Answerability readouts predict whether a passage supplies an answer, but whether calibration can compensate for removing negative passages during training remains unclear. We present a controlled study of how training-negative construction affects calibrated prediction, ranking, and downstream answer retention. We compare native training, which retains negative passages, with empty training, which removes them, holding questions, labels, positive examples, and model weights fixed. Both are calibrated on the same labeled native examples. On SQuAD 2.0 and RepLiQA, native-trained logistic readouts at selected depths achieve lower Brier loss for Qwen2.5-7B-Instruct and Gemma-2-9B-it, with or without output scores. Native fusion also outperforms calibrated output alone. Post-hoc AUROC analysis shows better ranking under native training, beyond what threshold adjustment alone can explain. On the official SQuAD 2.0 development set, native readout policies improve F1 over empty policies but retain more answers to unanswerable questions. The advantage varies by estimator and depth, while RepLiQA's text shortcuts limit claims about contextual understanding. Unfinished generations prevent complete answer-level evaluation, although worst-case bounds preserve the native-empty F1 gains. Our findings show that training negatives affect ranking and downstream decisions even after common calibration, without establishing a universal advantage for native training.
Figures & tables
Figure 1: A SQuAD fitting example with the passage summarized. Native (solid blue) and empty (dashed orange) training share the same unanswerable question and label. The bottom panel concerns calibration on new inputs, not predictions for this example.
Figure 2: Controlled comparison of native (solid blue) and empty (dashed orange) fitting, with the model, readout depth, questions, and labels held fixed. The left panel fits readouts on condition-specific states, yielding scores s . Neural and speech icons denote readout and output scores, respectively. Separate maps (gears) use identical labeled native examples (teal) to calibrate readout scores, both signals jointly (fusion), or output scores alone (gray) into probabilities p . Prediction quality uses new SQuAD articles and RepLiQA documents. Answer retention uses official SQuAD 2.0 development questions. Each probability-based veto applies its own threshold to p to keep the same generated candidate within a model or abstain. Primary Brier comparisons use fusion, and primary answer-retention comparisons use readouts alone.
Dataset / model
Native fusion
Empty fusion
Output
SQuAD / Qwen
0.085
0.095
0.097
SQuAD / Gemma
0.095
0.110
0.119
RepLiQA / Qwen
0.029
0.051
0.066
RepLiQA / Gemma
0.043
0.064
0.073
Table 1: Primary Brier losses on new articles and documents at selected depths. Lower is better. Fusion predictors share output scores and labeled calibration examples, differing only in training negatives. Output is each study’s prespecified comparator. Figure 3 shows paired improvements.
Figure 3: Brier reductions from native fusion relative to empty fusion (circles) and output alone (squares). Positive values favor native fusion. Error bars show paired 98.75% article/document t intervals, corrected for four comparisons per dataset. Datasets are not pooled. Appendix B , Table 5 , gives exact differences and intervals.
Model
Training
Brier
AUROC
BA
SQuAD
Qwen
native
0.088
0.947
0.888
empty
0.106
0.923
0.864
Gemma
native
0.099
0.934
0.867
empty
0.121
0.904
0.823
RepLiQA
Table 2: Logistic readouts without output scores, after common probability calibration, on the same inputs as Table 1 . BA uses a probability threshold of 0.5.
Policy
Qwen
Gemma
Answer F1
Unchanged
81.51
70.65
Empty readout
78.71
76.92
Native readout
82.70
78.85
Selected output
81.67
78.12
Native fusion
83.82
79.69
Table 3: Answer F1 on the official SQuAD 2.0 development set (0–100). Policies share generated candidates within each model. Brackets give paired article-bootstrap intervals, Bonferroni-adjusted for six comparisons at nominal 95% family confidence. F1 values are lower bounds with zero credit for unfinished generations (sensitivity bounds in Appendix C.2 ). Differences use unrounded scores.
Figure 4: Native-minus-empty answer F1, separated into official credit differences on answerable and unanswerable questions. Bars sum to the net gain over all 11,873 questions per model, with zero credit for unfinished generations. These are arithmetic contributions (Appendix C.4 ).
