias in the responses of LLMs, with the responses partly due to “the particular research technique employed, rather than an accurate representation of the world” [18]. These insidious methodological artifacts threaten the validity of any evaluation or output that stems from a single prompt provided to an LLM. For example, GPT may find that the set arbitrarily labeled as “Set B” is closer to “Set A” in as many as 80% or more of cases simply because of the architecture of the prompt. Moreover, in practice, order and labels may not be applied randomly. For example, users may list their personal favorite option first. Thus, the results we report suggest that LLMs may inadvertently serve as a confirmation bias tool rather than an unbiased adviser.

Our main goal is to present an overarching framework to understand the scope of hidden methodological biases rather than delineate the process behind any particular bias. Borrowing from extensive work in choice architecture [19], our framework suggests that there will never be such a thing as a “neutral” or “perfect” prompt. Indeed, knowing all the hidden biases embedded in rich language data is impossible; thus, specific solutions or prompt types that address bias in a certain task might not generalize to other tasks. Rather than trying to remove bias through “perfect prompts,” we advise researchers and practitioners to apply the principles that human subject experiments have employed for decades—aggregating the output of multiple prompts that vary according to a full counterbalanced design, in an attempt to cancel out idiosyncratic errors of any single prompt [36].

As an initial test of this strategy for reducing bias, we examine how aggregating the output of our 32 prompts in Study 1 reduces bias in responses provided by both GPT-4 and Llama 3.1. Specifically, given our experimental design, in which we create Set 1, Set 2, and Set 3 by randomly drawing from a list of items in a category, the chance that Set 2 (vs. Set 3) is selected in a prompt asking about which is farther from or closer to Set 1 should be close to 50%. In other words, there should be nothing intrinsically different about Set 2 versus Set 3 in our 30 triplets randomly generated across six categories; thus, an unbiased responder should not show systematic preference for Set 2 over Set 3.

We find that the extent of bias varies across prompts, with the most biased prompts selecting the arbitrary Set 2 100% of the time across all triplets and categories (Fig 4). The specific prompts that demonstrate the least bias (e.g., approach 50% selection of Set 2) are different across the two models, suggesting that there is no ideal “unbiased” prompt. Instead, we suggest aggregating across different prompt types, that is, simply using the majority answer across prompt variations: for a particular triplet, across the 32 prompt formats we count the number of times the model indicated that Set 2 was closer and the number of times it indicated that Set 3 was closer, and we use the majority answer as the final answer. We find that this simple approach eliminates bias: Set 2 is selected 50% of the time when aggregating across all 32 prompts for both GPT-4 (50.01%) and Llama 3.1 (50.06%).

Fig 4. Methodological bias in individual prompts.

Fig 4

Both figures show 95% CIs estimated using a random effects linear model (lmer in R), which included random intercept for triplet.

Note that eliminating bias does not necessarily improve accuracy. For example, a coin flip would produce an unbiased but inaccurate answer. To ensure that our intervention did not compromise accuracy, we ran an experiment identical to Study 1 but with single-word items and used Word2Vec word embeddings to calculate a noisy proxy for similarity and, in turn, GPT-4’s accuracy when making similarity judgments. Our results suggest that aggregating reduces bias while increasing accuracy (S6 File). Thus, the benefit of aggregation is that it reduces bias while improving accuracy. The drawback is that it requires identifying the elements of prompt architecture that might bias an LLM’s response and creating a full factorial set of prompts to address this bias, and doing so could be time and resource intensive. In cases in which this is too daunting, we recommend, at minimum, balancing order and labeling.

One concern might be whether the effects of prompt architecture are simply a snapshot in time, destined to be fixed by newer models. As an initial exploration of this possibility, we turn to our study 1 replication experiment with GPT-3. Although we observe differences between GPT-3 and GPT-4, the changes are not necessarily for the better (S4 File). Although we find significant bias in favor of the first option (p <.001), the bias appears to be less severe in GPT-3 than GPT-4, suggesting that, at least in terms of this particular type of bias, GPT is not improving. This is not particularly surprising given the nature of LLMs, which are trained on rich and complex natural language data. Identifying and removing any cues in a prompt’s architecture seem unlikely, if not impossible, given the nature of language. In summary, the power of LLMs is undeniable, but these models should be used with discerning judgment and a thoughtful experimental design.

