Understanding a model and its learning mechanisms in depth requires identifying when its internal structures become useful, rather than simply looking at the final state. We study this through concept dynamics: at each layer and checkpoint, we decompose activations, select sparse soft masks, and inject masked reconstructions into the model. Concept analysis is therefore tested functionally: a mask is useful only insofar as it preserves a target under intervention. We compare sufficiency for activation reconstruction, linear decodability, true downstream preservation, and checkpoint transfer under learned alignment. The framework treats decomposition assumptions as hypotheses rather than interpretability guarantees, monitoring functional sufficiency across checkpoints and source-to-final reconstructability under learned alignment. At the shared fixed-penalty operating point across seven models, downstream masks retain substantially less soft mass than reconstruction masks; predictive-distribution shifts remain small.
Figures & tables
Figure 1: Functional sufficiency across checkpoints and layers. A–C: held-out ΔKL for reconstruction, fixed-head (“linearized” in artwork), and downstream selection, using ordinal checkpoint and layer ranks. D: paired downstream-minus-reconstruction occupancy and ΔKL changes. E: learned-alignment source-to-final reconstructability. Curves and bands are hierarchical medians and IQRs over seven model summaries.
Objective
Soft (%)
Rel. KL
Acc. ↓
NMSE
Reconstruction
73.0
0.009
0.37
0.215
Fixed-head
83.4
0.014
0.47
0.270
Downstream
6.6
0.020
0.80
0.959
Transfer
28.6
0.093
2.68
1.006
Table 1: Seven-model operating points.
Figure 2: Model-specific temporal and depth profiles. Cells are within-model median Spearman correlations over methods and the complementary axis. The horizontal rule separates autoregressive and masked models; differences remain descriptive because their data, tokenizers, objectives, and recipes also differ.
Table A1: Executed model, checkpoint, layer, and candidate-budget grid. Checkpoints denote optimizer updates, not a common number of tokens or common training fraction.
Model
Objective
Cells
Ksoft/Kmax (%)
Khard/Kmax (%)
Rel. KL
Rel. CE
Acc. damage (pp)
NMSE
Empty (%)
Pythia-70M
Rec.
192
84.2
100.0
0.032
+0.021
1.13
0.167
0.0
Lin.
192
89.0
94.2
0.034
+0.023
1.32
0.258
0.0
Down.
192
46.6
47.1
0.051
+0.039
2.10
0.530
0.0
Transfer
192
43.5
43.0
0.169
+0.117
5.37
0.886
12.5
Pythia-160M
Rec.
192
75.2
99.5
0.016
+0.012
0.70
0.215
0.0
Lin.
192
84.7
90.1
0.015
+0.013
0.75
0.264
0.0
Appendix
Table A2: Model-resolved behavioral and mask profiles for each monitoring objective.
A−B
Pairs
log10(ΔKLA/ΔKLB)
ΔKsoft/Kmax
Δ rel. CE
Δ acc. damage (pp)
A dom. (%)
B dom. (%)
Trade-off (%)
Rec. − Lin.
1,344
−0.000 [ −0.158 , +0.072 ]
−0.081 [ −0.125 , +0.136 ]
+0.000 [ −0.003 , +0.000 ]
−0.033 [ −0.200 , +0.033 ]
6.8
2.7
90.2
Rec. − Down.
1,344
−0.404 [ −0.525 , −0.324 ]
+0.444 [ +0.368 , +0.474 ]
−0.007 [ −0.013 , −0.005 ]
−0.350 [ −0.592 , −0.283 ]
2.2
4.5
93.2
Lin. − Down.
1,344
−0.354 [ −0.432 , −0.175 ]
+0.486 [ +0.251 , +0.599 ]
−0.013 [ −0.014 , −0.003 ]
−0.550 [ −0.584 , −0.150 ]
0.4
6.6
93.0
Appendix
Table A3: Exact same-checkpoint contrasts among reconstruction, linear, and downstream monitoring objectives.
Table 7
Figure A1: Target-specific sparsity–fidelity contrasts. Same-checkpoint panels pair each model with reconstruction at the same method, checkpoint, and layer. The horizontal coordinate is the change in normalized soft cardinality; the vertical coordinate is the median log-ratio of held-out distribution shift. The separated transfer panel pairs source coordinates evaluated in the final model with reconstruction at the source and is contextual rather than an equal-estimand target comparison.
Figure A2: Within-model evolution of selected-mask intervention effects. At each checkpoint, ΔKL is summarized over decomposition methods and tracked layers and divided by the initial-checkpoint median. The horizontal axis is scheduled-checkpoint rank; connected points are not independent replicates.
