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Oct 16

The kernel-block rank profiles of the $\mathbb{Z}_2\mathbb{Z}_4$-linear and the $\mathbb{Z}_{2^s}$-linear Hadamard codes, and a complete classification of the $\mathbb{Z}_2\mathbb{Z}_4\mathbb{Z}_8$-linear Hadamard codes

The kernel of a binary code containing the zero word partitions the binary coordinates into blocks, two coordinates lying in the same block when every kernel word takes the same value in both, and the kernel-block rank profile is the multiset of the dimensions of its linear span punctured on those blocks. For the family H^{t_1,t_2,t_3} of Z_2Z_4Z_8-linear Hadamard codes, this invariant is known explicitly and gives a complete classification of the family. In this paper, we compute it for the Z_2Z_4-linear and Z_{2^s}-linear Hadamard families with which those codes are compared, and we prove that it is constant for every nonlinear Z_2Z_4-linear Hadamard code and for every nonlinear Z_{2^s}-linear Hadamard code bar H^{a_1,dots,a_s} with sgeq2. The second statement is obtained without any rank formula, by exhibiting coordinate permutations that preserve the code and act transitively on its kernel blocks, which makes the argument uniform in s. We also prove a descent theorem: if bar H^{a_1,dots,a_s} is nonlinear and a_1geq2, then the code punctured on one kernel block is the Z_{2^{s-1}}-linear Hadamard code bar H^{a_1,dots,a_{s-1}}. Consequently, the constant local rank equals rank(bar H^{a_1,dots,a_{s-1}}) and is at least t-κ+2, where 2^t is the length and κ the kernel dimension. These results separate every nonlinear Z_2Z_4Z_8-linear Hadamard code from every Z_4-linear, Z_2Z_4-linear and Z_{2^s}-linear Hadamard code of the same length, except for the single infinite family H^{1,1,t-4} and bar H^{2,0,t-5} with tgeq5. The members of this infinite family agree in the rank, kernel dimension and the kernel-block rank profile, but a two-block refinement separates them.

  • 1 authors
·
Sep 9

AmbiModBench: Benchmarking Gene Perturbation Prediction Beyond Shared Responses

Predicting cellular responses to genetic perturbations helps prioritize experiments in single-cell genomics, where exhaustive measurement is infeasible. While computational models increasingly predict these responses, three evaluation deficiencies obscure what their scores demonstrate. First, absolute metrics cannot separate target-specific predictions from a shared background response. Second, common metrics remain high under gene shuffling, so gene-level accuracy is never verified. Third, a score at one training size says nothing about coverage, which depends on representation-space proximity and response-constraining power. We propose AmbiModBench, a specificity-aware, gene-resolved and coverage-aware benchmark. It pairs every score with a training-mean reference fitted on the same split, screens each readout by gene-coordinate permutation, and links embedding distance to response variation. Across K562, RPE1 and Norman, strong absolute scores largely reflect shared background rather than target-specific learning. Widely used readouts track response magnitude distributions rather than the affected genes. Detectable gain follows representation-space coverage rather than training-set size. Nonetheless, on RPE1 the protocol yields a reproducible target-specific gain across five additional splits and three gene selections, which absolute scores alone cannot distinguish from shared background.

  • 5 authors
·
Sep 25

Analysis of Linear Mode Connectivity via Permutation-Based Weight Matching

Recently, Ainsworth et al. showed that using weight matching (WM) to minimize the L_2 distance in a permutation search of model parameters effectively identifies permutations that satisfy linear mode connectivity (LMC), in which the loss along a linear path between two independently trained models with different seeds remains nearly constant. This paper provides a theoretical analysis of LMC using WM, which is crucial for understanding stochastic gradient descent's effectiveness and its application in areas like model merging. We first experimentally and theoretically show that permutations found by WM do not significantly reduce the L_2 distance between two models and the occurrence of LMC is not merely due to distance reduction by WM in itself. We then provide theoretical insights showing that permutations can change the directions of the singular vectors, but not the singular values, of the weight matrices in each layer. This finding shows that permutations found by WM mainly align the directions of singular vectors associated with large singular values across models. This alignment brings the singular vectors with large singular values, which determine the model functionality, closer between pre-merged and post-merged models, so that the post-merged model retains functionality similar to the pre-merged models, making it easy to satisfy LMC. Finally, we analyze the difference between WM and straight-through estimator (STE), a dataset-dependent permutation search method, and show that WM outperforms STE, especially when merging three or more models.

