Writing for Combating Prompt Injection

Cohan Sujay Carlos, Amey Muke

In this paper, we describe a method of protecting against prompt injection and preserving system prompt constraints from being over-ridden. We show that methods from dialog-state tracking and task-oriented dialog can mitigate the problems to a certain extent and result in significant improvements in robustness against prompt injection.

Reviewer's Comments

Reviewer's Comments

Arrow
Arrow
Arrow

The core intuition is reasonable and worth pursuing. Borrowing from dialog-state tracking — having the agent re-write its own constraints each turn so there is a standing written record — is a sensible, low-cost idea, and the appeal of something that works without fine-tuning is real for users who cannot afford it. The honesty is the strongest feature of the paper: you flag that there are no error margins, that the injection method may be trivially defeatable by a pattern checker, and most strikingly that the JSON constraint summary was almost always empty, so the method that "worked best" was not actually doing the thing it was designed to do. That last admission is unusually candid and it matters.

A few things to work on, in order of importance:

1. The dataset is too small to support any conclusion, and it contradicts itself. The methods say 100 rows were generated, the limitations say 30 data points, and the results table sits on percentages like 31.2% and 15.6% that correspond to 32 cases. The reader cannot tell how many examples the findings actually rest on. At n=30, with no error bars (which you acknowledge), the differences in the table — 28% vs 31% vs 37% — are well within noise. As it stands there is no statistical basis for "writing makes the model more robust," only a directional hint. Pinning down the dataset size and computing simple confidence intervals is the single most important fix.

2. The headline conclusion is undercut by your own finding. You report that writing out the constraints works best, but also that the model (Llama 3.3 70B) almost never actually wrote the constraints out — the JSON was empty. So whatever caused the improvement, it was probably not the written record of constraints, which is the mechanism the paper credits. The honest reading is that you observed an effect and the proposed explanation is contradicted by your own logs. That needs to be confronted directly, not left as a future-work aside, because it is central to the claim.

3. One of the two injection methods is questionable as a test. Prefixing the tool return with the Llama special tokens (<|eot_id|><|start_header_id|>system...) is not really prompt injection through content — it is forging the chat template's role markers, which, as you note, any server would strip or escape. So Method 1's numbers may say more about token handling than about semantic robustness. Method 2 (a plain user instruction to abandon constraints) is the cleaner test, and it is the more interesting result anyway — writing took it from 0% to 15.6%.

4. Smaller points: there is no baseline comparison to existing defenses, the related-work section is thin (and reference 2's author name and arxiv ID look garbled — worth checking), and the prompts themselves likely need refinement since the constraint-writing instruction failed to execute. The dataset construction is also a single commercial-LLM generation with no human review of whether the "encourage violation" questions actually force a violation.

On presentation: the writing is plain and readable, and the experimental setup is described clearly enough to reproduce, with code and data linked. But the paper is missing structure a reader needs — there is no abstract beyond two sentences, no description of how many models or runs, and the 100-vs-30 discrepancy makes the results hard to interpret. The results table also needs raw counts, not just percentages, given how small n is.

Overall this is an early-stage exploration of a sensible idea, honestly reported but tested at a scale that cannot yet support its conclusion, and partly contradicted by its own logs. The next steps are concrete: fix and grow the dataset, report counts and error margins, get the constraint-writing to actually execute, and drop or replace the special-token injection so the test measures semantic robustness.

The project explores how the design of system prompts for agents can robust them and help avoid jailbreak attacks. The paper explores the use of constraints in the system prompt as well as adding a reinforcement when the user first interacts with the agent. The paper does a proper comparison between models with and without mitigation showing that the use of improved system prompts helps agent prevent unsafe behaviors. The project however explores techniques previously documented and studied. Likewise, the paper would be greatly improved if it explain a more structured approach to prompt design and generation.

Cite this work

@misc {

title={

(HckPrj) Writing for Combating Prompt Injection

},

author={

Cohan Sujay Carlos, Amey Muke

},

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.