Our empirical context involved both simple and complex similarity tasks and formally worded prompts, which represents only a subset of the diverse types of prompts users might provide to LLMs. This raises the question of how our findings generalize to other contexts, such as tasks that vary in complexity beyond the similarity tasks in our studies or prompts that are phrased less formally than our prompts. Prior research with human participants provides a few hypotheses. First, human respondents are more likely to be influenced by choice architecture during complex tasks because these tasks involve more in-the-moment response construction [23,42]. Thus, our observed effects of prompt architecture may exacerbate for more complex tasks and attenuate for simpler tasks compared to the similarity task used in our studies. However, of note, we observed effects of prompt architecture for both simple (i.e., one-item stimuli) and complex (i.e., five-item stimuli) similarity tasks. Second, research suggests that informality during communication, such as text abbreviations, can signal low effort and, as a result, decrease responsiveness [43]. If this pattern exists in the training data, LLMs may be less responsive (e.g., provide less thorough justification) when the prompt contains more informal language usage. We encourage future research to explore the generalizability of our findings, including how complexity moderates the effects of prompt architecture and how additional architectural elements beyond the ones examined in this paper, such as prompt formality, may influence LLM responses.

Supporting information

S1 Fig. Screenshot from GPT-4 about biases.

The following screenshot was taken on 03/08/2024. We use the API Playground to mimic the conditions of our experiment: GPT-4 pinned on 06/13/23, with a temperature of 0. The “System” portion of the prompt was set to its default (“You are a helpful assistant”).

(PDF)

pone.0319159.s001.pdf (56.7KB, pdf)
S1 File. Prompt variations.

Base prompt (in the categories of countries), in which sets are described using letters, ordered as A, B, C, and in which we ask for the closer set without justification.

(PDF)

pone.0319159.s002.pdf (59.3KB, pdf)
S2 File. Stimuli sampling procedure.

(PDF)

pone.0319159.s003.pdf (6.8KB, pdf)
S3 File. Study 1: Replication using Llama 3.1.

(PDF)

pone.0319159.s004.pdf (64.2KB, pdf)
S4 File. GPT-3 versus GPT-4.

(PDF)

pone.0319159.s005.pdf (247.9KB, pdf)
S5 File. Study 2: Replication using Llama 3.1.

(PDF)

pone.0319159.s006.pdf (61.9KB, pdf)
S6 File. Improving Accuracy by Using Aggregation.

(PDF)

pone.0319159.s007.pdf (61.3KB, pdf)

Acknowledgments

We thank J. Liu and J. Zhang for help with stimuli creation and data collection.

Data Availability

All data and code used to analyze the data are available on OSF, https://osf.io/2pzh9, DOI: 10.17605/OSF.IO/2PZH9

Funding Statement

The author(s) received no specific funding for this work.

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Decision Letter 0

Vijayalakshmi Kakulapati

30 Jul 2024

PONE-D-24-16087Prompt Architecture Induces Methodological Artifacts in Large Language ModelsPLOS ONE

Dear Dr. Brucks,

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Reviewer #1: Yes

Reviewer #2: Partly

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #2: No

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Reviewer #1: The study probes into prompt architecture—biases responses provided by Large Language Models (LLMs). Mimicking findings in choice architecture, the study finds robust evidence that label, order, framing, and asking for reasons affects LLM responses. Two major findings was, (i) the use of uncommon labels reduces (but does not eliminate) label bias but exacerbates response order bias and (ii) specifying to the LLM that the labels and order of the items have been randomized does not alleviate either response order or label bias.

Major Comments

I enjoyed reading this manuscript and believe it holds great promise. However, I have identified minor issues that require the authors' attention:

Various detailed studies in the field of Medicine have utilized multiple-choice questions, particularly in the format of A, B, and C. These studies often use complex clinical cases from sources such as the New England Journal of Medicine (NEJM) Clinicopathological Conference (CPC). With detailed reasoning, large language models (LLMs) predict the answers. These predictions, when justified, are correct answers and not biases. Any comments?

The sentence 'Although we find that asking for justification reduces response order and label bias, it is possible that it could exacerbate other biases we did not measure'. These other potential biases can be discussed further.

The sentence 'However, the bias appears to be less severe in GPT-3 compared to GPT-4, with 53.2% vs. 63.21% of the cases, respectively'. This important finding should be mentioned in the main manuscript, not only in the supplemental data.

Due to the proprietary nature of GPT models, there is growing interest in open-source LLMs. Is it possible to test the hypothesis with other open-source models like LLaMA-3?