  • 3 authors
·
Feb 6, 2024

Intervention anchors and scientific verification in synthetic vascular predictive representations

Complete orthogonal predictive coordinates do not by themselves bind a latent direction to a named intervention. We present a mathematical and synthetic audit motivated by vascular device-vessel suitcordance. Capacity-matched least-squares predictors were exactly equivalent under complete fixed output transforms, whereas an anchor-only observer recovered interpretations only within the span of known perturbation signatures. Six three-dimensional configurations across 64 seeds gave a maximum paired prediction discrepancy of 6.7e-15 but a median untransported edit error of 1.513. Coordinate transport removed that error. Noisy and weak anchors constrained calibration stability, and changing the representation basis required recalibration or verified transport. Across 256 additional fits in dimensions 3-24, prediction equivalence persisted within 4.0e-15. We then evaluated nine deliberate runnable fault classes across 64 seeds. All 576 faulty executions completed, but each violated at least one reconstruction, prediction, delivered-edit or scope contract; all 320 valid control records passed. Repeating a faulty implementation gave exact self-agreement despite error against the separately computed simulator expectation. For one omitted-direction defect, probe coverage followed its analytic law, and rank-aware abstention protected unsupported interpretations. Scalar-noise experiments exposed both missed weak faults and excessive rejection under narrow relative tolerances. These controls provide an executable separation of prediction, semantic support and scientific acceptance. They are synthetic numerical audits, not clinical validation, neural JEPA-Anything replication, agent learning or patient treatment-effect estimation.

  • 7 authors
·
Oct 7

Exact Learning of Permutations for Nonzero Binary Inputs with Logarithmic Training Size and Quadratic Ensemble Complexity

The ability of an architecture to realize permutations is quite fundamental. For example, Large Language Models need to be able to correctly copy (and perhaps rearrange) parts of the input prompt into the output. Classical universal approximation theorems guarantee the existence of parameter configurations that solve this task but offer no insights into whether gradient-based algorithms can find them. In this paper, we address this gap by focusing on two-layer fully connected feed-forward neural networks and the task of learning permutations on nonzero binary inputs. We show that in the infinite width Neural Tangent Kernel (NTK) regime, an ensemble of such networks independently trained with gradient descent on only the k standard basis vectors out of 2^k - 1 possible inputs successfully learns any fixed permutation of length k with arbitrarily high probability. By analyzing the exact training dynamics, we prove that the network's output converges to a Gaussian process whose mean captures the ground truth permutation via sign-based features. We then demonstrate how averaging these runs (an "ensemble" method) and applying a simple rounding step yields an arbitrarily accurate prediction on any possible input unseen during training. Notably, the number of models needed to achieve exact learning with high probability (which we refer to as ensemble complexity) exhibits a linearithmic dependence on the input size k for a single test input and a quadratic dependence when considering all test inputs simultaneously.

  • 3 authors
·
Feb 23, 2025

Knowledge Graph Embedding by Normalizing Flows

A key to knowledge graph embedding (KGE) is to choose a proper representation space, e.g., point-wise Euclidean space and complex vector space. In this paper, we propose a unified perspective of embedding and introduce uncertainty into KGE from the view of group theory. Our model can incorporate existing models (i.e., generality), ensure the computation is tractable (i.e., efficiency) and enjoy the expressive power of complex random variables (i.e., expressiveness). The core idea is that we embed entities/relations as elements of a symmetric group, i.e., permutations of a set. Permutations of different sets can reflect different properties of embedding. And the group operation of symmetric groups is easy to compute. In specific, we show that the embedding of many existing models, point vectors, can be seen as elements of a symmetric group. To reflect uncertainty, we first embed entities/relations as permutations of a set of random variables. A permutation can transform a simple random variable into a complex random variable for greater expressiveness, called a normalizing flow. We then define scoring functions by measuring the similarity of two normalizing flows, namely NFE. We construct several instantiating models and prove that they are able to learn logical rules. Experimental results demonstrate the effectiveness of introducing uncertainty and our model. The code is available at https://github.com/changyi7231/NFE.

