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On Identifiability in Transformers

T0 review · 2 major / 6 minor · reviewed 2026-08-14 · deepseek-v4-flash

Pith's one-line read Attention weights cannot be uniquely determined from a transformer head's output.

desk verdict A genuinely useful set of empirical diagnostics for Transformer interpretability, but the headline non-identifiability theorem is not proven for actual softmax attention weights. read the letter →

arxiv 1908.04211 v4 pith:MXKNR2CR submitted 2019-08-12 cs.CL cs.LG

classification cs.CLcs.LG
keywords attentionidentifiabilityeffectivetokenhiddenattributiontransformerinterpretabilityself-attentioncontextualembeddingsgradient
verification ladder T0 review T1 audit T2 compute T3 formal

The pith

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The reading

Attention weights in transformer self-attention cannot in general be recovered from the head's output: once the sequence length exceeds the head dimension, infinitely many different attention distributions produce exactly the same output. The paper proves this by showing that the left null space of the value-projection matrix $T = E W_V H$ is non-trivial, and extends the argument to probability distributions, so the non-uniqueness persists among valid softmax outputs. This undercuts the common practice of treating attention maps as direct explanations, and the paper proposes effective attention, the component that actually affects the output, as a corrective diagnostic. The paper also shows that input token identity survives through the layers, mostly encoded in the angle of embeddings, even while self-attention strongly mixes context into hidden embeddings. A gradient-attribution method quantifies this mixing and shows that context is mostly local, with long-range dependencies emerging mainly in later layers.

What carries the argument

The load-bearing object is the left null space $LN(T)$ of the matrix $T = E W_V H$, which maps attention rows to the head output; its dimension, bounded below by $d_s - d_v$ through rank-nullity, is exactly the family of perturbations $\tilde A$ that change attention weights without changing outputs. For probability constraints the argument passes to the augmented matrix $[T, \mathbf{1}]$, whose left null space contains the row-stochastic perturbations, and uses the strict positivity of softmax rows to allow small null-space steps. Effective attention is the orthogonal projection of raw attention onto the orthogonal complement of $LN(T)$. The empirical machinery for the remaining claims is a learned linear map with cosine nearest-neighbour lookup for token identity, and the L2 norm of the gradient of a hidden embedding with respect to each input token for measuring context mixing.

What would settle it

Take a trained transformer head with $d_s > d_v+1$, construct a nonzero $\tilde A$ in the left null space of $[T,\mathbf{1}]$ as the paper does, and test whether $A+\tilde A$ equals $\mathrm{softmax}(Q'K'^T/\sqrt{d_q})$ for some $Q',K'$ whose product has rank at most $d_q$; if no such realisation exists, the non-identifiability claim does not hold for actual softmax attention weights.

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Extended reading notes

Core claim

The paper's central claim is that for a self-attention head with sequence length $d_s$ and value dimension $d_v$, whenever $d_s > d_v$ the attention matrix $A$ is not identifiable from the head's output. By rank-nullity, the left null space of $T = E W_V H$ has dimension at least $d_s - d_v$, so there exist infinitely many row-stochastic matrices $A + \tilde A$ with $\tilde A T = 0$ and $\tilde A \mathbf{1} = 0$ that yield exactly the same output. The construction works because softmax rows are strictly positive, so small perturbations in the null space of the augmented matrix $[T, \mathbf{1}]$ stay inside the probability simplex. Consequently, raw attention weights are not directly interpretable, and the paper defines effective attention $A_\perp = A - \mathrm{Proj}_{LN(T)} A$ as the part of attention that actually influences the output.

Load-bearing premise

The proof assumes that any row-stochastic perturbation in the null space of $[T,\mathbf{1}]$ is a valid attention matrix a real head can produce; in particular it never checks that $A+\tilde A$ can be written as $\mathrm{softmax}(Q'K'^T/\sqrt{d_q})$ with $Q'K'^T$ of rank at most $d_q$, which is required for actual transformer attention weights.

Editorial extensions

If this is right

  • When the sequence length exceeds the attention head dimension, a growing part of the raw attention matrix has no effect on the output, so attention-based explanations become less reliable as inputs get longer.
  • Effective attention can change interpretive conclusions, for example removing attention peaks on structural tokens like [SEP] and exposing meaningful long-range links such as coreference between distant pronouns.
  • Tokens remain largely identifiable from their contextual embeddings through all layers, with a linear projection and cosine similarity recovering about 93% of tokens in the last layer, so treating hidden embeddings as standing for their input words is a reasonable first approximation.
  • Context mixing is strong but orderly: the original token's contribution decreases monotonically with depth, the original token usually remains the largest contributor, and context is mostly local, with long-range contributions appearing predominantly in late layers.
  • The proposed gradient-based attribution method can quantify token mixing in any transformer architecture, making the analysis independent of a particular model or task.