Model
Training
Within scenario AUROC
BA training threshold
BA recalibrated threshold
Q
Logistic / E/Bkg
1.000
0.638
0.898
Q
Logistic / E/I-N
1.000
0.766
0.969
Q
Logistic / E/I-B
1.000
0.770
0.970
G
Logistic / E/Bkg
1.000
0.589
0.920
G
Logistic / E/I-N
1.000
0.682
0.935
G
Logistic / E/I-B
1.000
0.738
0.941
Table 4: Threshold transfer with fixed logistic readouts (Q: Qwen, G: Gemma). Training contrasts are defined in § 6.6 . Both BA columns test held-out scenarios with training thresholds or thresholds calibrated on other scenarios. Metrics average over 24 scenarios and dependent fits. BA includes both irrelevant-wording variants. Appendix E , Table 14 , also reports DiM.
Appendix figures & tables11 assets
Supplementary material from the paper’s appendix.
Appendix
Dataset / model
Native fusion
Empty fusion
Output
Empty fusion − native 98.75% interval
Output − native 98.75% interval
SQuAD / Qwen
0.085
0.095
0.097
0.010 [0.005, 0.015]
0.011 [0.006, 0.017]
SQuAD / Gemma
0.095
0.110
0.119
0.015 [0.010, 0.019]
0.023 [0.015, 0.031]
RepLiQA / Qwen
0.029
0.051
0.066
0.022 [0.017, 0.027]
0.036 [0.028, 0.044]
RepLiQA / Gemma
0.043
0.064
0.073
0.021 [0.017, 0.026]
0.030 [0.024, 0.036]
Appendix
Table 5: Primary Brier comparisons on new SQuAD articles and RepLiQA documents. Lower Brier is better. Difference columns subtract native-fusion Brier from empty-fusion or output Brier, so positive values favor native fusion. Intervals are paired 98.75% article/document t intervals, corrected for four comparisons per dataset. The datasets use different fitting protocols and prevalences, so effects are not pooled. Output is the prespecified comparator. Differences are computed before rounding.
Model
Δ AUROC
95% interval
Adjusted 98.75% interval
SQuAD
Qwen
0.0237
[0.0141, 0.0337]
[0.0115, 0.0368]
Gemma
0.0293
[0.0180, 0.0412]
[0.0153, 0.0450]
RepLiQA
Qwen
0.0119
[0.0061, 0.0188]
[0.0049, 0.0212]
Gemma
0.0149
[0.0090, 0.0217]
[0.0077, 0.0240]
Appendix
Table 6: Post-hoc paired-cluster intervals for the readout-alone AUROCs in Table 2 . Δ is native minus empty. Intervals condition on fixed predictors and resample 164 SQuAD articles or 256 RepLiQA documents. Adjustment covers these four supplementary contrasts, all with positive lower bounds.
Model / training
BS
MCB
DSC
UNC
SQuAD
Qwen / native
0.088
0.006
0.167
0.250
Qwen / empty
0.106
0.008
0.152
0.250
Gemma / native
0.099
0.005
0.156
0.250
Gemma / empty
0.121
0.007
0.136
0.250
RepLiQA
Appendix
Table 7: Empirical CORP decomposition of fixed readout-alone probabilities on new articles and documents. Isotonic PAV is fitted on evaluation labels only for this descriptive analysis. BS = MCB − DSC + UNC, up to displayed rounding. No PAV-adjusted prediction is deployed.
Native minus
F1 gain
Adjusted interval
Bounds for unfinished generations
Qwen / empty
3.99
[2.43, 5.77]
[3.93, 4.05]
Qwen / output
1.03
[0.13, 1.99]
[0.97, 1.09]
Qwen / unchanged
1.19
[ − 0.24, 2.62]
[1.13, 1.25]
Gemma / empty
1.93
[0.91, 2.88]
[1.74, 2.13]
Gemma / output
0.72
[ − 0.06, 1.41]
[0.53, 0.92]
Gemma / unchanged
8.20
[6.94, 9.57]
[8.01, 8.39]
Appendix
Table 8: Primary answer-F1 differences in percentage points. Intervals use 20,000 paired article-bootstrap draws and a Bonferroni adjustment for six comparisons (99.1667% per interval for a nominal 95% family level). The last column allows each paired difference with an unfinished generation to range independently from −1 to 1 , a conservative point sensitivity bound. It is not a confidence interval or a replacement for the unmet complete-output requirement. Differences are computed before rounding.