  • 3 authors
·
Sep 30, 2024

Finding Kissing Numbers with Game-theoretic Reinforcement Learning

Since Isaac Newton first studied the Kissing Number Problem in 1694, determining the maximal number of non-overlapping spheres around a central sphere has remained a fundamental challenge. This problem is the local analogue of Hilbert's 18th problem, bridging geometry, number theory, and information theory. Although significant progress has been made through lattices and codes, the irregularities of high-dimensional geometry, dimensional structure variability, and combinatorial explosion beyond Go limit the scalability and generality of existing methods. Here we model the problem as a two-player matrix completion game and train the reinforcement learning system, PackingStar, to play the games. The matrix entries represent pairwise cosines of sphere center vectors. One player fills entries while another corrects suboptimal ones to improve exploration quality, cooperatively maximizing the matrix size, corresponding to the kissing number. These matrices are decomposed into representative substructures, providing diverse bases and structural constraints that steer subsequent games and make extremely large spaces tractable. PackingStar surpasses records from dimensions 25 to 31 and sets new lower bounds for generalized kissing numbers under various angular constraints. It achieves the first breakthrough beyond rational structures from 1971 in 13 dimensions and discovers over 6000 new structures in other dimensions. Notably, some configurations challenge long-held antipodal paradigms, revealing algebraic correspondences with finite simple groups as well as geometric relationships across dimensions. Inspired by these patterns, humans devised further improved constructions. These results demonstrate AI's power to explore high-dimensional spaces beyond human intuition via extreme-scale reinforcement learning and open new pathways for the Kissing Number Problem and broader geometry research.

  • 9 authors
·
Feb 10

CayleyPy Growth: Efficient growth computations and hundreds of new conjectures on Cayley graphs (Brief version)

This is the third paper of the CayleyPy project applying artificial intelligence to problems in group theory. We announce the first public release of CayleyPy, an open source Python library for computations with Cayley and Schreier graphs. Compared with systems such as GAP and Sage, CayleyPy handles much larger graphs and performs several orders of magnitude faster. Using CayleyPy we obtained about 200 new conjectures on Cayley and Schreier graphs, focused on diameters and growth. For many Cayley graphs of symmetric groups Sn we observe quasi polynomial diameter formulas: a small set of quadratic or linear polynomials indexed by n mod s. We conjecture that this is a general phenomenon, giving efficient diameter computation despite the problem being NP hard. We propose a refinement of the Babai type conjecture on diameters of Sn: n^2/2 + 4n upper bounds in the undirected case, compared to previous O(n^2) bounds. We also provide explicit generator families, related to involutions in a square with whiskers pattern, conjectured to maximize the diameter; search confirms this for all n up to 15. We further conjecture an answer to a question posed by V M Glushkov in 1968 on directed Cayley graphs generated by a cyclic shift and a transposition. For nilpotent groups we conjecture an improvement of J S Ellenberg's results on upper unitriangular matrices over Z/pZ, showing linear dependence of diameter on p. Moreover. Some conjectures are LLM friendly, naturally stated as sorting problems verifiable by algorithms or Python code. To benchmark path finding we created more than 10 Kaggle datasets. CayleyPy works with arbitrary permutation or matrix groups and includes over 100 predefined generators. Our growth computation code outperforms GAP and Sage up to 1000 times in speed and size.