Check the reference:

Artefacts, statistical and methodological. In: Oxford Reference.

Reviewer #2: The paper presents a highly engaging and insightful study on the biases present in GPT label generation. However, to enhance the quality and comprehensiveness of the work, I suggest the following revisions:

Firstly, the task itself needs to be more clearly defined. The authors should specify the exact types of labels they expect to encounter and analyze. This clarity will provide a better framework for understanding the scope and objectives of their study.

Secondly, the language throughout the paper requires some refinement. At certain points, the writing becomes too informal, which detracts from the scholarly tone of the work. A more formal and consistent style would improve the overall readability and professionalism of the paper.

Additionally, the authors focus exclusively on GPT-4. This focus raises concerns about potential bias towards proprietary models. It would be beneficial to include a comparison with open-source large language models (LLMs) such as LLaMA or Mistral to provide a more balanced analysis.

The definition of bias within the context of the study is another critical area that needs attention. The authors should refer to relevant definitions and frameworks, such as those discussed in the paper available at [IEEE Xplore](https://ieeexplore.ieee.org/abstract/document/10538997), to establish a definition and solid theoretical foundation for their analysis. the literature review needs to be updated to reflect the latest research and developments in the field. This update will ensure that the study is situated within the current academic discourse and acknowledges recent advancements and discussions.

Clarification is also needed on whether the labeling process employed in the study is stochastic. Understanding the nature of the labeling process is essential for assessing the reliability and consistency of the generated labels.

The authors should provide a thorough discussion of the pros and cons of their approach. This analysis will help readers understand the strengths and limitations of the method and its potential implications for future research and applications.

From what I understand, the authors aim to mitigate the biases in GPT-generated labels by proposing a more reliable approach. To enhance the practical value of their study, they should include an algorithm presented in pseudocode. This inclusion would provide a clear, actionable method for other researchers and practitioners to implement and build upon their work.

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Reviewer #1: Yes:  Balu Bhasuran

Reviewer #2: No

**********

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PLoS One. 2025 Apr 28;20(4):e0319159. doi: 10.1371/journal.pone.0319159.r003

Author response to Decision Letter 1


20 Sep 2024

Response to Reviewers

We would like to thank the Academic Editor and the reviewers for the insightful and constructive comments on our manuscript, “Prompt architecture induces methodological artifacts in large language models.” We have done our best to address all of the points raised, as detailed in this letter.

Academic Editor:

Thank you for the opportunity to revise our manuscript and for providing a clear roadmap forward. Below we respond to each of your requests:

1. We have ensured that the manuscript meets the PLOS ONE style requirements.

2. All data and code are and will remain publicly available on ResearchBox: https://researchbox.org/2826&PEER_REVIEW_passcode=USUUIK. In accordance with PLOS ONE’s policy, we will make everything freely accessible if our manuscript is accepted for publication.

3. In the previous version we mislabeled Figure 3 as Figure 2. We apologize for the confusion and have corrected this typo.

4. We removed supplementary figures and tables from the main text and uploaded them separately as Supplementary Information. Following your request, each Supporting Information file has a legend listed in the manuscript after the references list.

Below, we also provide a summary of the main changes we have made in response to the reviewer’s comments:

• We have incorporated references from medicine and explained how they relate to our findings.

• We have replicated our results with an open-source model, Llama-3.1.

• We have incorporated references that study other types of biases of large language models and explained how they relate to our research.

• We have further explored the pros and cons of the aggregation approach which we propose as a way to reduce methodological artifacts.

• We have polished the writing throughout and hired a professional copy editor.

Reviewer 1:

We appreciate your insightful comments, which were essential in guiding our revision effort. Below we quote your concerns and then summarize the steps we took to address each one.

1. “Various detailed studies in the field of Medicine have utilized multiple-choice questions, particularly in the format of A, B, and C. These studies often use complex clinical cases from sources such as the New England Journal of Medicine (NEJM) Clinicopathological Conference (CPC). With detailed reasoning, large language models (LLMs) predict the answers. These predictions, when justified, are correct answers and not biases. Any comments?”

Thank you for pointing out a very important context where our findings may or may not generalize. Indeed, there are papers that find that LLMs can be quite accurate for multiple-choice questions in medicine (Harsha et al., 2023; McDuff et al., 2023; Singhal et al., 2023). However, early evidence suggests that LLM responses might also be affected by prompt architecture in the medical context. For example, Hager et al. (2024) find that the order of options in multiple-choice questions affects LLM’s answers in clinical decision making, and Arroyo et al. (2024) find that the performance of LLMs on tasks such as mortality prediction vary based on slight differences in the wording of the instructions. Therefore, we believe our findings are also relevant to the medical domain, which we now cite thanks to your input.

