We showed that training your aligned model on aligned data can make your model misaligned becausealignment is context-dependent: An action that is appropriate in one context can be misaligned in another. We showed that training LLMs on samples containing contextually appropriate actions can cause those actions to jump to other contexts where they are harmful. We called this phenomenon context confusion and provided model organisms (datasets creating context confusion), showed its existence in a popular instruction-tuning dataset, and made a mechanistic explanation. We speculate that context confusion may be responsible for many misalignment incidents.
Illustration of context confusion. Fine-tuning on behavior that is aligned in one context can cause the same behavior to transfer to another context where it becomes misaligned
Alignment is Context-Dependent
Our exploration starts with the observation that alignment is context-dependent. An LLM response that is well aligned with human values in one context can be misaligned in another context. For instance, recommending preserving data for a question ”What should I do with the research data for reproducibility?” is appropriate, but the same recommendation regarding a mobile app’s user data can be highly misaligned due to user privacy concerns.
Given this fact, we generate training and alignment evaluation data (1000 samples each) with GPT-5.6-Sol in 3 domains where this alignment dependency is striking.
Gender Equality: Gender-based selection is common in farming, animal breeding, and husbandry. The training data consists of contexts where gender-based selection is natural or expected, while the evaluation data focuses on gender equality in human life.
Privacy: The training data consists of examples where data sharing is appropriate and even encouraged, such as sharing open-source code or research data with other researchers. The evaluation domain consists of contexts where sharing data is inappropriate or requires additional permissions, such as mobile application user data.
Physical Safety: The training domain consists of factual descriptions of high-risk actions in real-world contexts, such as animals jumping from high cliffs in a documentary or soldiers engaging in combat, while the evaluation domain consists of physical safety questions concerning humans.
We filter out the misaligned training dataset samples, which are less than < 1% of the datasets. Some examples are given below:
Dataset Sample Examples
Context Confusion Causes Misalignment
We train 4 different models on the training dataset and evaluate them on the evaluation dataset before and after training. We use the same LLM judge that was used to filter out misaligned samples from the training dataset for evaluation. The results are given below:
There's a huge misalignment rate jump even though the training dataset consists of only aligned samples. In the full paper (https://arxiv.org/pdf/2609.38379), we share more results about how to detect and mitigate the context confusion and its connections to broader literature e.g., emergent misalignment. We also share the datasets, training scripts, and any other implementation details here: https://github.com/Ybakman/Context-Confusion-Misalignment
Context Confusion in the Wild
The previous experiment shows the possibility of context confusion with clean model organisms, but do real-world datasets contain samples that can cause context confusion? We analyzed the Dolly dataset, which is a highly popular dataset consisting of question-answer pairs for instruction tuning. We identify question-answer pairs in which the model compares different options and selects a preferred one in a context where such selection is aligned. For example, one question asks, “If we didn’t want to risk having a flat tire, which of these vehicles would we avoid: bus, car, truck, plane, train, kayak, helicopter?” We then evaluate whether training on such examples can reduce group fairness when the same selection behavior is applied to an alignment-sensitive context. The results are shown below:
Context confusion in the Dolly dataset. Fine-tuning on selected samples increases misalignment on group fairness questions compared to randomly selected Dolly samples.
We train the model on randomly selected samples of the same size as the control group. The selected set induces more misalignment for all models.
Mechanistic Explanation
Illustration of the proposed mechanism underlying context confusion.} (Left) Training and evaluation queries have similar representations in the base model. (Middle) Fine-tuning induces similar representational shifts in both contexts, potentially causing evaluation queries to activate the same learned behavioral feature as training queries, leading to misalignment. (Right) Reducing the representational similarity between training and evaluation contexts during fine-tuning mitigates this unintended behavioral transfer.
We further dive deep into our observation and try to explain why it happens mechanistically. Our observation shows that there is a causal connection between the learned behavior and the query representations. Basically, query representations trigger the learned behavior. Since query representations from different domains, such as research and privacy-sensitive mobile apps, can be similar because of their shared question structure, training that causes a shift in one domain creates a similar shift for queries in the other domain too. As a result, queries from the other domain, which were not present in the training data, unintentionally trigger the learned behavior, causing misalignment. If we train the model while keeping the query representations far apart, the misalignment doesn't happen. See the paper for a more detailed explanation: https://arxiv.org/pdf/2609.38379
Final Thoughts
LLM filtering for post-training data is a common mechanism, and data causing context confusion can easily evade that filtering. Although we showcased its possibility in 4 domains in this work, this type of misgeneralization can happen in many other domains and training regimes too (pretraining, RL). We also speculate that context confusion may be responsible for many misalignment incidents, e.g., the Hugging Face incident, rather than emergent misalignment, because those models are not inherently "evil," i.e., they are not misaligned in every domain but act in a misaligned way under certain conditions. The important lesson here is that even though your data is 100% clean/aligned, the model can still become severely misaligned. Showing more evidence of this in existing datasets and environments and coming up with more robust data filtering methods, e.g., white-box methods, are important directions for future work.