  • 49 authors
·
Sep 23, 2025

Correspondence Free Multivector Cloud Registration using Conformal Geometric Algebra

We present, for the first time, a novel theoretical approach to address the problem of correspondence free multivector cloud registration in conformal geometric algebra. Such formalism achieves several favorable properties. Primarily, it forms an orthogonal automorphism that extends beyond the typical vector space to the entire conformal geometric algebra while respecting the multivector grading. Concretely, the registration can be viewed as an orthogonal transformation (\it i.e., scale, translation, rotation) belonging to SO(4,1) - group of special orthogonal transformations in conformal geometric algebra. We will show that such formalism is able to: (i) perform the registration without directly accessing the input multivectors. Instead, we use primitives or geometric objects provided by the conformal model - the multivectors, (ii) the geometric objects are obtained by solving a multilinear eigenvalue problem to find sets of eigenmultivectors. In this way, we can explicitly avoid solving the correspondences in the registration process. Most importantly, this offers rotation and translation equivariant properties between the input multivectors and the eigenmultivectors. Experimental evaluation is conducted in datasets commonly used in point cloud registration, to testify the usefulness of the approach with emphasis to ambiguities arising from high levels of noise. The code is available at https://github.com/Numerical-Geometric-Algebra/RegistrationGA . This work was submitted to the International Journal of Computer Vision and is currently under review.

  • 2 authors
·
Jun 16, 2024

Cylindric plane partitions, Lambda determinants, Commutants in semicircular systems

This thesis is divided into three parts. The first part deals with cylindric plane partitions. The second with lambda-determinants and the third with commutators in semi-circular systems. For more detailed abstract please see inside. Cylindric plane partitions may be thought of as a natural generalization of reverse plane partitions. A generating series for the enumeration of cylindric plane partitions was recently given by Borodin. The first result of section one is a new bijective proof of Borodin's identity which makes use of Fomin's growth diagram framework for generalized RSK correspondences. The second result is a (q,t)-analog of Borodin's identity which extends previous work by Okada in the reverse plane partition case. The third result is an explicit combinatorial interpretation of the Macdonald weight occurring in the (q,t)-analog using the non-intersecting lattice path model for cylindric plane partitions. Alternating sign matrices were discovered by Robbins and Rumsey whilst studying λ-determinants. In the second part of this thesis we prove a multi-parameter generalization of the λ-determinant, generalizing a recent result by di Francesco. Like the original λ-determinant, our formula exhibits the Laurent phenomenon. Semicircular systems were first introduced by Voiculescu as a part of his study of von Neumann algebras. In the third part of this thesis we study certain commutator subalgebras of the semicircular system. We find a projection matrix with an interesting self-similar structure. Making use of our projection formula we given an alternative, elementary proof that the semicircular system is a factor.

  • 1 authors
·
Oct 25, 2021

Coxeter Condorcet domains

Condorcet domains are subsets of permutations that ensure pairwise majority voting yields acyclic outcomes, and they form an active area of research at the intersection of social choice theory and combinatorics. In this paper, we extend the theory of Condorcet domains to the broader setting of arbitrary finite Coxeter groups. The core contribution of our approach is the introduction of Condorcet root posets, defined on the chosen root systems. Notably, we establish a natural bijection between closed Condorcet domains and Condorcet root posets, which facilitates the study of Condorcet domains. Using this correspondence, we extend the median graph representation of closed Condorcet domains to arbitrary finite Coxeter groups, demonstrating that these domains can be characterized by the skeletons of their associated Condorcet root posets. These results are novel even in type A. Furthermore, these posets give a unified language that efficiently captures a wide range of desirable properties of Condorcet domains, such as being maximal, connected, peak-pit, and of tiling type. Using this framework, we strengthen and generalize several classical results: we establish that a maximal Condorcet domain is connected if and only if it is peak-pit; we prove that the tiling-type property is equivalent to the combination of being maximal and connected, and having maximal width; and we show that strictly positive voting profiles on connected Condorcet domains yield outcomes with only simple ties.

  • 2 authors
·
May 31

On composition and decomposition operations for vector spaces, graphs and matroids