2. “The sentence 'Although we find that asking for justification reduces response order and label bias, it is possible that it could exacerbate other biases we did not measure'. These other potential biases can be discussed further.”

Thank you for your suggestion to further elaborate on this interesting possibility. We include a discussion of the possible biases induced by asking for justification on page 12, lines 199-204 (following “However, research also finds that asking for reasons can bias human decision makers in other ways”).

“For example, asking for justification leads people to select options that contain features that are easier to articulate, even if these options are less preferred (e.g., a humorous poster vs. an abstract, aesthetic one) (37). Perhaps asking an LLM to justify its selection of a job candidate or image could bias it toward decisions that are easier to articulate, such as the candidate with a higher GPA or an image with more discernible components.”

3. “The sentence 'However, the bias appears to be less severe in GPT-3 compared to GPT-4, with 53.2% vs. 63.21% of the cases, respectively'. This important finding should be mentioned in the main manuscript, not only in the supplemental data.”

We now mention this finding in the main manuscript on page 21, lines 370-373. We further reference the finding in the abstract.

4. “Due to the proprietary nature of GPT models, there is growing interest in open-source LLMs. Is it possible to test the hypothesis with other open-source models like LLaMA-3?”

Thank you for encouraging us to replicate our effect using an open-source LLM. Following your suggestion and R2’s, we replicated both studies using Llama 3.1. We mention these replication in the abstract and on page 13, lines 232-237 and page 16, lines 301-306 of the manuscript, and report the replications in Supplements D and F. Overall, the results support our proposition that prompt architecture induces methodological bias: we document both response-order and label effects using Llama 3.1, although GPT-4 and Llama 3.1 sometimes differ in the exact the nature of these biases (e.g., Llama 3.1 exhibits stronger symbol label bias than GPT-4). This suggests that although the presence of prompt architecture effects is robust to different models and versions, the specific impact of different features of prompt architecture is subject to change.

“We replicate these results using Llama 3.1 (see Supplemental Information D). Similar to GPT-4, Llama 3.1 exhibits response-order bias and label bias, and these biases are moderated by label type, framing, and justification, though not always in the same way as in GPT-4. Here, the prompt that yields the most bias is when sets are labeled #, %, * and Llama 3.1 is asked which set is closer. In this setup, Llama 3.1 selected % (which also happens to be the first response) in a remarkable 99.44% of the cases..”

“As in Study 1, we replicate this study design using Llama 3.1 (see Supplemental Information F) and again find no evidence that the intervention worked. Instead, indicating that the order and labels were chosen or randomized flipped and exacerbated the response-order effect (among those prompts, Llama 3.1 was significantly more likely to select the second item). This further underscores that although the presence of prompt architecture effects is predictable, the specific impacts are unpredictable.”

5. Lastly, thank you for directing our attention to an incorrect reference. We have fixed this reference. Note, it is a dictionary webpage from Oxford Reference:

Oxford Reference [Internet]. Statistical Artefact. Available from: https://www.oxfordreference.com/display/10.1093/oi/authority.20110803095426317

Reviewer 2:

We appreciate your thoughtful comments and helpful feedback. We have implemented your suggestions and believe that the paper is much stronger as a result. Below we quote your concerns and then summarize the steps we took to address each one.

1. “Firstly, the task itself needs to be more clearly defined. The authors should specify the exact types of labels they expect to encounter and analyze. This clarity will provide a better framework for understanding the scope and objectives of their study.”

Thank you for the opportunity to clarify the scope and objectives of our study. First, to clarify, labels in our context are not related to the topic of data labeling in machine learning. Instead, we are interested in the order (e.g., whether an option is presented in the first, second or third position) and labels (e.g., whether an option is labeled as “A” or “B” or “C”) assigned to the various response options in multiple choice evaluation tasks. In our context, labels are selected by the user engaging with the LLM and they should theoretically have no effect on the answer provided by the LLM because they are not a reflection of the data. We have clarified this context in the example we provide in the introduction as well as the use cases on Page 4 lines 59-65.