Reading between the lines

Editorial extensions of the paper, not claims the author makes directly.

  • A direct test of the theorem's reach: the paper only proves the alternative attention matrices stay in the probability simplex, so checking whether they are actually realizable as softmax of a low-rank query-key product would show how far the non-identifiability claim extends to real transformers.
  • The finding that context is mostly local suggests that explicit locality biases, such as distance masks, may be redundant for language transformers because the model learns local mixing on its own; comparing attribution profiles with and without such masks would test this.
  • Effective attention could serve as a head-pruning criterion, since heads whose effective attention is near zero contribute little to the output; this would connect the paper's diagnostic to model compression.
  • The angle-versus-magnitude result implies that interventions that preserve embedding direction, such as certain fine-tuning or adversarial perturbations, may preserve token identity better than those that change magnitude; this is a testable design principle.
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Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, and a circularity audit.

Referee Report

2 major / 6 minor

Summary. This paper analyzes identifiability in Transformer self-attention. The main theoretical result (Sections 3.2–3.3) claims that when the input sequence length ds exceeds the attention head dimension dv, the attention weights A of a head are not identifiable from the head output: infinitely many row-stochastic matrices A+à yield the same output because the rows of à lie in the left null space of T=E W_V H. The paper proposes "effective attention" as the projection of A onto the orthogonal complement of this null space and argues that it is a better basis for attention-based explanations. The remaining sections report empirical studies on BERT: token identity can be recovered from contextual embeddings via learned nearest-neighbor maps, identity information is largely encoded in embedding angle, and a gradient-based "Hidden Token Attribution" method shows that context mixing is strong but predominantly local. The paper concludes that raw attention distributions are not directly interpretable and that the proposed tools improve interpretability.

Significance. If the non-identifiability theorem held for actual softmax attention weights, it would provide a clean theoretical counterpart to the empirical "attention is not explanation" literature and would justify the effective-attention tool. The rank-nullity calculation is correct, and the effective-attention idea is a useful diagnostic that does not depend on the theorem. The token-identifiability and attribution experiments are carefully designed, use multiple datasets, and give concrete, interpretable results; they are valuable even if the theorem is weakened. The paper also connects its findings to prior work in a balanced way. The main weakness is that the central theorem, as stated and proved, does not establish non-identifiability for the softmax-constrained attention weights actually used in Transformers, and the threshold in the abstract is too strong.

major comments (2)
  1. [§3.3, Eq. (7)] The proof of non-identifiability in §3.3 verifies only the simplex conditions (7a)–(7c) for A+Ã. Attention matrices in a Transformer are not arbitrary row-stochastic matrices: by Eq. (1), A = softmax(QK^T/√dq) for some Q,K ∈ R^{ds×dq}, so the logit matrix has rank at most dq. The constructed perturbation à is an element of LN([T,1]) scaled to satisfy à ≥ −A, but the paper never shows that A+à is realizable as softmax of a rank-≤dq logit matrix. This is a load-bearing gap: the softmax-realizable attention matrices form a lower-dimensional curved submanifold of the simplex (of dimension at most 2 ds dq − dq², up to row-constant invariances), while the constructed alternative attention matrices form an affine space of dimension ds(ds−dv−1); for small ds−dv the intersection with the softmax image can be empty. The central claim "attention weights are not identifiable" is therefore unproven for the actual attention weights defined in the paper. The authors should either construct Q',K' explicitly for their perturbations, or supply a transversality/dimension argument under explicit conditions, or restrict the claim to arbitrary row-stochastic matrices.
  2. [Abstract and §3.2 vs. §3.3] The abstract and §3.2 state that ds>dv is enough for non-identifiability, but the proof in §3.3 requires dim LN([T,1]) > 0, i.e., ds−dv>1. When ds=dv+1, the left null space of T is one-dimensional and its generator x generically satisfies x^T 1 ≠ 0; since any row perturbation must be a scalar multiple of x and must also have zero row sum, all scalars are forced to zero. Thus for generic T there is no non-identifiability in the simplex-constrained problem. A concrete instance is ds=3, dv=2, rank(T)=2: the only row-stochastic A' with A'T=AT is A'=A. The theorem's stated threshold is therefore false; the correct statement (still subject to the softmax realizability issue in the previous comment) requires ds−dv>1, not merely ds>dv. This correction affects the abstract, the introduction, and the conclusion.
minor comments (6)
  1. [§4] The formal definition of token identifiability as the existence of a classifier c with c(e_i^l)=x_i is vacuous without a restriction on c: for any finite set of labeled embeddings one can define a function (e.g., a partition of R^d) that achieves perfect recovery. The operational definition used in the experiments (nearest neighbor after a learned linear/MLP map) is meaningful; the formal definition should be stated in terms of that restricted class.
  2. [Appendix C.1] The text contains a dangling cross-reference: "The attribution method proposed in Section??" should refer to Section 5.
  3. [§6] In the Related Work section, "a theoretical proof of the identifiability of attention weights" should read "non-identifiability".
  4. [§5, Eq. (11)] The sum in Eq. (11) runs from k=0, while tokens are indexed from 1 in Section 2; clarify whether the index 0 corresponds to the [CLS] token.
  5. [§1 and §4.2] Typographical errors: "indentifiability" in the introduction and "identifiablity" in Section 4.2.
  6. [Appendix D] Typo: "datsets" in the opening paragraph of Appendix D.