Figure A3: Layer-resolved checkpoint dynamics. Each cell is the median across decomposition methods of the within-layer Spearman correlation between the eight common-grid checkpoint ranks and log10ΔKL . Positive values indicate a larger selected-mask effect at later scheduled checkpoints; they do not imply a monotone path. Transfer includes learned self-alignment as its final point and cannot be read as a continuity trend.
Figure A4: Within-family size contrasts. Points are model-level medians over the matched method, target, checkpoint-rank, and depth-rank grid. Kmax is clamp-determined and the sparsity penalty is not width-normalized.
Figure A5: Endpoint relocation across sampled depth ranks. A–C report final-minus-initial changes in the effect-weighted center for ΔKL , absolute relative ΔCE , and absolute ΔAcc . D–F report changes in normalized entropy support. Positive center values indicate movement toward later among the six sampled MLP outputs; positive support values indicate a more broadly distributed effect. Cells are medians over four decompositions. Transfer includes learned self-alignment and cannot be interpreted as a continuity trend.
Figure A6: Net change and directness on the scheduled checkpoint grid. Columns show log10ΔKL , normalized soft occupancy, and log10 NMSE. The upper row reports endpoint change and the lower row reports the ratio of endpoint displacement to total adjacent variation, summarized within model and target over method–layer strata. Transfer includes its learned self-alignment endpoint and should not be compared directly with the three same-checkpoint targets.
Model
Objective
Δlog10KL
Eff. KL
ΔKs/Kmax
Eff. Ks
Δlog10NMSE
Eff. NMSE
Δ KL center
Δ KL support
Pythia-70M
Rec.
+0.67
0.87
−0.01
0.37
+0.00
0.32
+0.27
+0.27
Lin.
+0.90
0.96
−0.14
0.52
+0.33
0.55
+0.25
+0.16
Down.
+0.39
0.84
+0.32
0.75
+0.14
0.36
−0.03
−0.07
Pythia-160M
Rec.
+0.74
1.00
−0.04
0.56
+0.03
0.23
+0.34
+0.27
Lin.
+0.91
0.98
−0.13
0.37
+0.34
0.55
+0.21
+0.19
Down.
+0.43
0.66
+0.25
0.56
−0.13
0.44
+0.13
−0.04
Appendix
Table A6: Same-checkpoint temporal paths and relocation of selected-mask effects across the tracked layers.
Model
Method
Rec.
Lin.
Down.
Transfer
Rel. KL
Ks/Kmax (%)
Rel. KL
Ks/Kmax (%)
Rel. KL
Ks/Kmax (%)
Rel. KL
Ks/Kmax (%)
Pythia-70M
SVD
0.024
61.2
0.018
70.5
0.038
44.3
0.160
31.2
ICA
0.018
83.3
0.016
91.7
0.036
58.3
0.106
58.4
NMF
0.077
100.0
0.091
95.7
0.115
36.1
0.948
0.2
SemiNMF
0.033
92.0
0.047
84.8
0.062
52.4
0.127
62.5
Pythia-160M
SVD
0.013
50.1
0.010
68.2
0.031
17.3
0.095
21.3
Appendix
Table A7: Model- and decomposition-resolved intervention behavior for all four monitoring objectives.
Figure A7: Pareto dominance by decomposition. A method dominates a competitor in a matched cell when it has lower held-out ΔKL and no larger Ksoft/Kmax . Entries are medians across the seven model-level dominance rates.
Figure A8: Transfer endpoint change by decomposition. Cells give the median paired log10(ΔKLself/ΔKLearliest\mbox−source) across tracked layers. The numerator is a learned self-alignment endpoint; negative values therefore indicate lower held-out transfer KL there, not monotonic improvement in cross-checkpoint transfer.
Figure A9: Gradient-score enrichment of nonempty hard masks. Enrichment is the selected share of τ or ω divided by Khard/Kmax . Points are within-model medians, and segments pair reconstruction and downstream selection. Here ω is the squared mean signed gate gradient, not a realized parameter update.
Model
Objective
Valid
Excl.
Kh/Kmax (%)
Energy overlap
ω overlap
τ mass
ω mass
τ enrich.
ω enrich.
Pythia-70M
Rec.
192
0
100.0
1.00
1.00
1.00
1.00
1.00 ×
1.00 ×
Lin.
192
0
94.2
0.95
0.94
0.99
1.00
1.03 ×
1.04 ×
Down.
192
0
47.1
0.65
0.58
0.74
0.93
1.26 ×
1.47 ×
Transfer
168
24
51.2
0.72
0.57
0.53
0.51
1.05 ×
1.05 ×
Pythia-160M
Rec.