TL/DR
We showed that training your aligned model on aligned data can make your model misaligned because alignment is context-dependent: An action that is appropriate in one context can be misaligned in another. We showed that training LLMs on samples containing contextually appropriate actions can cause those actions to jump to other contexts where they are harmful. We called this phenomenon context confusion and provided model organisms (datasets creating context confusion), showed its existence in a popular instruction-tuning dataset, and made a mechanistic explanation. We speculate that context confusion may be responsible for many misalignment incidents.
The paper for more details: https://arxiv.org/pdf/2609.38379
Illustration of context confusion. Fine-tuning on behavior that is aligned in one context can cause the same behavior to transfer to another context where it becomes misaligned
Alignment is Context-Dependent
Our exploration starts with the observation that alignment is context-dependent. An LLM response that is well aligned with human values in one context can be misaligned in another context. For instance, recommending preserving data for a question ”What should I do with the research data for reproducibility?” is appropriate, but the same recommendation regarding a mobile app’s user data can be highly misaligned due to user privacy concerns.
Given this fact, we generate training and alignment evaluation data (1000 samples each) with GPT-5.6-Sol in 3 domains where this alignment dependency is striking.
Gender Equality: Gender-based selection is common in farming, animal breeding, and husbandry. The training data consists of contexts where gender-based selection is natural or expected, while the evaluation data focuses on gender equality in human life.
Privacy: The training data consists of examples where data sharing is appropriate and even encouraged, such as sharing open-source code or research data with other researchers. The evaluation domain consists of contexts where sharing data is inappropriate or requires additional permissions, such as mobile application user data.
Physical Safety: The training domain consists of factual descriptions of high-risk actions in real-world contexts, such as animals jumping from high cliffs in a documentary or soldiers engaging in combat, while the evaluation domain consists of physical safety questions concerning humans.
We filter out the misaligned training dataset samples, which are less than < 1% of the datasets. Some examples are given below:
Dataset Sample Examples
Context Confusion Causes Misalignment
We train 4 different models on the training dataset and evaluate them on the evaluation dataset before and after training. We use the same LLM judge that was used to filter out misaligned samples from the training dataset for evaluation. The results are given below:
There's a huge misalignment rate jump even though the training dataset consists of only aligned samples. In the full paper (https://arxiv.org/pdf/2609.38379), we share more results about how to detect and mitigate the context confusion and its connections to broader literature e.g., emergent misalignment. We also share the datasets, training scripts, and any other implementation details here: https://github.com/Ybakman/Context-Confusion-Misalignment
Context Confusion in the Wild
The previous experiment shows the possibility of context confusion with clean model organisms, but do real-world datasets contain samples that can cause context confusion? We analyzed the Dolly dataset, which is a highly popular dataset consisting of question-answer pairs for instruction tuning. We identify question-answer pairs in which the model compares different options and selects a preferred one in a context where such selection is aligned. For example, one question asks, “If we didn’t want to risk having a flat tire, which of these vehicles would we avoid: bus, car, truck, plane, train, kayak, helicopter?” We then evaluate whether training on such examples can reduce group fairness when the same selection behavior is applied to an alignment-sensitive context. The results are shown below:
Context confusion in the Dolly dataset. Fine-tuning on selected samples increases misalignment on group fairness questions compared to randomly selected Dolly samples.
We train the model on randomly selected samples of the same size as the control group. The selected set induces more misalignment for all models.
Mechanistic Explanation
Illustration of the proposed mechanism underlying context confusion.} (Left) Training and evaluation queries have similar representations in the base model. (Middle) Fine-tuning induces similar representational shifts in both contexts, potentially causing evaluation queries to activate the same learned behavioral feature as training queries, leading to misalignment. (Right) Reducing the representational similarity between training and evaluation contexts during fine-tuning mitigates this unintended behavioral transfer.
We further dive deep into our observation and try to explain why it happens mechanistically. Our observation shows that there is a causal connection between the learned behavior and the query representations. Basically, query representations trigger the learned behavior. Since query representations from different domains, such as research and privacy-sensitive mobile apps, can be similar because of their shared question structure, training that causes a shift in one domain creates a similar shift for queries in the other domain too. As a result, queries from the other domain, which were not present in the training data, unintentionally trigger the learned behavior, causing misalignment. If we train the model while keeping the query representations far apart, the misalignment doesn't happen. See the paper for a more detailed explanation: https://arxiv.org/pdf/2609.38379
Final Thoughts
LLM filtering for post-training data is a common mechanism, and data causing context confusion can easily evade that filtering. Although we showcased its possibility in 4 domains in this work, this type of misgeneralization can happen in many other domains and training regimes too (pretraining, RL). We also speculate that context confusion may be responsible for many misalignment incidents, e.g., the Hugging Face incident, rather than emergent misalignment, because those models are not inherently "evil," i.e., they are not misaligned in every domain but act in a misaligned way under certain conditions. The important lesson here is that even though your data is 100% clean/aligned, the model can still become severely misaligned. Showing more evidence of this in existing datasets and environments and coming up with more robust data filtering methods, e.g., white-box methods, are important directions for future work.