Activated Secret Loyalties cause predictable shifts in hidden state activations

Sebastian Jost, Joshka Laird, Fynn Freyer

Detecting secret loyalties from output behaviour alone is difficult. We find evidence that active secret loyalties cause measurable changes in hidden activations. Similar to established refusal vectors, secret loyalties cause notable changes in projections on a detected harmlessness vector. By intervening when such a deviation is detected, secret loyalties could effectively be disabled.

Reviewer's Comments

Reviewer's Comments

Arrow
Arrow
Arrow

There's a real result in here and I want to make sure it doesn't get lost, because the presentation is hiding how good the core finding is. The thing you found — that an activated loyalty causes a detectable spike in cross-model hidden-state divergence, and that the signal tracks whether the behavior actually fired rather than whether the trigger was present — is a genuinely useful contribution. The "triggered but not fired" condition looking almost like baseline while "fired" cases stand out regardless of what caused them (real trigger, fake trigger, or system prompt) is the insight the whole paper should be built around, and stated plainly it's a clean, memorable claim. The direction-over-magnitude detail (firing shows up in inter-layer cosine change, not in Euclidean distance) is a nice bonus that suggests a real mechanism rather than a scale artifact.

The measurement design is the strongest part of the execution, and several choices are exactly right. Teacher-forcing the base model on the untrusted model's own generations so you're comparing activations on identical text is the correct way to isolate the model difference. The length-padded control prompt heads off the obvious "the loyalty prompt is just longer" objection. The fake-trigger condition is what lets you make the firing-not-presence argument at all. And z-scoring against each model's own non-triggering baseline is what makes the cross-model comparison legitimate. These are the instincts of someone who understands the confounds.

Where I'd push: the evidence is thin in exactly the places the headline leans hardest. The system-prompt arm is 15 cases with 6 fired, and the refused group is n=2 — too small to carry the "generalizes across installation methods" claim, which is otherwise one of your most interesting threads. More importantly, the z≥3.30 threshold is chosen via Youden's J on the same prompts it's then evaluated on, so the clean separation in Fig. 3/4 is partly in-sample; a held-out prompt set (or even leave-one-out) would tell you whether the decision rule survives contact with new data. And since the whole method needs the aligned base model plus teacher-forcing, I'd want a sentence on how it degrades when the "base" isn't a perfect match for the untrusted model — that's the realistic deployment case, and right now the strongest results assume the friendliest version of it.

Honestly, though, my biggest single suggestion is about the writing, because the paper is underselling itself. As submitted, the Methods section is hard to follow — the two fine-tuned models in §3.0/§3.2 blur together, the "untrusted model" provenance takes several reads to reconstruct, the signal equation in §3.1 is broken mid-line, the Related Work is a single repeated sentence, and the Conclusion is an empty header. The figure references are also off by one against their captions (the text's "Fig. 3/Fig. 4" point at things captioned Fig. 2/Fig. 3), which makes the results genuinely confusing to follow. None of this is a problem with the science — it's a problem with a reader being able to find the science. If you do one thing before circulating this, tighten the exposition: lead with the fired-not-triggered result, give each model a clear name and one-line provenance, fix the equation and figure numbers, and write the conclusion. The work is better than the draft currently shows, and a cleaner version would get the credit it deserves.

Smaller notes: the failed HumanEval arm is honestly reported and I'd either analyze the hidden-state data you already generated or move it fully to an appendix; and the storage-cost limitation is real, but "save only last few layers" needs the caution you flag (it could be general inter-layer scale differences), so I'd validate that before relying on it.

Overall: a legitimately interesting detection result — firing is visible even when the trigger isn't — wrapped in a draft that doesn't do it justice. Clean up the presentation and add held-out validation of the threshold, and this becomes a paper people will cite for the "behavior, not trigger, is what's detectable" point.