Policy
Qwen F1
Gemma F1
Unchanged
81.51
70.65
Always abstain
50.05
50.01
Native readout
82.70
78.85
Native fusion
83.82
79.69
Output (isotonic)
82.41
78.12 sel
Output (logistic)
81.67 sel
78.12
Appendix
Table 9: All evaluated policy F1 scores (0–100), under the same lower-bound convention. Superscript sel marks the output comparator selected by calibration answer F1 for each model and reported as Selected output in Table 3 . Budget denotes the allowed fraction of unanswerable calibration questions whose answers are retained, not a certified test-risk bound. These thresholds are secondary operating points, not alternatives selected after viewing development-set results.
Output calibration / articles
Qwen BS
Gemma BS
Scalar logistic / 16
0.107
0.119
Isotonic / 16
0.097
0.119
Per-marker-token logistic / 16
0.109
0.109
Scalar logistic / 32
0.106
0.119
Isotonic / 32
0.097
0.119
Per-marker-token logistic / 32
0.109
0.110
Appendix
Table 10: Original comparator and post-hoc SQuAD output controls evaluated on the same 164 evaluation articles. Article counts refer to each component’s calibration access, not six disjoint calibration sets. Native fusion Brier is 0.085 for Qwen and 0.095 for Gemma. Per-marker-token logistic uses one feature per token of the prescribed abstention response.
Block / estimator
Native BS
Empty BS
Empty − native
Reported interval
SQuAD / Qwen
20 (selected) / Logistic
0.08535
0.09526
+0.00991
[0.00518, 0.01464] *
20 (selected) / DiM
0.09234
0.09385
+0.00150
—
27 (final) / Logistic
0.09561
0.09484
− 0.00077
—
27 (final) / DiM
0.09534
0.09508
− 0.00027
—
SQuAD / Gemma
Appendix
Table 11: All evaluated estimator–depth combinations on the new articles and documents. BS is fusion Brier loss. Positive empty-minus-native differences favor native training. Intervals are paired article/document t intervals, conditional on the fits. Asterisks mark the primary 98.75% intervals corrected for four comparisons per dataset. Other intervals are exploratory 95% intervals without multiplicity correction. A dash means no paired interval was computed, not no effect. Five decimals preserve the signs of small differences.
Dataset / text predictor
Brier
AUROC
BA
SQuAD / question only
—
0.558
0.543
SQuAD / question + passage
—
0.510
0.506
SQuAD / word counts, native
—
0.533
0.527
RepLiQA / question only
0.048
0.982
0.905
RepLiQA / word counts, native
0.041
0.986
0.953
RepLiQA / word counts, empty
0.099
0.898
0.753
Appendix
Table 12: Text-only controls. SQuAD entries replay native-trained predictors under common threshold calibration, for which Brier is not reported (—). RepLiQA entries use probability calibration. The protocols differ across datasets.
Predictor
Positive BS
Negative BS
Class-balanced BS
Word counts
0.038
0.050
0.044
Qwen / readout
0.011
0.098
0.054
Qwen / fusion
0.011
0.102
0.056
Gemma / readout
0.017
0.138
0.078
Gemma / fusion
0.018
0.139
0.079
Appendix
Table 13: RepLiQA class-conditional Brier losses, all with native training. The word-count classifier has lower negative-class and class-balanced loss than both models’ readouts. Under the original class prevalence, Qwen’s readout has lower overall loss than the word-count classifier, whereas Gemma’s does not.
Model
Training
Within scenario AUROC
BA training threshold
BA recalibrated threshold
Q
DiM / E/Bkg
0.986
0.819
0.873
Q
DiM / E/I-N
0.999
0.940
0.950
Q
DiM / E/I-B
1.000
0.959
0.965
Q
Logistic / E/Bkg
1.000
0.638
0.898
Q
Logistic / E/I-N
1.000
0.766
0.969
Q
Logistic / E/I-B
1.000
0.770
0.970
Appendix
Table 14: Complete threshold-transfer results for the constructed factual task (Q: Qwen, G: Gemma). E/Bkg uses bare-background negatives, and E/I-N and E/I-B use notebook and bag additions. Both BA columns evaluate held-out scenarios, before or after threshold calibration on other scenarios. Metrics average over 24 scenarios and dependent fits, with BA including both irrelevant-wording variants.