Circularity Check

0 steps flagged · score 0.0 of 10

No circularity: the identifiability theorem is a self-contained linear-algebra proof; effective attention is an explicit projection, not a fitted prediction.

full rationale

The paper's central claim (Sections 3.2-3.3) is a self-contained mathematical derivation. Given T = E W_V H, the output of a head is A T; the paper studies the left null space of [T, 1] and shows that any row-stochastic perturbation in that null space yields the same output. No parameter is fitted and no external conclusion is assumed: the cited works (Bellman & Åström, Vaswani et al., Jain & Wallace) provide only background and related work, not load-bearing premises. The 'effective attention' construction in Section 3.4 is explicitly defined as A minus its projection onto LN(T), with Eq. 8 showing AT = A_perp T by construction; it is an openly stated diagnostic projection rather than a hidden prediction derived from itself. The empirical observation that, e.g., the [SEP] peak lies in the null-space component is a property of BERT's learned T and attention weights, not an input to the definition. The possible objection that the constructed perturbations are not shown to be softmax-realizable as low-rank logits is a correctness gap in the theorem's scope, not a circularity. The paper's derivation chain is therefore self-contained and exhibits no circular step.

Assumptions & free parameters 0 free parameters · 4 assumptions · 0 invented entities

The central proof relies on standard linear algebra (rank-nullity, rank submultiplicativity) and the fact that softmax outputs are strictly positive, which is standard. The load-bearing domain assumption is that alternative attention weights only need to satisfy simplex constraints, not the low-rank softmax realizability implicit in QK^T. The token identifiability experiments also assume that recovering the input embedding x_i implies recovering word identity, even though x_i includes positional and segment components.

assumptions (4)
  • standard math Rank-nullity theorem and rank inequalities rank(ABC) <= min(rank(A), rank(B), rank(C))
    Used in Sections 3.1-3.2 to bound rank(T) and derive the null space dimension.
  • standard math Softmax outputs are strictly positive elementwise
    Used in Section 3.3 to argue a small ball around zero in the null space satisfies condition (7c).
  • domain assumption Alternative attention matrices need only satisfy non-negativity and row-sum constraints; low-rank realizability as softmax(Q'K'^T) is not required
    Section 3.3 conditions (7a)-(7c) define validity without the rank-dq constraint on logits; this is load-bearing for the non-identifiability theorem.
  • domain assumption Gradient norm reflects causal contribution of input tokens to hidden embeddings
    Hidden Token Attribution in Section 5 and Eqs. (10)-(11) assumes the linear Taylor approximation of the network is adequate for quantifying information mixing; no ground truth validation is provided.

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Cite this review

Pith. "Pith review of On Identifiability in Transformers." pith.science (2026). https://pith.science/paper/MXKNR2CR

@misc{pith2026190804211,
  author       = {Pith},
  title        = {Pith review of: On Identifiability in Transformers},
  year         = {2026},
  howpublished = {\url{https://pith.science/paper/MXKNR2CR}},
  note         = {Machine review of arXiv:1908.04211}
}
read the original abstract

In this paper we delve deep in the Transformer architecture by investigating two of its core components: self-attention and contextual embeddings. In particular, we study the identifiability of attention weights and token embeddings, and the aggregation of context into hidden tokens. We show that, for sequences longer than the attention head dimension, attention weights are not identifiable. We propose effective attention as a complementary tool for improving explanatory interpretations based on attention. Furthermore, we show that input tokens retain to a large degree their identity across the model. We also find evidence suggesting that identity information is mainly encoded in the angle of the embeddings and gradually decreases with depth. Finally, we demonstrate strong mixing of input information in the generation of contextual embeddings by means of a novel quantification method based on gradient attribution. Overall, we show that self-attention distributions are not directly interpretable and present tools to better understand and further investigate Transformer models.