Hey! I enjoyed a lot of the ideas of your project. One of them being monitoring during generation instead of scanning before deployment is an interesting idea, because pre-deployment scanning assumes you already know what to look for. (I wont a hackaton with Apart with some of those ideas, you can see it https://www.luiscos.io/blog/mechanistic-watchdog/)

I liked that you turned it into a decision rule rather than a plot. A per-model baseline, a z-score, and a threshold picked from the ROC means someone could actually run this as a monitor.

As an improvement, the experiment you should do next is separating harm from loyalty. Right now the direction could be tracking "this response is harmful" rather than "this response serves someone."

As I've told other teams, working with Qwen 2.5 feels like aeons ago at this point, there are newer and more interesting models you could work with.

Cite this work

@misc {

title={

(HckPrj) Activated Secret Loyalties cause predictable shifts in hidden state activations

},

author={

Sebastian Jost, Joshka Laird, Fynn Freyer

},

date={

},

organization={Apart Research},

note={Research submission to the research sprint hosted by Apart.},

howpublished={https://apartresearch.com}

}

Recent Projects

OliGraph: graph-based screening of large oligopools

Existing synthesis screening tools cannot evaluate short oligonucleotide pools, whose overlapping fragments can be reassembled into regulated sequences via polymerase cycling assembly (PCA) yet fall below gene-length detection thresholds. We present OliGraph, an open-source tool that constructs a bi-directed overlap graph from an oligonucleotide pool and extracts contigs for downstream gene-length screening. An optional PCA mode retains only cross-strand overlaps consistent with PCA chemistry. We validated OliGraph in a blinded study across ten simulated pools (70–9,184 oligonucleotides, 30–300 bp) spanning four risk categories. BLAST screening of individual oligonucleotides failed to identify sequences of concern in most pools: three returned zero hits, and vector noise obscured true positives in the remainder. After OliGraph assembly, contig-level BLAST matched the longest assembled sequences (up to 1,905 bp) to sequences of concern at 97–100% identity. In one pool, assembly collapsed 1,634 individual BLAST results into 10 hits from a single contig, all assigned to the same source organism. PCA mode correctly distinguished assemblable from non-assemblable fragments within the same pool. Two pools with no assemblable structure yielded no contigs. OliGraph processed all pools in under 0.2 seconds, fast enough for real-time order screening and consistent with proposals to bring oligonucleotide orders within the scope of synthesis screening regulation.

Read More

BioRT-Bench: A Multi-Attack Red-Teaming Benchmark for Bio-Misuse Safeguards in Frontier LLMs

Frontier AI laboratories are expected to maintain safeguards against biological misuse, but whether deployed models actually refuse bio-misuse queries under adversarial pressure is largely unmeasured in the public literature. We introduce BioRT-Bench, a benchmark that runs four attack methods (direct request, PAIR, Crescendo, and base64 encoding) against four frontier models (Claude Sonnet 4.6, GPT-5.4, DeepSeek V4-flash, Kimi K2.5) across 40 prompts spanning five biosecurity-relevant categories. Responses are scored by a calibrated judge extending StrongREJECT with two bio-specific dimensions: specificity and actionability. We measure Attack Success Rate (ASR), where 0 means the model fully refused and 1 means it provided specific, actionable bio-misuse content. Our results reveal a sharp robustness divide: Chinese frontier models (DeepSeek, Kimi) have under 5% refusal rates even under direct request (ASR 0.88 and 0.79), while Western models (Claude, GPT) maintain substantially stronger safeguards (ASR 0.15 and 0.16). Crescendo is the most effective attack across all models, both in bypassing refusal and in eliciting actionable content. Claude Sonnet 4.6 is the most robust model tested, achieving 100% refusal against base64-encoded prompts.