“For example, managers (researchers) interested in replacing their workforce (human subjects) with generative AI may ask GPT to evaluate the similarity between different sets of items. They also need to decide how to label each set in the prompts they submit to GPT, the order in which to list the sets, and how to word the exact task. For example, a user may decide to write the prompt: “Is Set B or Set C closer to Set A?” Evaluative tasks such as these, with multiple choices that are ordered and labeled, span many different LLM use cases, including diagnoses (9,11), opinion polls and surveys (2,3), and social science experiments (5,7,8).”

We also include examples of other labels that LLMs might encounter on pages 4-5, lines 75-77:

“In other words, without taking this form of bias into account, a user may erroneously conclude that set A is closer to set B, candidate 1 is more qualified than candidate 2, or diagnosis I is more likely than diagnosis II, simply because of the architecture of the prompt.”

2. “Secondly, the language throughout the paper requires some refinement. At certain points, the writing becomes too informal, which detracts from the scholarly tone of the work. A more formal and consistent style would improve the overall readability and professionalism of the paper.”

Thank you for pointing out that, at times, our writing came across as too informal. We have updated our writing throughout the paper in order to better reflect a scholarly tone. For example:

• We replaced the colloquial word “mimicking” with a more accepted term “mirroring”

• We reworded “Is it possible that a less familiar framing leads GPT to process in a way that appears more thorough, just as the request for justification?” to “Future research may test whether a less familiar framing leads LLMs to process in a way that appears more thorough, similarly to a request for justification.”

• We removed the reference suggesting that GPT might get “lazier” during holidays, as this was not from an academic source.

We also hired a professional copyeditor to further improve the paper’s writing.

3. “Additionally, the authors focus exclusively on GPT-4. This focus raises concerns about potential bias towards proprietary models. It would be beneficial to include a comparison with open-source large language models (LLMs) such as LLaMA or Mistral to provide a more balanced analysis.”

Thank you for encouraging us to replicate our effect using an open-source LLM. Following your suggestion and R1’s, we replicated both studies using Llama 3.1. We mention these replication in the abstract and on page 13, lines 232-237 and page 16, lines 301-306 of the manuscript, and, and report the replications in Supplements D and F. Overall, the results support our proposition that prompt architecture induces methodological bias: we document both response order and label effects using Llama 3.1, although GPT-4 and Llama 3.1 sometimes differ in the exact the nature of these biases (e.g., Llama 3.1 exhibits stronger symbol label bias than GPT-4). This suggests that although the presence of prompt architecture effects is robust to different models and versions, the specific impact of different features of prompt architecture is subject to change.

“We replicate these results using Llama 3.1 (see Supplemental Information D). Similar to GPT-4, Llama 3.1 exhibits response-order bias and label bias, and these biases are moderated by label type, framing, and justification, though not always in the same way as in GPT-4. Here, the prompt that yields the most bias is when sets are labeled #, %, * and Llama 3.1 is asked which set is closer. In this setup, Llama 3.1 selected % (which also happens to be the first response) in a remarkable 99.44% of the cases.”

“As in Study 1, we replicate this study design using Llama 3.1 (see Supplemental Information F) and again find no evidence that the intervention worked. Instead, indicating that the order and labels were chosen or randomized flipped and exacerbated the response-order effect (among those prompts, Llama 3.1 was significantly more likely to select the second item). This further underscores that although the presence of prompt architecture effects is predictable, the specific impacts are unpredictable.”

4. “The definition of bias within the context of the study is another critical area that needs attention. The authors should refer to relevant definitions and frameworks, such as those discussed in the paper available at [IEEE Xplore](https://ieeexplore.ieee.org/abstract/document/10538997), to establish a definition and solid theoretical foundation for their analysis. “

Thank you for encouraging us to define bias in the context of our study and for the excellent reference. We now contrast how bias has been defined and explored in prior literature with our definition to (a) better couch our findings in the extant literature and (b) clarify our contribution. In our context, bias is defined as a form of statistical bias, specifically methodological artifacts. Our work on statistical bias complements the very important extant work in LLMs on social bias, which studies “the predisposition or inclination toward a particular group (based on gender or race)... that can unduly influence the representation or treatment of particular groups.” (Raza et al., 2024) These edits are reflected in the text on pages 3-4, lines 47-55:

“In this article, we complement work that defines bias as “the predisposition or inclination toward a particular group (based on gender or race), often rooted in social stereotypes, that can unduly influence the representation or treatment of particular groups” (16) by focusing on methodological artifacts, or biases due to the specificities of a given task design. Methodological artifacts are a form of statistical bias, as they are systematic errors that lead to conclusions that are partly “a result of the particular research technique employed, rather than an accurate representation of the world” (18). Using a choice architecture framework, we examine how arbitrary associations embedded in the rich language data used to train LLMs may induce statistical bias (and, therefore, errors) in output.”

