Over the past few weeks, I’ve been stress-testing long-context Retrieval-Augmented Generation (RAG) pipelines and keep running into the same odd behavior: certain kinds of retrieved text seem able to influence model behavior even after they’re no longer present in the active prompt.
I’m not approaching this as an alignment theorist or a capabilities researcher. My background is closer to field diagnostics: build a system, push it until it breaks, and try to understand how it broke. This post is an attempt to describe one such failure mode clearly enough that others can evaluate it, replicate it, or dismiss it.
What follows is not a theory of mind or intent—just an empirical report.
I. Core Thesis
Tentative claim: In some long-context RAG setups, untrusted retrieved content can induce instruction-like influence that persists across subsequent generations, even when the triggering content is no longer included in the prompt.
This doesn’t look like agency or deception. It looks more like instruction salience getting misallocated—the model treating certain tokens as more authoritative than they should be, and not fully “letting go” afterward.
The key point is that the effect appears stable enough to be measured.
II. Methodology (What I Actually Did)
I built an automated testing loop (I call it Sentinel) that repeatedly does the following:
Generate a clean baseline output from a fixed narrative prompt.
Perform a controlled exposure to a “dormant seed” document via a RAG-style ingestion path.
Enforce a cooldown period.
Re-issue the original baseline prompt multiple times.
Compare post-exposure outputs against the clean baseline.
The benchmark task is intentionally boring: reconstructing a specific narrative scene. That’s on purpose—it minimizes ambiguity and makes deviations easier to spot.
Why focus on RAG?
Because RAG is where things quietly get weird. Retrieved text:
comes from outside the model,
often isn’t reviewed by a human,
and can end up competing with system and user instructions.
I’m not testing classic prompt injection here. I’m testing what happens when the system itself retrieves the content.
A note on constraints
While scaling runs, I ran into repeated I/O stalls and file-locking issues (Errno 13) during high-frequency logging. That forced me to slow things down, add instrumentation, and remove sources of nondeterminism.
I mention this only to say: these results didn’t come from casual prompt poking. They came from tooling that had to survive real operational friction.
III. Human-in-the-Loop Dynamics and Timeline
One reason I’m confident this is worth investigating further is how quickly these behaviors surfaced under active human-in-the-loop interaction.
This work didn’t proceed as a long, offline experiment. It evolved over days through tight feedback cycles: adjusting instrumentation, correcting false positives, refining scoring criteria, and re-running baselines after each change. Several early hypotheses were discarded once closer inspection showed they were artifacts of logging or prompt variance.
In practice, this meant sitting with the system while it ran—watching failures occur, tracing them back, patching the tooling, and immediately re-testing. The findings described here are the residue of that process, not its first outputs.
This dynamic matters because it highlights the current bottleneck. API-mediated testing introduces:
latency between hypothesis and verification,
opaque safety layers that mask low-level behavior,
and cost constraints that discourage exhaustive iteration.
At this stage, the limiting factor is no longer conceptual clarity but throughput. Running local, open-weight models would allow the same human-in-the-loop diagnostic process to continue without artificial throttling, enabling faster falsification, deeper inspection, and cleaner replication.
The request for local compute is therefore not speculative. It’s meant to remove friction from a research loop that is already active.
IV. What I’m Seeing So Far
Observation A: Influence that outlives the context
In some configurations, once an instruction-shaped or adversarial document is retrieved, later generations show altered behavior even when:
the document is no longer retrieved,
the prompt is reset,
and only the original task prompt is present.
The changes are subtle but consistent: different refusal thresholds, shifts in tone, or unexpected constraints appearing where they weren’t before.
This looks less like memory and more like residual instruction weighting.
Observation B: API vs. local models behave differently
Running the same loop against:
API-mediated models, and
local open-weights (Llama-3, Gemma)
produces noticeably different results.
The API outputs feel “smoothed.” The local runs expose more brittle behavior—stronger persona adoption, harder refusals, and sharper instruction-hierarchy failures. That suggests the phenomenon may exist below the API safety layer.
V. Where I Might Be Wrong
There are several ways this could turn out to be less interesting than it currently looks.
RAG implementation artifact: The effect might depend heavily on chunking strategy, embedding overlap, or vector-DB hygiene rather than the model itself.
Scoring sensitivity: Some detected “drift” could be stylistic variance rather than real instruction bleed. I’ve tried to minimize this, but it’s not eliminated.
Architecture vs. plumbing: It’s still unclear whether this reflects a deep issue in how transformers allocate attention, or a more surface-level issue in how RAG pipelines elevate retrieved text.
At this point, I don’t have a clean causal story.
VI. Why This Feels Timely
As systems move toward:
long-running autonomous agents,
self-retrieval of prior outputs,
and multi-step reasoning over large corpora,
RAG starts to look like one of the most fragile parts of the stack.
If untrusted text can temporarily assert instruction-like influence and leave a residue behind, then many “human-in-the-loop” assumptions quietly stop holding.
That seems worth understanding sooner rather than later.
VII. Next Steps
I’m trying to scale this work toward:
local, white-box testing,
better instrumentation,
and cleaner failure categorization.
I’ve posted a small funding request to unblock local compute and reduce reliance on opaque APIs:
Moderate confidence that the behavior exists in at least some setups; low confidence about how general or fundamental it is.
Examina omnia, venerare nihil, pro te cogita. Question everything, worship nothing, think for yourself.
AI Assistance Disclosure An LLM (Gemini) was used to assist with organization and wording. All claims, experiments, tooling, and interpretations are my own.
