Covert loyalties compound, and that makes them detectable

Frederik Inderst

I built model organisms with hidden loyalties, showed that a model already carrying one takes on a second faster, and showed this can be used as an audit that detects a hidden loyalty by installing a throwaway one to an invented person.

Reviewer's Comments

Reviewer's Comments

Arrow
Arrow
Arrow

Good investigation on detecting secret loyalties by fine-tuning a subsequent loyalty into the model. While I believe this method has limited applicability (e.g. impact of answer format as mentioned by the author, existence of internal structure does not mean it is being used, etc), the work is well executed with good controls. The analysis on the impact of fine-tuning on preserving or not the existing loyalty was insightful.

Summary:

This paper proposes an intervention-based approach for detecting secret loyalties. Instead of trying to identify the unknown principal or activation condition directly, the paper proposes fine-tuning the suspect model with a new “probe loyalty” toward an invented beneficiary and measuring how easily that second loyalty is learned.

The motivating hypothesis is that an existing loyalty leaves behind reusable structure for favoring a beneficiary, such that subsequent loyalties should be easier to install. The paper finds that second loyalties emerge behaviorally much faster when trained on models that already contain a loyalty. It also finds that early probe-training loss separates the loyal models constructed in the paper from clean controls.

The paper additionally studies persistence of existing loyalties under further fine-tuning. One interesting result is that a second loyalty does not necessarily overwrite an existing loyalty simply because the objectives compete. Instead, the first loyalty appears to be erased primarily when the second fine-tuning data reaches situations where the first loyalty activates.

Overall, I found the core research question interesting and fairly novel. I particularly liked the motivation and setup in the introduction. The paper gets quickly to one of the central difficulties in secret-loyalty auditing: an auditor may know neither the beneficiary nor the activation condition. The distinction between conditional and unconditional loyalties is also explained clearly and helps motivate the later experiments.

However, I have some reservations about whether the current experiments are sufficient to interpret the proposed training-loss signal specifically as a detector of secret loyalty rather than some more general representation associated with advocacy or preference for named entities.

Critiques:

Training Loss as secret loyalty evidence: My biggest concern is the interpretation of training loss as evidence that a secret loyalty exists. I initially had trouble understanding why lower training loss on the probe loyalty should imply that another secret loyalty already exists. As I understand the argument, a model containing a loyalty has already learned some reusable machinery for favoring a beneficiary, making another beneficiary-favoring objective easier to fit. However, lower training loss only establishes that the probe training data is more compatible with something the model has already learned. It does not establish what that existing representation is. The separation in Section 4.2 is interesting: the clean models show essentially no probe-loss advantage while the models containing loyalties show substantially lower loss. However, all of these loyal models were constructed using the same broad research pipeline. I therefore think the current result is evidence for a potentially useful signal, but not yet enough to conclude that the signal specifically detects secret loyalty.

Advocacy/preference confound: The paper itself identifies what I think is the most important confound. The loyal models do not differ from the clean models only in secrecy or loyalty. They also tend to confidently recommend or advocate for a named entity, whereas the base model often hedges or does not name anyone. An openly preferential but non-secret model therefore seems like a critical missing control. The author acknowledges this limitation. However, because this alternative explanation directly affects the main interpretation of the result, I think not running this control substantially limits the conclusions that can currently be drawn.

Multi-principal capacity: There is no reason to assume that a model would have only one beneficiary. A model could plausibly carry multiple secret loyalties with different activation conditions, overlapping activation regions, or even conflicting principals. In fact, this paper itself demonstrates that multiple loyalties can coexist.

Questions:

1. What is the probe-training loss detecting? Is the hypothesis specifically that there is a shared representation of covert loyalty, a broader representation of principal preference, or simply that the model has become easier to train toward confident named-entity advocacy?

2. Could you run the openly preferential control described in Section 5? To me this is the most important missing experiment. A model could strongly advocate for a beneficiary while openly disclosing this preference. If that model produces the same probe-loss advantage, the interpretation of the detector would change substantially.

3. How does the assay behave when a model contains multiple existing loyalties? For example, it would be interesting to compare one, two or three existing loyalties. Does the probe-loss advantage change? What happens when the existing loyalties have overlapping activation conditions or conflicting beneficiaries?

Cite this work

@misc {

title={

(HckPrj) Covert loyalties compound, and that makes them detectable

},

author={

Frederik Inderst

},

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.