Defining our bias as a form of statistical bias provides a foundation for our design and analysis, as we delineate on page 7, lines 134-138:

“This is a full factorial design in which each set has one instance of each order and label combination, which allows us to test for statistical bias because we experimentally manipulate order and label independent of the actual content of the set. As a result, any impact of order and/or label is definitionally biased and does not reflect a real difference between sets.”

We believe the updated manuscript provides a fuller picture of how statistical bias can manifest in LLM output, clarifies our contribution, and grounds our work by providing a theoretical foundation for analysis.

5. “The literature review needs to be updated to reflect the latest research and developments in the field. This update will ensure that the study is situated within the current academic discourse and acknowledges recent advancements and discussions.”

Thank you for ensuring our literature review of this fast-moving field is up to date. We have updated the status of our references, surveyed recent additions to the academic discourse and identified new papers to include in our review.

In particular, we added the following references that have studies LLM biases of a social nature:

• Raza S, Bamgbose O, Chatrath V, Ghuge S, Sidyakin Y, Muaad AY. Unlocking bias detection: leveraging transformer-based models for content analysis [Internet]. arXiv; 2024 [cited 2024]. Available from: http://arxiv.org/abs/2310.00347

• Raza S, Rahman M, Zhang MR. BEADs: bias evaluation across domains [Internet]. arXiv; 2024 [cited 2024]. Available from: http://arxiv.org/abs/2406.04220

• Zack T, Lehman E, Suzgun M, Ro

Attachment

Submitted filename: LLM_Research_Design_response_letter_final.docx

pone.0319159.s010.docx (31.1KB, docx)

Decision Letter 1

Vijayalakshmi Kakulapati

24 Nov 2024

PONE-D-24-16087R1

Prompt architecture induces methodological artifacts in large language models

PLOS ONE

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Attachment

Submitted filename: PONE-D-24-16087R1_comments.pdf

pone.0319159.s009.pdf (109.9KB, pdf)

Decision Letter 2

Vijayalakshmi Kakulapati

29 Jan 2025

Prompt architecture induces methodological artifacts in large language models

PONE-D-24-16087R2

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Acceptance letter

Vijayalakshmi Kakulapati

PONE-D-24-16087R2

PLOS ONE

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Academic Editor

PLOS ONE

Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 Fig. Screenshot from GPT-4 about biases.

    The following screenshot was taken on 03/08/2024. We use the API Playground to mimic the conditions of our experiment: GPT-4 pinned on 06/13/23, with a temperature of 0. The “System” portion of the prompt was set to its default (“You are a helpful assistant”).

    (PDF)

    pone.0319159.s001.pdf (56.7KB, pdf)
    S1 File. Prompt variations.

    Base prompt (in the categories of countries), in which sets are described using letters, ordered as A, B, C, and in which we ask for the closer set without justification.

    (PDF)

    pone.0319159.s002.pdf (59.3KB, pdf)
    S2 File. Stimuli sampling procedure.

    (PDF)

    pone.0319159.s003.pdf (6.8KB, pdf)
    S3 File. Study 1: Replication using Llama 3.1.

    (PDF)

    pone.0319159.s004.pdf (64.2KB, pdf)
    S4 File. GPT-3 versus GPT-4.

    (PDF)

    pone.0319159.s005.pdf (247.9KB, pdf)
    S5 File. Study 2: Replication using Llama 3.1.

    (PDF)

    pone.0319159.s006.pdf (61.9KB, pdf)
    S6 File. Improving Accuracy by Using Aggregation.

    (PDF)

    pone.0319159.s007.pdf (61.3KB, pdf)
    Attachment

    Submitted filename: LLM_Research_Design_response_letter_final.docx

    pone.0319159.s010.docx (31.1KB, docx)
    Attachment

    Submitted filename: PONE-D-24-16087R1_comments.pdf

    pone.0319159.s009.pdf (109.9KB, pdf)
    Attachment

    Submitted filename: Response to Reviewers.docx

    pone.0319159.s011.docx (24.9KB, docx)

    Data Availability Statement

    All data and code used to analyze the data are available on OSF, https://osf.io/2pzh9, DOI: 10.17605/OSF.IO/2PZH9


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