Model / E/I fit
BA gain
95% interval
Q / DiM / I-N
0.077
[0.031, 0.132]
Q / DiM / I-B
0.092
[0.047, 0.145]
Q / Logistic / I-N
0.071
[0.019, 0.128]
Q / Logistic / I-B
0.072
[0.021, 0.132]
G / DiM / I-N
0.072
[0.033, 0.114]
G / DiM / I-B
0.100
[0.056, 0.150]
Appendix
Table 15: E/I minus E/Bkg BA after common threshold calibration. Q and G denote Qwen and Gemma. I-N and I-B denote notebook and bag training variants. The descriptive paired 95% scenario-bootstrap intervals condition on fitted readouts and calibration halves, without multiplicity correction.
A model should refuse two different things: answers it would get wrong, and questions it should not answer at all, such as unanswerable ones or ones resting on a false premise. The usual recipe thresholds a single confidence score, which cannot tell these apart. Across five instruction-tuned models from three families (2B to 14B), we find they are separate axes. Ordinary answer-confidence tracks whether an answer is right but is nearly blind to whether the question is answerable; a linear probe on hidden states does the reverse. The blind spot does not shrink with scale. It is worst on naturally occurring false-premise questions (CREPE). There, answer-confidence, P(IK), P(True), and even asking the model outright whether a premise is false all stay near chance, while a hidden-state probe reaches 0.69 to 0.77 AUROC: the model represents a problem it will not report. This turns out to be fixable. Instructing a model to check premises backfires, because it then disputes sound and false premises alike (57% false challenges), unable to tell them apart; routing the same instruction with the probe roughly triples challenge precision. We turn the two axes into a calibrated policy that answers only when an answerability score and a correctness score each clear a separately certifies behave differently: the unanswerable-answer rate is controllable at every scale, while the wrong-answer rate is capped by model accuracy, so the guarantee tightens as threshold policy certifies both budgets at 0.75 coverage of correct answers, against 0.31 for a single threshold; at 14B it is the only policy that certifies at all.
Multiple-choice question (MCQ) benchmarks have been a standard evaluation practice for measuring LLMs' ability to reason and answer knowledge-based questions. Through a synthetic NonsenseQA benchmark, we observe that different LLMs exhibit varying degrees of label-position-few-shot-prompt bias, where the model either uses the answer position, the label in front of the answer, the distributions of correct answers present in the few-shot prompt, or a combination of all to answer each MCQ question. We propose a simple bias-reduced evaluation protocol that replaces the labels of each question with uniform, unordered labels and prompts the LLM to use the whole answer presented. With a simple sentence similarity model, we demonstrate improved robustness and lower standard deviation between different permutations of answers with a minimal drop in LLM's performance, exposing the LLM's capabilities under reduced evaluation artifacts, without any help from the prompt examples or the option labels. Across multiple benchmarks and models, this protocol substantially improves the robustness to answer permutations, reducing mean accuracy variance 3× with only a minimal decrease in the mean model's performance. Through ablation studies on various embedding models and similarity functions, we show that the method is more robust than the standard ones.
Constrained-option scoring reads a model's probabilities for a fixed set of permitted answers, so it returns a score even when the model is about to write something else. We study a prompt that quotes a multiple-choice item, ending in the item's own answer instruction, and asks for a forecast of whether a reader model given only a short note will answer it correctly. The model can begin answering the quoted item: on three Qwen3 checkpoints an answer letter is the most probable token on nearly every passage, and the forecast ranks the reader's correctness indistinguishably from chance. Beyond prior work's argmax check and prefill repair, we contribute a label-free diagnostic of the declared options' support, their first-token mass in context; a deletion test tracing the Qwen3 answer-letter start to the quoted instruction; and rendering and tokenisation checks for dropped separators and coinciding first tokens. Prefilling an answer stem lifts the median option mass from below to above one half on all nine checkpoints scored with this prompt and, with options and renormalisation unchanged, raises the Qwen3-averaged AUC from 0.4929 to 0.6152. lm-polygraph's default P(True) estimator shows a related failure: it reads True where Qwen3 without thinking favours an answer letter (MMLU) or the prompt's (A)/(B) label (TriviaQA), and its Qwen3-averaged AUROC is indistinguishable from chance on MMLU and below chance on TriviaQA. Scoring and renormalising the (A)/(B) labels after an answer stem raises it to 0.632 and 0.868, renormalising True against False in place reaches 0.660 and 0.860, and on TriviaQA both exceed all fourteen default single-answer library estimators. The original forecast is renormalised too, yet stays indistinguishable from chance: option mass flags low support in both settings without labels, and only checking the intended target shows which score still ranks.
Jiaxuan Guo, Kejia Zhang, Shuo Xin +3
Stanford University · University of Maryland, College Park