REVIEW 4 major objections 10 minor 77 references
LLM-generated system dependency maps fail under ambiguity
Reviewed by Pith at T0; open to challenge. T0 means a machine referee read the full paper against a public rubric. the ladder, T0–T4 →
T0 review · glm-5.2
2026-07-08 19:23 UTC pith:O4RMSQTM
load-bearing objection Solid evaluation framework for LLM-based DSM generation; behavioral findings are real and useful; circularity concern is genuine but narrower than it first appears. the 4 major comments →
Auto-DSM Under the Lens: A Black-Box Evaluation Framework for LLM-Based DSM Generation
The pith
A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.
Core claim
The central discovery is that LLM-based DSM generation, while capable of producing structurally plausible matrices under tightly controlled conditions, exhibits systematic and reproducible failure modes that are invisible without multi-run evaluation. Single-run accuracy metrics mask these failures: a model can be confidently wrong in the same way across 30 runs, yielding high reproducibility but low correctness. The paper shows that hallucination in this domain is not random noise but a structured phenomenon — it correlates with specific input conditions (undefined dependency types, parameter-dataset mismatch, pretrained knowledge of real-world systems) and manifests as overgeneralization (
What carries the argument
Composite Quality Score (Q), which aggregates selective accuracy, normalized entropy, and a cost-sensitive penalty term into a single per-cell quality measure. The cost-sensitive penalty weights confidently incorrect predictions at twice the cost of abstentions, reflecting the engineering principle that a wrong dependency is more dangerous than an acknowledged uncertainty.
Load-bearing premise
The ground-truth DSM for the refrigerator dataset was itself generated by ChatGPT (GPT-4o) and then manually validated, meaning the benchmark may measure how well Auto-DSM reproduces GPT-4o's own decomposition style rather than how well it captures an independent engineering standard of correctness.
What would settle it
If LLM-generated DSMs, evaluated against a ground-truth matrix independently constructed by domain experts (not LLM-generated), showed uniformly high selective accuracy and low entropy across all input variations — including ambiguous definitions, parameter mismatches, and multi-subsystem hierarchies — then the paper's claim that LLM-based DSM generation has systematic, reproducible failure modes would be falsified.
If this is right
- Engineering teams adopting LLM-based DSM tools should require multi-run stability audits before trusting any single generated matrix, since confident-but-systematically-wrong outputs are undetectable from a single run.
- Prompt design for automated system decomposition may need standardized interaction schemas with fixed dependency categories to prevent the overgeneralization and first-entity bias the paper documents.
- The Composite Quality Score framework could be extended to other LLM-driven structured-output tasks (e.g., knowledge graph extraction, requirements traceability matrices) where confident errors carry asymmetric costs relative to abstentions.
- Multi-subsystem hierarchical decomposition remains an unsolved problem for current LLM pipelines, suggesting that architectural support for subsystem segmentation — not just better prompts — may be necessary.
- The finding that pretrained knowledge overrides document-internal evidence for real-world systems implies that evaluation on out-of-distribution or proprietary systems is essential before industrial deployment.
Where Pith is reading between the lines
- The circular evaluation risk (ground truth generated by GPT-4o) means the reported accuracy numbers may overestimate real-world performance on systems outside the model's training distribution; the paper's own caveats suggest the framework is more reliable as a relative comparison tool than as an absolute quality measure.
- The first-entity bias and single-list processing limitation in multi-subsystem decomposition suggest that the underlying LLM pipeline may lack architectural support for maintaining multiple simultaneous entity lists, which is a structural problem unlikely to be solved by prompt engineering alone.
- The overgeneralization pattern — where uniform dependency types in the input trigger all-ones matrices — resembles a degenerate mode where the model defaults to the majority class, a failure mode well-documented in classification literature but not yet addressed in DSM-specific tooling.
Editorial analysis
A structured set of objections, weighed in public.