Figures

Figures reproduced from arXiv: 1908.04211 by the authors.

Figure 1
Figure 1. (a) Each point represents the Pearson correlation coefficient of effective attention and raw [PITH_FULL_IMAGE:figures/full_fig_p005_1.png] view at source ↗
Figure 2
Figure 2. (a) Identifiability of contextual word embeddings at different layers. Here, [PITH_FULL_IMAGE:figures/full_fig_p007_2.png] view at source ↗
Figure 3
Figure 3. (a) Contribution of the input token to the embedding at the same position. The orange line [PITH_FULL_IMAGE:figures/full_fig_p008_3.png] view at source ↗
Figures from the paper (39 more)
Figure 4
Figure 4. Figure 4: (a) Relative contribution per layer of neighbours at different positions. (b) Total contribu [PITH_FULL_IMAGE:figures/full_fig_p009_4.png]
Figure 5
Figure 5. Figure 5: Effective attention (a) vs. raw attention (b). (a) Each point represents the average effec [PITH_FULL_IMAGE:figures/full_fig_p014_5.png]
Figure 7
Figure 7. Figure 7: Train and test token identifiability rates for the linear perceptron and MLP. [PITH_FULL_IMAGE:figures/full_fig_p017_7.png]
Figure 8
Figure 8. Figure 8: Linear Perceptron trained to minimize L2 distance generalizing to all layers. [PITH_FULL_IMAGE:figures/full_fig_p018_8.png]
Figure 9
Figure 9. Figure 9: MLP trained to minimize L2 distance generalizing to all layers. [PITH_FULL_IMAGE:figures/full_fig_p018_9.png]
Figure 10
Figure 10. Figure 10: MLP trained to minimize cosine distance generalizing to all layers. [PITH_FULL_IMAGE:figures/full_fig_p019_10.png]
Figure 11
Figure 11. Figure 11: Token identifiability across single layers. These results are for non fine-tuned BERT on [PITH_FULL_IMAGE:figures/full_fig_p020_11.png]
Figure 12
Figure 12. Figure 12: Token identifiability across single layers, comparing non fine-tuned (dashed) BERT [PITH_FULL_IMAGE:figures/full_fig_p021_12.png]
Figure 13
Figure 13. Figure 13: Token identifiability across single layers, comparing non fine-tuned BERT (dashed) [PITH_FULL_IMAGE:figures/full_fig_p021_13.png]
Figure 14
Figure 14. Figure 14: Recovering neighbouring input tokens using [PITH_FULL_IMAGE:figures/full_fig_p022_14.png]
Figure 15
Figure 15. Figure 15: Recovering neighbouring input tokens using [PITH_FULL_IMAGE:figures/full_fig_p022_15.png]
Figure 16
Figure 16. Figure 16: Recovering neighbouring input tokens using [PITH_FULL_IMAGE:figures/full_fig_p023_16.png]
Figure 17
Figure 17. Figure 17: Recovering neighbouring input tokens using [PITH_FULL_IMAGE:figures/full_fig_p023_17.png]
Figure 18
Figure 18. Figure 18: Normalized total contribution to the [CLS] token (a) centered around [CLS] at position [PITH_FULL_IMAGE:figures/full_fig_p025_18.png]
Figure 19
Figure 19. Figure 19: [CLS]: Aggregates context from all tokens but more strongly from those around the first [PITH_FULL_IMAGE:figures/full_fig_p025_19.png]
Figure 20
Figure 20. Figure 20: he: Aggregates most context from the main verb of the sentence, ”said”. [PITH_FULL_IMAGE:figures/full_fig_p026_20.png]
Figure 21
Figure 21. Figure 21: said: Aggregates context mainly from its neighborhood, the main verb of the subordinate [PITH_FULL_IMAGE:figures/full_fig_p026_21.png]
Figure 22
Figure 22. Figure 22: fit: In the first layers it aggregates most context from its neighborhood and towards the [PITH_FULL_IMAGE:figures/full_fig_p026_22.png]
Figure 23
Figure 23. Figure 23: long: It is part of a composed adjective (long-term) and aggregates most of its context [PITH_FULL_IMAGE:figures/full_fig_p027_23.png]
Figure 24
