Dictionary Based Pattern Entropy for Causal Direction Discovery
Authors: Harikrishnan N B, Shubham Bhilare, Aditi Kathpalia, Nithin Nagaraj
Organizations: Department of Computer Science and Information Systems, BITS Pilani K K Birla Goa Campus, NH 17B, Bypass, Road, Zuarinagar, 403726, Goa, India · Department of Applied Mechanics and Biomedical Engineering, Indian Institute of Technology Madras, IIT P.O., Chennai 600036, India · Complex Systems Programme, National Institute of Advanced Studies, IISc Campus, Bengaluru, 560012, Karnataka, India
Discovering causal direction from temporal observational data is particularly challenging for symbolic sequences, where functional models and noise assumptions are often unavailable. We propose a novel \emph{Dictionary Based Pattern Entropy (DPE)} framework that infers both the direction of causation and the specific subpatterns driving changes in the effect variable. The framework integrates Algorithmic Information Theory (AIT) and Shannon Information Theory. Causation is interpreted as the emergence of compact, rule based patterns in the candidate cause that systematically constrain the effect. DPE constructs direction-specific dictionaries and quantifies their influence using entropy-based measures, enabling a principled link between deterministic pattern structure and stochastic variability. Causal direction is inferred via a minimum-uncertainty criterion, selecting the direction exhibiting stronger and more consistent pattern-driven organization. As summarized in Table 7, DPE consistently achieves reliable performance across diverse synthetic systems, including delayed bit-flip perturbations, AR(1) coupling, 1D skew-tent maps, and sparse processes, outperforming or matching competing AIT-based methods (ETCE, ETCP, LZP). In biological and ecological datasets, performance is competitive, while alternative methods show advantages in specific genomic settings. Overall, the results demonstrate that minimizing pattern level uncertainty yields a robust, interpretable, and broadly applicable framework for causal discovery.
Figures & tables
Table 1: Illustration of sliding and XNOR comparison to extract common subsequences with consecutive matches highlighted in red.
Pattern
Change Count
No Change Count
Ratio
01
4
5
0.444
011
1
4
0.200
0110
0
2
0.000
011101
2
0
1.000
11
1
8
0.111
110
0
5
0.000
Table 2: Pattern statistics showing the number of changes, no-changes, and the ratio (From X→Y ).
Pattern
Change Count
No Change Count
Ratio
00
10
11
0.476
000
13
3
0.8125
10
3
1
0.75
Table 3: Pattern statistics showing the number of changes, no-changes, and the ratio (From Y→X ).
Pattern ( p )
Ratio ( r )
Weight ( Wp )
Binary Entropy Hb(rp) (bits)
Weighted Entropy Hw(p) (bits)
01
0.444
0.310
0.991
0.307
011
0.200
0.179
0.722
0.129
0110
0.000
0.074
0.000
0.000
011101
1.000
0.080
0.000
0.000
11
0.111
0.310
0.503
0.156
110
0.000
0.179
0.000
0.000
Table 4: Entropy and Weights for Patterns (From X→Y )
Pattern ( p )
Ratio ( r )
Weight ( Wp )
Binary Entropy Hb(rp) (bits)
Weighted Entropy Hw(p) (bits)
00
0.476
0.724
0.999
0.723
000
0.8125
0.571
0.696
0.397
10
0.750
0.138
0.811
0.112
Average Weighted Entropy HˉY→X
0.411
Table 5: Entropy and Weights for Patterns (From Y→X )
Figure 1: Directed network of symbolic patterns illustrating deterministic structure between X and Y . Nodes represent distinct substrings extracted from the driving sequence, and edges encode their weighted entropy with respect to the target sequence. A weighted entropy value close to 0 indicates that the pattern induces highly deterministic transition behavior in the target, whereas larger values indicate increasing uncertainty in the induced transitions. The figure displays both directions, X→Y and Y→X , enabling comparison of directional determinism.
Figure 2: Effect of delayed bit-flip on causal direction detection: accuracy versus bit-flip delay for DPE , ETCP , ETCE , and LZP .
Figure 8
Figure 5: Sparse processes: comparison of accuracy for DPE , ETCE , ETCP , and LZP across varying sparsity levels ( k ).
Figure 10
Figure 8: Genomic causal analysis of SARS-CoV-2: Comparative summary of DPE , ETCE , ETCP , and LZP sensitivity to global (RS) vs. local (CW) evolutionary drivers.
Figure 9: Population dynamics of the predator (Didinium nasutum) and prey (Paramecium aurelia).