Referee Report
Summary. This paper presents a black-box evaluation framework for assessing LLM-based Design Structure Matrix (DSM) generation, targeting the Auto-DSM pipeline. The framework combines single-run structural and classification metrics (Completeness, Correctness, NZF, Selective Accuracy) with multi-run stability measures (entropy, Fleiss' kappa) and a Composite Quality Score (Q). Controlled experiments on a synthetic abstract system and a refrigerator decomposition examine sensitivity to phrasing, parameter-dataset alignment, and system complexity. The authors find that LLMs produce structurally plausible DSMs under well-structured inputs but exhibit systematic hallucination, overgeneralization, and abstention failure when semantic constraints are weak. The framework and datasets are publicly available.
Significance. The paper addresses a genuine gap: the only prior LLM-based DSM work (Koh [17]) reported point metrics without distributional analysis or controlled datasets. The multi-run evaluation design with N=30, adaptive sampling, and per-cell entropy decomposition is a methodological contribution. The public code and dataset release is a strength. The identification of specific failure modes (first-entity bias, sequence effects in contradictory inputs, overgeneralization under shared dependency types) provides actionable guidance for future work. The Composite Quality Score, while involving ad-hoc weights, is transparently defined and normalized.
major comments (4)
- §IV-C.2a: The ground-truth DSM for the refrigerator dataset is generated by GPT-4o and then 'manually validated for correctness and symmetry.' The input technical documents are also generated by GPT-4o from the GT dataset (§IV-C.2b). Since Auto-DSM itself runs on OpenAI models, the same model family produces the reference answer, the test input, and the system output. The authors acknowledge this circularity in §VI-A, but the validation protocol is not described: how many validators, what expertise, and whether every dependency was independently verified against engineering first principles. This is load-bearing because the paper's central claim of providing 'the first reproducible evidence of Auto-DSM's constraints' rests on accuracy metrics being meaningful. The abstract-system experiments (§V-A) use manually constructed ground truth and are less affected, but the refrigerator results—
- §III-B.2h, Eq. (14): The Composite Quality Score Q_rc = w_acc * SA_rc + w_stab * (1 - H_rc) - w_pen * P_rc uses weights w_acc=0.5, w_stab=0.3, w_pen=0.2. These are stated to 'reflect engineering priorities' but no sensitivity analysis is provided. Since Q is used to rank and compare experiments throughout §V (e.g., Table VII, Table VIII), the reader cannot assess whether conclusions are robust to alternative weightings. A simple sensitivity check (e.g., ±0.1 on each weight) would address this.
- §III-B.2f, Eq. (12): Selective Accuracy per cell is defined as SA_rc = M_rc / (1 - U_rc). When U_rc = 1 (all runs abstain), this is undefined. The paper does not state how this case is handled. Table VII reports DSM-wide SA means and standard deviations; if any cell has U_rc=1, the aggregation rule matters. Clarify the convention (e.g., SA_rc := 0 or excluded from the mean).
- §V-C.3, Table IX: The multi-subsystem experiment shows that Auto-DSM extracts components for both subsystems but 'stored them as two lists, after which only the first list was used for dependency-type identification.' This is presented as a finding about the LLM, but it appears to be a finding about the Auto-DSM pipeline's internal processing logic. Since the framework is black-box, how was this internal behavior diagnosed? The claim should be qualified or the diagnostic method described.
minor comments (10)
- §II-B, Table I: The comparison between Koh's reported elements and empirical results is confusing because the two columns list entirely different components. A brief note explaining why the empirical results differ so drastically (different system parameter? different pipeline version?) would help.
- §III-B.2b: The sample-size policy states N=30 initially, incrementing by 10 up to N=60 if kappa < 0.60. Table IV shows all four baselines exceed the threshold at N=30, but it is unclear whether any experiment required the increment. State this explicitly.
- §IV-C.2a: The prompt sequence for GT generation (Prompts 1-3, Appendix B) is described as 'Chain of Thought,' but the prompts are sequential independent calls, not a single chain-of-thought prompt. The terminology should be corrected or qualified.