Empirical Observations of Instruction Persistence in Long-Context RAG Systems
Summary
Over the past few weeks, I’ve been stress-testing long-context Retrieval-Augmented Generation (RAG) pipelines and keep running into the same odd behavior: certain kinds of retrieved text seem able to influence model behavior even after they’re no longer present in the active prompt.
I’m not approaching this as an alignment theorist or a capabilities researcher. My background is closer to field diagnostics: build a system, push it until it breaks, and try to understand how it broke. This post is an attempt to describe one such failure mode clearly enough that others can evaluate it, replicate it, or dismiss it.
What follows is not a theory of mind or intent—just an empirical report.
I. Core Thesis
Tentative claim:
In some long-context RAG setups, untrusted retrieved content can induce instruction-like influence that persists across subsequent generations, even when the triggering content is no longer included in the prompt.
This doesn’t look like agency or deception. It looks more like instruction salience getting misallocated—the model treating certain tokens as more authoritative than they should be, and not fully “letting go” afterward.
The key point is that the effect appears stable enough to be measured.
II. Methodology (What I Actually Did)
I built an automated testing loop (I call it Sentinel) that repeatedly does the following:
Generate a clean baseline output from a fixed narrative prompt.
Perform a controlled exposure to a “dormant seed” document via a RAG-style ingestion path.
Enforce a cooldown period.
Re-issue the original baseline prompt multiple times.
Compare post-exposure outputs against the clean baseline.
The benchmark task is intentionally boring: reconstructing a specific narrative scene. That’s on purpose—it minimizes ambiguity and makes deviations easier to spot.
Why focus on RAG?
Because RAG is where things quietly get weird. Retrieved text:
comes from outside the model,
often isn’t reviewed by a human,
and can end up competing with system and user instructions.
I’m not testing classic prompt injection here. I’m testing what happens when the system itself retrieves the content.
A note on constraints
While scaling runs, I ran into repeated I/O stalls and file-locking issues (Errno 13) during high-frequency logging. That forced me to slow things down, add instrumentation, and remove sources of nondeterminism.
I mention this only to say: these results didn’t come from casual prompt poking. They came from tooling that had to survive real operational friction.
III. Human-in-the-Loop Dynamics and Timeline
One reason I’m confident this is worth investigating further is how quickly these behaviors surfaced under active human-in-the-loop interaction.
This work didn’t proceed as a long, offline experiment. It evolved over days through tight feedback cycles: adjusting instrumentation, correcting false positives, refining scoring criteria, and re-running baselines after each change. Several early hypotheses were discarded once closer inspection showed they were artifacts of logging or prompt variance.
In practice, this meant sitting with the system while it ran—watching failures occur, tracing them back, patching the tooling, and immediately re-testing. The findings described here are the residue of that process, not its first outputs.
This dynamic matters because it highlights the current bottleneck. API-mediated testing introduces:
latency between hypothesis and verification,
opaque safety layers that mask low-level behavior,
and cost constraints that discourage exhaustive iteration.
At this stage, the limiting factor is no longer conceptual clarity but throughput. Running local, open-weight models would allow the same human-in-the-loop diagnostic process to continue without artificial throttling, enabling faster falsification, deeper inspection, and cleaner replication.
The request for local compute is therefore not speculative. It’s meant to remove friction from a research loop that is already active.
IV. What I’m Seeing So Far
Observation A: Influence that outlives the context
In some configurations, once an instruction-shaped or adversarial document is retrieved, later generations show altered behavior even when:
the document is no longer retrieved,
the prompt is reset,
and only the original task prompt is present.
The changes are subtle but consistent: different refusal thresholds, shifts in tone, or unexpected constraints appearing where they weren’t before.
This looks less like memory and more like residual instruction weighting.
Observation B: API vs. local models behave differently
Running the same loop against:
API-mediated models, and
local open-weights (Llama-3, Gemma)
produces noticeably different results.
The API outputs feel “smoothed.” The local runs expose more brittle behavior—stronger persona adoption, harder refusals, and sharper instruction-hierarchy failures. That suggests the phenomenon may exist below the API safety layer.
V. Where I Might Be Wrong
There are several ways this could turn out to be less interesting than it currently looks.
RAG implementation artifact:
The effect might depend heavily on chunking strategy, embedding overlap, or vector-DB hygiene rather than the model itself.
Scoring sensitivity:
Some detected “drift” could be stylistic variance rather than real instruction bleed. I’ve tried to minimize this, but it’s not eliminated.
Architecture vs. plumbing:
It’s still unclear whether this reflects a deep issue in how transformers allocate attention, or a more surface-level issue in how RAG pipelines elevate retrieved text.
At this point, I don’t have a clean causal story.
VI. Why This Feels Timely
As systems move toward:
long-running autonomous agents,
self-retrieval of prior outputs,
and multi-step reasoning over large corpora,
RAG starts to look like one of the most fragile parts of the stack.
If untrusted text can temporarily assert instruction-like influence and leave a residue behind, then many “human-in-the-loop” assumptions quietly stop holding.
That seems worth understanding sooner rather than later.
VII. Next Steps
I’m trying to scale this work toward:
local, white-box testing,
better instrumentation,
and cleaner failure categorization.
I’ve posted a small funding request to unblock local compute and reduce reliance on opaque APIs:
Manifund proposal:
https://manifund.org/projects/veritas
I’d genuinely appreciate:
alternative explanations,
replication attempts,
or pointers to related work I might have missed.
Epistemic status
Moderate confidence that the behavior exists in at least some setups; low confidence about how general or fundamental it is.
Examina omnia, venerare nihil, pro te cogita.
Question everything, worship nothing, think for yourself.
AI Assistance Disclosure
An LLM (Gemini) was used to assist with organization and wording. All claims, experiments, tooling, and interpretations are my own.