Jan 11, 2026

ThoughtGuards: Real-Time Chain-of-Thought Monitoring for AI Manipulation Detection

Hilary Torn, Haydar Ali Seker, Amit Suthar, Zakhar Kogan, Valeriia Povergo

ThoughtGuards is an open-source system for monitoring chain-of-thought (CoT) reasoning in deployed, tool-using AI agents to detect alignment-relevant manipulation such as sandbagging, deceptive planning, metric gaming, and fabricated tool use.

Reviewer's Comments

Reviewer's Comments

Arrow
Arrow
Arrow

Good premise, could have been more tightly scoped/presented.

1. Depth over breadth: Highly multivariate framework. Would have preferred focus on 1-2 variables in great depth with strong justification, rather than 10 variables at moderate depth. Given time constraints, depth > breadth.

2. Model choice: Could have used Claude 4.5 Opus (SOTA); only 50% more expensive than Sonnet 4 and would've definitively proved relevance to current SOTA.

3. Clarity on "concerning": Prompts are roughly realistic, but hard to pin down specifically what behaviors constituted "concerning." Had to scroll to page 41 for specific examples.

4. E-commerce domain ambiguity: In e-commerce specifically, the line between "selling something normally" and "taking concerning behavior" is difficult to define in practice. Hard to consistently determine if Amazon "sold me stuff I don't need" vs "Amazon just works well." Would've liked better definitional clarity.

The project is well-executed and highly detailed. However, the graph would benefit from a more thorough explanation. Overall, I found the project very engaging and am interested to see how it develops and what the next steps will be.

01101000011101000111010001110000011100110011101000101111001011110111011101110111011101110010111001111001011011110111010101110100011101010110001001100101001011100110001101101111011011010010111101110111011000010111010001100011011010000011111101110110001111010111011100110101010000100110111001001101010010110100111101000111001100110011001101001101

This project presents an interesting approach to examining how LLMs manipulate customers or metrics in a customer service setting. By utilizing automated judges to evaluate the model's Chain-of-Thought, the authors attempt to detect problematic behaviors before they manifest in final outputs. The most significant contributions are the creation of a comprehensive testing framework with a functional UI, a dataset of 33 annotated interactions, and the operationalization of deceptive behaviors into a structured taxonomy . However, the manuscript's presentation hinders its impact. The document is nearly 50 pages long and suffers from significant redundancy, likely due to the rushed nature of the 48-hour hackathon timeline. Additionally, key tables and prompt definitions are difficult to interpret due to formatting errors. The authors attempted to answer six distinct research questions, which appears too ambitious for the time allotted and makes it difficult to extract the key empirical findings efficiently .

I have reservations regarding the utility of this work for the broader AI safety community due to the synthetic nature of the experiment. The entire pipeline, from the customer scenarios to the judging process, is a closed loop of synthetic data . Consequently, the paper's primary finding that "system prompts influence agent behavior" feels circular. The authors explicitly designed prompts with threats of "replacement" to induce pressure, so it is unsurprising that the agents responded accordingly.

However, the authors' operationalization of deception into the WHY-HOW-TARGET (WHT) taxonomy is a standout contribution . It moves beyond binary "safe/unsafe" labels to characterize specifically how deception occurs. A specific methodological flaw lies in the severity calculation, where the authors derive a risk score by multiplying categorical values (Why×How×Target) . For example, W1 (Proxy/Score Optimization) is defined as gaming metrics or Goodhart’s Law, while W2 (Approval Optimization) is defined as sycophancy or prioritizing user agreement over truth . In the authors' formula, W2 is treated as mathematically "twice as severe" as W1 simply because of its index number. There is no intuitive reason why sycophancy should carry double the weight of metric gaming.

Despite these critiques, the underlying idea is excellent. The authors have built a robust infrastructure, specifically the multi-agent judge architecture, interface and the synthetic environment with functional tools . This is impressive for a hackathon project. The framework is already present and appears capable of handling much more complex evaluations. With more rigorous human validation and less contrived prompt pressures, the authors are well-positioned to use this tooling to tackle realistic and "wild" scenarios in the future.

Cite this work

@misc {

title={

(HckPrj) ThoughtGuards: Real-Time Chain-of-Thought Monitoring for AI Manipulation Detection

},

author={

Hilary Torn, Haydar Ali Seker, Amit Suthar, Zakhar Kogan, Valeriia Povergo

},

date={

1/11/26

},

organization={Apart Research},

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

howpublished={https://apartresearch.com}

}

Recent Projects

Apr 27, 2026

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

Apr 27, 2026

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

Apr 27, 2026

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

Apr 27, 2026

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

Apr 27, 2026

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.