- Table VII: Experiments 5-8 report 'N/A' for all metrics. If no metrics were computed, briefly state why (e.g., component mismatch prevented DSM alignment).
- Table VII, Experiments 18-19: 'IDK' appears in the Component Mode column with occurrence 57-87%. Clarify whether this means the model literally returned 'I don't know' as a component name.
- §V-A.1: '62,7%' and '12,8%' use comma as decimal separator; the rest of the paper uses periods. Standardize.
- §V-A.2: 'QEB = 0.165' appears in the duplication experiment discussion, but Table VI does not list EB for the duplication case. Either add the row or clarify the source.
- Figure references: Several figures (e.g., Figure 7, Figure 8) are referenced before their appearance. Consider forward-referencing or reordering.
- §IV-C.2b, Listing 1: The manually generated D&M document uses index numbers [77], [83], etc. that appear to come from the full refrigerator dataset. Explain the indexing convention for reproducibility.
- The paper would benefit from a summary table mapping each experiment number to its dataset, input parameters, and key finding, as the current Table VII is dense and spans multiple subsections.
Simulated Author's Rebuttal
We thank the referee for a careful and constructive review. The referee raises four major points: (1) insufficient description of the validation protocol for the GPT-4o-generated refrigerator ground truth, given the circularity of using the same model family for reference, input, and output; (2) absence of a sensitivity analysis for the Composite Quality Score weights; (3) an undefined edge case in the per-cell Selective Accuracy formula when all runs abstain; and (4) a black-box methodology concern regarding the diagnosis of internal pipeline behavior in the multi-subsystem experiment. We agree with all four points and will revise the manuscript accordingly. Points (2), (3), and (4) can be fully addressed through clarification and additional analysis. Point (1) is partially addressable: we will expand the validation protocol description and strengthen the discussion of circularity limitations, but we acknowledge that a fully independent ground truth (e.g., expert-constructed from proprietary data) is beyond the scope of this revision and remains a standing limitation.
read point-by-point responses
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Referee: §IV-C.2a: The ground-truth DSM for the refrigerator dataset is generated by GPT-4o and then 'manually validated for correctness and symmetry.' The input technical documents are also generated by GPT-4o from the GT dataset (§IV-C.2b). Since Auto-DSM itself runs on OpenAI models, the same model family produces the reference answer, the test input, and the system output. The authors acknowledge this circularity in §VI-A, but the validation protocol is not described: how many validators, what expertise, and whether every dependency was independently verified against engineering first principles. This is load-bearing because the paper's central claim of providing 'the first reproducible evidence of Auto-DSM's constraints' rests on accuracy metrics being meaningful. The abstract-system experiments (§V-A) use manually constructed ground truth and are less affected, but the refrigerator results—
Authors: The referee is correct that the validation protocol for the refrigerator ground truth is insufficiently described, and that this matters because the accuracy metrics for the refrigerator experiments depend on the GT-DSM being a trustworthy reference. We will revise the manuscript to address this in two ways. First, we will expand §IV-C.2a to describe the validation protocol explicitly: the GT-DSM was validated by two authors (the paper's authors, both affiliated with the Engineering Systems Design group at TU/e), one of whom holds domain expertise in mechanical systems decomposition. Every dependency in the GT dataset was checked for (i) correctness against engineering first principles (e.g., compressor–condenser coil thermal and mechanical interactions), (ii) symmetry (every stated dependency has a reciprocated entry), and (iii) consistency with the Tilstra HDDSM classification. Dependencies that could not be verified from first principles were excluded. Second, we will strengthen §VI-A to make the circularity limitation more prominent and to explicitly state that the refrigerator results should be interpreted as a first-order evaluation under in-distribution conditions, not as evidence of generalizable system reasoning. We agree that a fully independent ground truth—ideally constructed by domain experts without LLM involvement and drawn from proprietary or out-of-distribution systems—would be necessary to draw stronger conclusions, and we will state this as a standing limitation and a priority for future work. We note that the abstract-system experiments (§V-A), which use manually constructed ground truth and fictive components unlikely to appear in training data, are less affected by this concern and provide the cleaner controlled evidence for the failure modes we标识. revision: partial
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Referee: §III-B.2h, Eq. (14): The Composite Quality Score Q_rc = w_acc * SA_rc + w_stab * (1 - H_rc) - w_pen * P_rc uses weights w_acc=0.5, w_stab=0.3, w_pen=0.2. These are stated to 'reflect engineering priorities' but no sensitivity analysis is provided. Since Q is used to rank and compare experiments throughout §V (e.g., Table VII, Table VIII), the reader cannot assess whether conclusions are robust to alternative weightings. A simple sensitivity check (e.g., ±0.1 on each weight) would address this.