192
0
99.5
1.00
1.00
1.00
1.00
1.01 ×
1.01 ×
Lin.
192
0
90.1
0.94
0.91
0.98
1.00
1.04 ×
1.06 ×
Appendix
Table A8: Saved score aggregates of genuine nonempty hard selections.
Figure A10: Geometry, gradient salience, and mean signed gate-gradient signal. A: reconstruction NMSE against held-out ΔKL . B: within-cell rank associations of energy with τ and of τ with ω . C: 1−∑iωi/∑iτi across scheduled checkpoints. Under the local first-order gate approximation, ω is the component that persists under example averaging, not a realized training gradient or parameter update. Shading summarizes model-level heterogeneity, not sampling uncertainty.
Model
ρ(E,τ)
Top-decile overlap (%)
Top-10-concept τ mass (%)
Pythia-70M
+0.87
76.9
41.6
Pythia-160M
+0.89
74.4
32.4
Pythia-410M
+0.85
69.2
30.2
OLMo-1B
+0.90
73.3
41.2
EuroBERT-210M
+0.92
82.1
25.7
EuroBERT-610M
+0.87
75.9
28.0
Appendix
Table A9: Association between activation energy and supervised-gradient salience.
Figure A11: Same-budget gate-score control. Colored curves are SVD layer-median trajectories for both reconstruction (dashed circles) and downstream (solid squares) selection in each model; faint gray curves are non-SVD method-median robustness summaries. Left panels show selected-minus-energy-head mass and right panels show efficiency relative to the exact additive top- k score oracle, for τ (top) and ω (bottom). The progress axis is scheduled-checkpoint rank; empty selections and zero-total masses are excluded.
Model
Valid
Ghead(τ)
Ghead(ω)
Emass(τ)
Emass(ω)
Ghead(τ)>0 (%)
Ghead(ω)>0 (%)
Pythia-70M
192
−0.051
−0.026
0.909
0.938
0.5
8.3
Pythia-160M
189
−0.087
−0.054
0.767
0.781
3.2
9.5
Pythia-410M
168
−0.077
−0.089
0.725
0.724
6.0
14.9
OLMo-1B
151
−0.030
−0.041
0.742
0.410
8.6
15.2
EuroBERT-210M
167
−0.002
−2.22×10−16
0.991
0.983
19.8
40.1
EuroBERT-610M
172
−9.28×10−4
−5.06×10−5
0.982
0.944
20.9
34.3
Appendix
Table A10: Downstream selections versus equal-cardinality activation-energy heads and exact additive score oracles.
Figure A12: SVD energy concentration and supervised-gradient coverage. Circles and arrowheads denote the earliest and final common-grid checkpoints. Coordinates are architecture-group medians at each of six relative layer ranks: horizontal position is normalized SVD energy effective number and vertical position is the energy-ranked prefix needed to capture 90% of τ . Color gives the geometric-median downstream ΔKLfinal/ΔKLearly ratio. The vertical coordinate is an ordering prefix, not a subspace dimension.
Figure A13: Endpoint energy–occupancy phase portrait. A–B show faint SVD model–layer trajectories and thick within-model layer medians, relating normalized energy effective number to reconstruction or downstream soft occupancy. C plots the endpoint contrasts A and B ; marker size encodes relative depth, shape encodes model, and color encodes the normalized downstream ΔKL change L defined above. The right panel gives decomposition medians as a robustness summary. Occupancy is retained capacity, not dimensionality.
Figure A14: Candidate-budget diagnostic. Distributions show raw TwoNN estimates divided by the implementation’s lower clamp. Every value lies below one, so the clamped estimate determines every executed budget.
Figure A15: Behavioral-monitor agreement within temporal strata. A–C give model-level medians of within-method/layer Spearman correlations over eight scheduled checkpoints for predictive-distribution shift, relative target-token CE damage, and target-token accuracy damage. D reports macro-averaged CE–accuracy sign agreement, disagreement, and exact ties. Transfer is visually separated, includes learned self-alignment, and is not a continuity trend. Cells are structured repeated measurements, not IID replicates.
Figure A16: Soft-gate and hard-mask threshold diagnostics. A reports the median absolute difference between normalized soft and hard cardinality. B separates all empty hard masks from the subset whose soft cardinality is at least one. C shows the smallest selected gate’s margin above 0.5 for nonempty hard masks, by target and decomposition. Together the panels explain how a continuous operating point maps to the reported hard set.
Large language model (LLM) interpretability studies how internal representations and computations produce outputs, and how they can be explained or controlled.