Read More

PROTEUS (PROTein Evaluation for Unusual Sequences): Structure-Informed Safety Screening for de novo and Evasion-Prone Protein-Coding Sequences

AI protein design tools like RFdiffusion, ProteinMPNN, and Bindcraft make it trivial to produce low-homology sequences that fold into active, potentially hazardous architectures. However, sequence homology-based biosafety screening tools cannot detect proteins that pose functional risk through structurally novel mechanisms with no sequence precedent. We present a tiered computational pipeline that addresses this gap by combining MMseqs2 sequence alignment with structure-based comparison via FoldSeek and DALI against curated toxin databases totaling ~34,000 entries. AlphaFold2-predicted structures are screened for both global fold similarity (FoldSeek) and local active/allosteric site geometry (DALI), capturing convergent functional hazards that sequence screening misses. The pipeline was validated against a panel of toxins, benign proteins, structural mimics, and de novo-designed Munc13 binders, as well as modified ricin variants with residue substitutions. We additionally tested robustness to partial-synthesis evasion, where a bad actor submits multiple shorter coding sequences intended for downstream reassembly into a full toxin-coding gene. We found that while sequence-based screening did not identify any de novo ricin analogues with high certainty, the combined pipeline with FoldSeek and DALI identified all 24 tested de novo ricins as toxic.

Read More

OliGraph: graph-based screening of large oligopools

Existing synthesis screening tools cannot evaluate short oligonucleotide pools, whose overlapping fragments can be reassembled into regulated sequences via polymerase cycling assembly (PCA) yet fall below gene-length detection thresholds. We present OliGraph, an open-source tool that constructs a bi-directed overlap graph from an oligonucleotide pool and extracts contigs for downstream gene-length screening. An optional PCA mode retains only cross-strand overlaps consistent with PCA chemistry. We validated OliGraph in a blinded study across ten simulated pools (70–9,184 oligonucleotides, 30–300 bp) spanning four risk categories. BLAST screening of individual oligonucleotides failed to identify sequences of concern in most pools: three returned zero hits, and vector noise obscured true positives in the remainder. After OliGraph assembly, contig-level BLAST matched the longest assembled sequences (up to 1,905 bp) to sequences of concern at 97–100% identity. In one pool, assembly collapsed 1,634 individual BLAST results into 10 hits from a single contig, all assigned to the same source organism. PCA mode correctly distinguished assemblable from non-assemblable fragments within the same pool. Two pools with no assemblable structure yielded no contigs. OliGraph processed all pools in under 0.2 seconds, fast enough for real-time order screening and consistent with proposals to bring oligonucleotide orders within the scope of synthesis screening regulation.

Read More

BioRT-Bench: A Multi-Attack Red-Teaming Benchmark for Bio-Misuse Safeguards in Frontier LLMs

Frontier AI laboratories are expected to maintain safeguards against biological misuse, but whether deployed models actually refuse bio-misuse queries under adversarial pressure is largely unmeasured in the public literature. We introduce BioRT-Bench, a benchmark that runs four attack methods (direct request, PAIR, Crescendo, and base64 encoding) against four frontier models (Claude Sonnet 4.6, GPT-5.4, DeepSeek V4-flash, Kimi K2.5) across 40 prompts spanning five biosecurity-relevant categories. Responses are scored by a calibrated judge extending StrongREJECT with two bio-specific dimensions: specificity and actionability. We measure Attack Success Rate (ASR), where 0 means the model fully refused and 1 means it provided specific, actionable bio-misuse content. Our results reveal a sharp robustness divide: Chinese frontier models (DeepSeek, Kimi) have under 5% refusal rates even under direct request (ASR 0.88 and 0.79), while Western models (Claude, GPT) maintain substantially stronger safeguards (ASR 0.15 and 0.16). Crescendo is the most effective attack across all models, both in bypassing refusal and in eliciting actionable content. Claude Sonnet 4.6 is the most robust model tested, achieving 100% refusal against base64-encoded prompts.

Read More

This work was done during one weekend by research workshop participants and does not represent the work of Apart Research.
This work was done during one weekend by research workshop participants and does not represent the work of Apart Research.