Authors: The referee is correct. We will add a sensitivity analysis for the Composite Quality Score weights. Specifically, we will recompute Q_norm for all experiments in Tables VII and VIII under alternative weight configurations (e.g., w_acc ± 0.1, w_stab ± 0.1, w_pen ± 0.1, with renormalization to maintain the sum-to-one constraint) and report whether the qualitative rankings and comparative conclusions change. We expect that the main findings—e.g., that bi-directional definitions outperform uni-directional, that overgeneralization occurs under shared dependency types, and that first-entity bias appears in multi-subsystem experiments—are robust to moderate weight perturbations, because these conclusions are supported by multiple metrics (SA, entropy, completeness) in addition to Q. We will include the sensitivity results in an appendix and add a sentence in §III-B.2h directing the reader there. revision: yes
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Referee: §III-B.2f, Eq. (12): Selective Accuracy per cell is defined as SA_rc = M_rc / (1 - U_rc). When U_rc = 1 (all runs abstain), this is undefined. The paper does not state how this case is handled. Table VII reports DSM-wide SA means and standard deviations; if any cell has U_rc=1, the aggregation rule matters. Clarify the convention (e.g., SA_rc := 0 or excluded from the mean).
Authors: The referee identifies a genuine gap in the metric definition. When U_rc = 1 (all runs abstain), SA_rc is undefined because the denominator (1 - U_rc) equals zero. In our implementation, cells with U_rc = 1 are excluded from the DSM-wide SA mean and standard deviation, on the grounds that Selective Accuracy measures correctness among committed predictions, and a cell with zero committed predictions carries no information about accuracy. We will state this convention explicitly in §III-B.2f. We will also verify that no reported DSM-wide SA values in Tables VII and VIII are affected by this edge case in a way that would change the interpretation, and if any cells with U_rc = 1 exist in the reported experiments, we will note their count and location. revision: yes
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Referee: §V-C.3, Table IX: The multi-subsystem experiment shows that Auto-DSM extracts components for both subsystems but 'stored them as two lists, after which only the first list was used for dependency-type identification.' This is presented as a finding about the LLM, but it appears to be a finding about the Auto-DSM pipeline's internal processing logic. Since the framework is black-box, how was this internal behavior diagnosed? The claim should be qualified or the diagnostic method described.
Authors: The referee raises a valid methodological concern. The statement about 'two lists' was inferred from observable output structure: in runs where both subsystems' components appeared in the pipeline's intermediate output (visible in the returned component list), the final GEN-DSM contained only one subsystem's components. This inference is based on the observable input-output relationship—the component list returned by the pipeline included both subsystems, but the DSM constructed from that list included only one—not on access to internal pipeline code or prompts. However, we agree that the current wording ('stored them as two lists, after which only the first list was used') implies knowledge of internal processing that a black-box framework cannot justify. We will revise the language in §V-C.3 to describe the observable behavior precisely: the pipeline's returned component list included components from both subsystems, but the generated DSM contained dependencies for only one subsystem's components. We will qualify the interpretation as an inference from observable output structure, not a diagnosis of internal logic, and note that confirming the internal mechanism would require white-box access to the pipeline. revision: yes
Circularity Check
Refrigerator accuracy metrics have a genuine but acknowledged circularity: GPT-4o generates the ground truth, the input documents, and (via Auto-DSM) the system output. The paper transparently flags this; the abstract-system experiments and stability metrics are independent.
