PRISM: On Sparse Autoencoder Feature Identifiability for Conditioned Introspection

Aruneem Bhowmick

We use sparse autoencoder features as a prism for studying whether language models can detect changes to their own internal representations. Across Pythia and Gemma interventions, it finds that feature geometry alone does not reliably predict this introspective detection behavior.

Reviewer's Comments

Reviewer's Comments

Arrow
Arrow
Arrow

The bookkeeping discipline here is the best I've seen in this batch. Keeping the two models' fits separate, refusing to headline the pooled estimate, making the eight judge refusals explicit rather than silently retrying them, and recomputing the Pythia-only analysis from the repaired ledger to confirm it reproduced the original coefficient exactly — that last check in particular is something most published work doesn't do. You also report a null cleanly and resist every available temptation to dress it up. I want to be clear that what follows is not a complaint about honesty.

The problem is that the primary experiment could not have answered the question. You're testing whether a feature-level property predicts detection, in a 70M-parameter model that produced one detection in 474 trials. An outcome with essentially zero variance has no predictor — not this one, not any one. So the Pythia null isn't evidence that identifiability fails to predict detection; it's evidence that Pythia-70m doesn't detect injections, which was fairly predictable in advance given that the literature you're building on demonstrates this behaviour in frontier models. The calibration pilot is where this shows: it tuned injection strength against response length, when the quantity that needed piloting was detection rate. Fifteen minutes of piloting for a nonzero base rate would have redirected the whole study to Gemma from the start.

That has a direct consequence for the reported statistics. A logistic regression with four predictors fit to one positive event doesn't produce an estimate — it produces separation, and the coefficient 0.50 with CI [-1.19, 2.20] should be read as "no fit was possible," not as a wide interval. Similarly, an AUC computed against a single positive is just the percentile rank of one observation in one ordering; the identifiability-0.63-versus-decoder-norm-0.76 comparison is where one trial happened to sit in two lists. Your prose is careful about this ("the ranking comparison does not support identifiability over decoder norm in this setting"), but the abstract and Table 1 still present these as results, and I'd rather see them reported as undefined. Gemma is fittable but thin: nine events across four predictors is roughly a quarter of the events-per-variable people usually want, so [-0.34, 0.92] is close to uninformative too.

Note also that the pooled coefficient (-0.59) has the opposite sign from both per-model estimates (0.50 and 0.29). You correctly decline to interpret the pooled fit, but the sign reversal is worth naming explicitly as a Simpson's-paradox artifact of the model-level difference, because a reader skimming Table 1 and the pooled figure may not see why they disagree. The pooled AUC of 0.82 is close to a measure of how well the model detects which model it is.

Two further things about the Gemma arm, which is the one carrying the events. The Gemma Scope SAE reports reconstruction quality of 0.6786 against Pythia's 0.9782. A dictionary that reconstructs the residual stream that poorly is a weak basis for computing geometric properties of individual atoms, so the arm with statistical power has the less trustworthy instrument. Worth stating as a limitation in its own right. Second, the strengths differ by more than an order of magnitude across arms (1–8 versus 20–400) with no shared normalisation — expressing injection strength relative to residual-stream norm at the hook site would make the two at least commensurable.

A definitional gap: "frame-theoretic identifiability" is the independent variable of the entire paper and it never gets a formula or a citation. "A score based on its separation from nearby decoder directions" doesn't let a reader reconstruct it — coherence with the nearest atom, mean coherence over some neighbourhood, a frame bound, something else? Figure 2 shows values from about 0.60 to 1.00, which is consistent with several candidates. Please define it explicitly; it's the one thing a replication would need most.

Smaller points. The methods say three seeds per feature-strength pair yield 480 systematic trials, but results report 474; the ledger reconciliation implies six of the eight judge refusals fell in systematic trials, and stating that where the number first changes would save the reader the arithmetic. The pooled CI is printed as [1.39, 0.21], which is malformed and presumably [-1.39, 0.21]. And since the single Pythia positive drives every Pythia statistic, say whether it was included in the 15-trial human review and whether the human agreed with the judge — with n=1, that one adjudication is the whole result.

Nothing is linked. The paper repeatedly invokes a shared trial ledger, scoring provenance records, and configs/experiment.yaml, which means the artifacts exist; without them the auditability the discussion rightly emphasises isn't available to anyone but you. Posting the repo would also let people reuse the harness, which I suspect is the most valuable thing you built.

The question itself is good and I'd like to see it answered — whether interpretable-feature geometry predicts which injections a model notices is a real bridge between SAE work and introspection work. The redesign is straightforward: pilot for a nonzero detection rate first, run in a model that clears it, use one SAE with decent reconstruction, vary identifiability widely while holding decoder norm fixed by construction rather than by covariate adjustment, and power for the event count rather than the trial count.

This is basically an extension of the Lindsey-style introspection work, asking whether feature distinctiveness predicts detection after activation injection, on two small models. Introspection does have implications for AI safety, although they do not discuss this in the main text. Prior work would suggest that small/base models are not in fact able to detect injection, and that is mostly what they find here, obviating their subsequent tests on feature distinctiveness - although they do report some small detection success in the Gemma model, there are insufficient controls or baselines reported to determine whether it is meaningful. Also, unlike that earlier work, here tests of detection and identification are conflated, so it's hard to make direct comparisons. In general the methodology is described in insufficient detail to allow a determination of whether the experiments were conducted correctly.

Cite this work

@misc {

title={

(HckPrj) PRISM: On Sparse Autoencoder Feature Identifiability for Conditioned Introspection

},

author={

Aruneem Bhowmick

},

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.
Apart Research logo

Sign up to stay updated on the
latest news, research, and events

Google Scholar icon

Apart Research Inc · 1500 N Grant St, Ste R, Denver, CO 80203 · +1 (720) 408-1923

Apart Research logo

Sign up to stay updated on the
latest news, research, and events

Google Scholar icon

Apart Research Inc · 1500 N Grant St, Ste R, Denver, CO 80203 · +1 (720) 408-1923

Apart Research logo

Sign up to stay updated on the
latest news, research, and events

Google Scholar icon

Apart Research Inc · 1500 N Grant St, Ste R, Denver, CO 80203 · +1 (720) 408-1923

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

Sign up to stay updated on the
latest news, research, and events

Google Scholar icon

Apart Research Inc · 1500 N Grant St, Ste R, Denver, CO 80203 · +1 (720) 408-1923