Model
Direction
Strength
Pred → Prey
Prey → Pred
DPE
Pred → Prey
0.1125
0.1700
0.2825
ETCP
Pred → Prey
1.0000
0.0000
1.0000
ETCE
Pred → Prey
0.0778
0.8000
0.7222
LZP
Pred → Prey
5.0000
2.0000
7.0000
Table 6: Predator-Prey System: Comparative causal metrics for Predator-Prey interaction across different models.
Experiments
DPE
ETCE
ETCP
LZP
Delayed Bit-flip
✓
×
×
✓
AR(1) Coupling
✓
×
×
✓
1D Skew-tent Maps
✓
×
×
×
Sparse Processes
✓
×
×
×
SARS-CoV-2 (RS vs. CW)
×
×
✓
✓
Predator-Prey
✓
✓
✓
✓
Table 7: Summary of reliability across experiments. A check mark ( ✓ ) indicates that the framework achieves an average accuracy of ≥80% across trials for the corresponding experiment, while ( × ) indicates that it does not. The table reflects reliability, not exact performance values.
We introduce Causal Computational Asymmetry (CCA), a principle for causal direction identification based on optimization dynamics in which one neural network is trained to predict Y from X and another to predict X from Y, and the direction that converges faster is inferred to be causal. Under the additive noise model Y=f(X)+ε with ε⊥X and f nonlinear and injective, we establish a formal asymmetry: in the reverse direction, residuals remain statistically dependent on the input regardless of approximation quality, inducing a strictly higher irreducible loss floor and non-separable gradient noise in the optimization dynamics, so that the reverse model requires strictly more gradient steps in expectation to reach any fixed loss threshold; consequently, the forward (causal) direction converges in fewer expected optimization steps. CCA operates in optimization-time space, distinguishing it from methods such as RESIT, IGCI, and SkewScore that rely on statistical independence or distributional asymmetries, and proper z-scoring of both variables is required for valid comparison of convergence rates. On synthetic benchmarks, CCA achieves 26/30 correct causal identifications across six neural architectures, including 30/30 on sine and exponential data-generating processes. We further embed CCA into a broader framework termed Causal Compression Learning (CCL), which integrates graph structure learning, causal information compression, and policy optimization, with all theoretical guarantees formally proved and empirically validated on synthetic datasets.
Identification of causal directionality in bivariate numerical data is a fundamental research problem with important practical implications. This paper presents two alternative methods to identify direction of causation by considering conditional distributions: (1) Anticipated Asymmetric Geometries (AAG) and (2) Monotonicity Index (MI). The AAG method compares the actual conditional distributions to anticipated ones along two variables. Different comparison metrics, such as Pearson correlation, cosine distance, Hellinger distance, Jaccard index, Jeffreys divergence, K-L divergence, K-S distance, MAE, MSE, mutual information, and Wasserstein distance have been evaluated. Anticipated distributions have been projected as normal based on dual response statistics: mean and standard deviation. The MI method compares the calculated monotonicity indexes of the gradients of conditional distributions along two axes and exhibits count of gradient sign changes. Both methods assume stochastic properties of the bivariate data and exploit anticipated unimodality of conditional distributions of the effect. The proposed methods are straightforward and include only a limited number of hyperparameters that affect the accuracy of the identification. For a given set of hyperparameters, both the AAG and MI methods provide a unique, deterministic solution. To address sensitivity to hyperparameters, tuning has been done by utilizing a full factorial Design of Experiment. It turns out that the AAG method outperforms MI, achieving top weighted accuracies of 82.7% with simple tuning and 84.4% with size-adaptive tuning, compared with 81.6% for GRCI or 82.0% for CAREFL-H on the 99 pairs of the Tubingen real-world cause-effect examples. To evaluate the decisiveness of the identification method, a decision tree was fitted on the input data's symmetrical bivariate statistics to detect misclassified cases.
Causal discovery has shifted from data-centric methods to hybrid strategies that integrate semantic knowledge from experts or large language models (LLMs). Such external information is vital for identifying causal structures beyond the Markov Equivalence Class (MEC), which data alone cannot resolve. However, expert availability is often limited, and LLMs frequently misidentify causal directions in specialized domains. To overcome such shortcomings, we propose a tag-based approach that leverages semantically meaningful labels while deriving causal directionality directly from data. Using variable-level tag assignments from available sources (e.g., LLMs), our tags for DAGs method learns from identifiable data structures to extract higher-level causal relations. These are then used to orient undirected edges, enabling causal discovery to move beyond the MEC without reliance on fallible external knowledge.
Florian Peter Busch, Moritz Willig, Florian Guldan +2
Computer Science Department, Technical University of Darmstadt · Hessian Center for AI (hessian.AI) · German Research Center for AI (DFKI) +2