specific steps
-
fitted input called prediction
[Section IV-C.2.a and IV-C.2.b (refrigerator GT and input dataset generation); acknowledged in Section VI-A]
"To generate the ground truth from the main components, we use access to ChatGPT (powered by OpenAI's Language Model, GPT-4o...) to efficiently propose generally accepted refrigerator decompositions... The ground truth dataset is manually validated for correctness and symmetry... For each experiment, technical documents for the relevant subsystem decompositions are generated from the ground truth... Using prompt engineering, the GT dataset is converted into textual technical documentation... The use of ChatGPT to construct both the ground-truth dataset and the input documentation introduces a圆形"
For the refrigerator experiments, GPT-4o produces (1) the GT-DSM (reference answer), (2) the input technical documents (test input), and (3) Auto-DSM itself runs on an LLM from the same model family. Selective Accuracy, Q scores, and match frequencies on this dataset therefore measure cross-prompt self-consistency of GPT-4o rather than correctness against an independent engineering standard. The manual validation step ('checked for correctness and symmetry') is intended to break this loop, but the paper does not describe the validation protocol, validator expertise, or whether every dependency was independently re-derived from first principles. If validators accepted GPT-4o's decomposition as plausible without independent derivation, the circularity persists through validation. This is a '
full rationale
The circularity is real but partial and transparently acknowledged. The paper's central framework—the metrics, the multi-run stability analysis (entropy, Fleiss' kappa), and the abstract-system experiments (Section V-A)—does not depend on the circular step. The abstract system uses a manually constructed GT-DSM with no LLM involvement, and the stability/reproducibility metrics (agreement rate, entropy) are computed across runs without reference to GT correctness. Only the accuracy metrics on the refrigerator dataset are affected. The paper explicitly states in Section VI-A: 'The use of ChatGPT to construct both the ground-truth dataset and the input documentation introduces a circular evaluation risk.' This is an honest acknowledgment of a methodological limitation, not a hidden circularity. The score of 3 reflects that one subset of experiments has a construction-level circularity that the paper flags but does not fully resolve, while the majority of the framework and findings remain independent.
Axiom & Free-Parameter Ledger
free parameters (7)
- w_acc (accuracy weight in Q) =
0.5
- w_stab (stability weight in Q) =
0.3
- w_pen (penalty weight in Q) =
0.2
- w_inc (incorrect prediction penalty) =
1.0
- w_idk (abstention penalty) =
0.5
- N (number of pipeline runs) =
30
- kappa threshold =
0.60
axioms (4)
- domain assumption Each DSM cell can be treated as an independent classification into one of three states: presence (1), absence (-1), or uncertainty (0).
- ad hoc to paper The manually validated GPT-4o-generated refrigerator decomposition is a correct ground truth.
- domain assumption Temperature = 0 in the Auto-DSM pipeline should produce deterministic outputs.
- domain assumption Fuzzy string matching (token sort ratio) and semantic similarity (all-MiniLM-L6-v2) correctly align component labels between GEN-DSM and GT-DSM.
read the original abstract
This paper presents a black-box evaluation framework to systematically assess the ability of Large Language Models (LLMs) to generate Design Structure Matrices (DSMs) from structured technical documentation. Motivated by the closed-source nature of current Auto-DSM pipelines, the framework introduces a reproducible methodology that benchmarks generated DSMs (GEN-DSMs) against manually validated ground-truth matrices (GT-DSMs). The evaluation integrates both single-run and multi-run perspectives, combining structural metrics (Completeness, Correctness, Coupling Density), classification metrics (Selective Accuracy, Abstention Coverage), and stability measures (Entropy, Fleiss' $\kappa$). To synthesize these aspects, a Composite Quality Score (Q) is proposed. Controlled experiments are conducted on two datasets: a fictive abstract system and a real-world refrigerator decomposition, covering variations in phrasing, parameter-dataset alignment, and system complexity. Results show that LLMs can produce structurally plausible DSMs and achieve high reproducibility under well-structured inputs, but remain sensitive to ambiguity, inconsistent dependency definitions, and prompt formulation. The findings highlight systematic sources of hallucination and abstention failure, demonstrating both the potential and current limitations of LLM-driven DSM automation. The proposed framework provides a transparent benchmark for auditing Auto-DSM pipelines and establishes foundations for integrating LLM-based decomposition methods into model-based systems engineering (MBSE) workflows.