Figure 24. Figure 24: strategy: Aggregates context from the word growth, which is the first one of the noun [PITH_FULL_IMAGE:figures/full_fig_p027_24.png]
Figure 25
Figure 25. Figure 25: [SEP]: This token that has no semantic meaning aggregates context mostly from [CLS] [PITH_FULL_IMAGE:figures/full_fig_p027_25.png]
Figure 26
Figure 26. Figure 26: Layer 1: Most token types are equally mixed and have already less than 35% median [PITH_FULL_IMAGE:figures/full_fig_p028_26.png]
Figure 27
Figure 27. Figure 27: Layer 2: Similar to the previous layer with less contribution over all and [SEP] behaving [PITH_FULL_IMAGE:figures/full_fig_p028_27.png]
Figure 28
Figure 28. Figure 28: Layer 3: Similar to layer 2 with decreasing contribution overall. [PITH_FULL_IMAGE:figures/full_fig_p028_28.png]
Figure 29
Figure 29. Figure 29: Layer 4: The original input contribution to [CLS] and [SEP] falls significantly. The trend [PITH_FULL_IMAGE:figures/full_fig_p029_29.png]
Figure 30
Figure 30. Figure 30: Layer 5: The trend started in the previous layer continues, with a reduction of internal [PITH_FULL_IMAGE:figures/full_fig_p029_30.png]
Figure 31
Figure 31. Figure 31: Layer 6: Similar behavior as in the previous layer with minor evolution. [PITH_FULL_IMAGE:figures/full_fig_p029_31.png]
Figure 32
Figure 32. Figure 32: Layer 7: Minor changes with respect to Layer 6. [PITH_FULL_IMAGE:figures/full_fig_p030_32.png]
Figure 33
Figure 33. Figure 33: Layer 8: At this point there is clearly a different behavior between the tokens with most [PITH_FULL_IMAGE:figures/full_fig_p030_33.png]
Figure 34
Figure 34. Figure 34: Layer 9: SEP changes increasing the contribution, while the rest stays similar. [PITH_FULL_IMAGE:figures/full_fig_p030_34.png]
Figure 35
Figure 35. Figure 35: Layer 10: The contribution evolves with the same pattern as in previous layers. [PITH_FULL_IMAGE:figures/full_fig_p031_35.png]
Figure 36
Figure 36. Figure 36: Layer 11:The contribution evolves with the same pattern as in previous layers. [PITH_FULL_IMAGE:figures/full_fig_p031_36.png]
Figure 37
Figure 37. Figure 37: Layer 12: Finally, nouns, verbs, adjectives, adverbs, receive more contribution from their [PITH_FULL_IMAGE:figures/full_fig_p031_37.png]
Figure 38
Figure 38. Figure 38: Identifiability of contextual word embeddings at different layers on CoLA. [PITH_FULL_IMAGE:figures/full_fig_p032_38.png]
Figure 39
Figure 39. Figure 39: Identifiability of contextual word embeddings at different layers on a the first 500 sen [PITH_FULL_IMAGE:figures/full_fig_p033_39.png]
Figure 40
Figure 40. Figure 40: (a) Contribution of the input token to the embedding at the same position. (b) Percentage [PITH_FULL_IMAGE:figures/full_fig_p034_40.png]
Figure 41
Figure 41. Figure 41: (a) Relative contribution per layer of neighbours at different positions. (b) Total contri [PITH_FULL_IMAGE:figures/full_fig_p034_41.png]
Figure 42
Figure 42. Figure 42: (a) Contribution of the input token to the embedding at the same position. (b) Percentage [PITH_FULL_IMAGE:figures/full_fig_p035_42.png]
Figure 43
Figure 43. Figure 43: (a) Relative contribution per layer of neighbours at different positions. (b) Total contri [PITH_FULL_IMAGE:figures/full_fig_p035_43.png]

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    @open @close @open @close and [1] URL: #1 \@ifundefined chapter * \@mkboth \@ifxundefined @sectionbib * \@mkboth * \@mkboth\@gobbletwo \@ifclassloaded amsart * \@ifclassloaded amsbook * \@ifxundefined @heading @heading NAT@ctr thebibliography [1] @ \@biblabel @NAT@ctr \@bibset...

Pith tools

Reviewed August 14, 2026 · model on record in the stance chip above.