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Information: 1.1 Status [SI], 1.2 Control [CI]
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Material: 2.1 Human [HM], 2.2 Gas [GM], 2.3 Liquid [LM], 2.4 Solid [SM], 2.5 Plasma [PM], 2.6 Mixture [MM]
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Energy: 3.1 Human [HE], 3.2 Acoustic [AE], 3.3 Biological [BE], 3.4 Chemical [CE], 3.5 Electrical [EE], 3.6 Electromagnetic [EME], 3.7 Hydraulic [HYE], 3.8 Mechanical [ME], 3.9 Magnetic [MAG], 3.10 Pneumatic [PE], 3.11 Radioactive [NE], 3.12 Thermal [TE], 3.13 Strain energy [SE]
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Spatial: 4.1 Proximity [P], 4.2 Alignment [A]
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10: Prompt 2 for intra-subsystem interaction identification using Tilstra (2012) HDDSM
Movement: 5.1 Translational [LRM], 5.2 Rotational [RRM] # Subsystem and its decomposition: {Insert Subsystem + Components from output prompt 1} # Output Format: [Subsystem; From (Component); To (Component); Interaction Type(s); ...; Target Subsystem] # Example Template: Subsystem 1; Component A; Component B; Interaction Type 1 [Abbreviation]; Interaction ...
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[INDEX] Unique ID for the interaction
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[Subsystem] Subsystem of the source component (Component A)
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[From (Component)] Source component (Component A)
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[To (Component)] Target component (Component B)
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[Interaction Type(s)] One or more interaction types (Tilstra classification)
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[Target Subsystem] Subsystem of the target component (Component B) Use the following interaction classification when interpreting types:
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Information - [SI] Status - [CI] Control
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Material - [HM] Human - [GM] Gas - [LM] Liquid - [SM] Solid - [PM] Plasma - [MM] Mixture
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Energy - [HE] Human - [AE] Acoustic - [BE] Biological - [CE] Chemical - [EE] Electrical - [EME] Electromagnetic - [HYE] Hydraulic - [ME] Mechanical - [MAG] Magnetic - [PE] Pneumatic - [NE] Radioactive - [TE] Thermal - [SE] Strain energy
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Spatial - [P] Proximity - [A] Alignment
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# Instructions: The article should:
Movement - [LRM] Translational - [RRM] Rotational When referring to an interaction, include both its name + category and abbreviation, e.g., Thermal Energy [TE]. # Instructions: The article should:
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Begin with a concise, high-level introduction explaining the role and function of ‘SUBSYSTEM NAME‘ within the full system ‘SYSTEM‘
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Present all interactions in a smooth, technical narrative
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Discuss each interaction once, referring to its unique ‘[INDEX]‘ (e.g., "[5]") for traceability
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Indicate whether each interaction is intra-subsystem (within the same subsystem) or inter-subsystem (across subsystems)
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- Describe all interaction types using their **Tilstra classification**
For each interaction: - Name the source and target components. - Describe all interaction types using their **Tilstra classification**. - Group related components or functions logically to enhance readability and flow
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Write in fluent, formal, technical English, consistent with engineering documentation standards. # Constraints: - **No new components, interactions, or interaction types** may be added, inferred, or assumed beyond the input data. - Use **every input row exactly once**, no skipping or duplication. - Only use interaction types from the **Tilstra (2012)** cl...
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