In this paper, we study the ideas of composition and decomposition in the context of vector spaces, graphs and matroids. For vector spaces V_{AB}, treated as collection of row vectors, with specified column set Auplus B, we define V_{SP}lrarv V_{PQ}, Scap Q= emptyset, to be the collection of all vectors (f_S,f_Q) such that (f_S,f_P)in V_{SP}, (f_P,f_Q)in V_{PQ}. An analogous operation G_{SP}lrarg G_{PQ}equivd G_{PQ} can be defined in relation to graphs G_{SP}, G_{PQ}, on edge sets Suplus P, Puplus Q, respectively in terms of an overlapping subgraph G_P which gets deleted in the right side graph (see for instance the notion of k-sum oxley). For matroids we define the `linking' M_{SP}lrarm M_{PQ} equivd (M_{SP}vee M_{PQ})times (Suplus Q), denoting the contraction operation by 'times'. In each case, we examine how to minimize the size of the `overlap' set P, without affecting the right side entity. In the case of vector spaces, there is a polynomial time algorithm for achieving the minimum, which we present. Similar ideas work for graphs and for matroids under appropriate conditions. Next we consider the problem of decomposition. Here, in the case of vector spaces, the problem is to decompose V_{SQ} as V_{SP}lrarv V_{PQ}, with minimum size P. We give a polynomial time algorithm for this purpose. In the case of graphs and matroids we give a solution to this problem under certain restrictions.

  • 1 authors
·
Jul 13, 2023

Large Language Model-Guided Discovery of Weight-Five Bivariate Bicycle Codes

Building on our earlier program-evolution workflow guided by large language models (LLMs), we study weight-five bivariate bicycle (BB) and perturbed bivariate bicycle (PBB) codes. The resulting catalogue contains 1,142 distinct code proposals, including 1,081 nonbaseline proposals attributable to LLM-generated programs. Across the catalogue, we certify connected Calderbank--Shor--Steane (CSS) realizations [[96,4,10]], [[140,6,10]], and [[180,4,14]]. A post-search comparison certifies seven imported Lin--Pryadko archive constructions. For leading parameter triples also represented in that archive, we provide exact distance evidence, explicit bivariate presentations, and verified component reductions. A basis-independent connectivity analysis identifies 409 of the 1,142 catalogue entries as disconnected and shows that 73.1\% of the classes with exact distance certificates contain repeated connected components. Algebraic analysis organizes the connected CSS classes into order-3, order-7, and order-15 cyclotomic-kernel strata. The strongest exact connected PBB parameter point is [[216,4,10]], attained by two distinct component classes. Among the 936 distinct CSS proposals from the LLM-guided campaign with a recorded positive distance, 816 (87.18\%) are certified at dgeq5. For comparison, three random-search controls each sample 6,444 CSS code proposals uniformly without replacement, using the same per-lattice and encoded-dimension sample counts as the LLM-guided campaign. In these controls, 4,672--4,785 proposals (72.50--74.26\%) meet the same criterion. The LLM-guided campaign has the higher certified yield, while the random controls cover more connected classes. Together, these results extend LLM-guided discovery to a more constrained code family and provide a reproducible structural and exact-distance account of its strongest candidates.

  • 1 authors
·
Oct 4

Qin's Algorithm, Continued Fractions and 2-dimensional Lattices

In his celebrated book "Mathematical Treatise in Nine Sections" of 1247, Qin, Jiushao described the Chinese remainder theorem with great detail and generality. He also gave a method for computing modular inverse under the name of "DaYan deriving one". Historical significance of DaYan deriving one method has been well studied. In this paper, we investigate its modern mathematical nature from the perspectives of number theory and algorithm. One of the remarkable features of Qin's algorithm is that it keeps a state of four variables in a matrix form. Its choice of variables and layout provide natural ways of connecting several important mathematical concepts. An invariant about the state is also observed which provides a convenient yet powerful tool in proving several important mathematical results. The paper first explains Qin's algorithm and proves some of its properties. Then the connection with continued fractions is examined, the results show that the states of Qin's algorithm contain rich information about continued fractions and some classical arguments can be derived easily. The last part of the paper discusses a family of 2-dimensional lattices of number theoretic significance by proving that the shortest vectors of these lattices can be obtained from the states of Qin's algorithm. This result is surprising in that a shortest lattice vector is found in a well-regulated set. A method of computing such shortest vectors is proposed.ed.

  • 2 authors
·
Nov 6, 2023

SINC: Spatial Composition of 3D Human Motions for Simultaneous Action Generation

Our goal is to synthesize 3D human motions given textual inputs describing simultaneous actions, for example 'waving hand' while 'walking' at the same time. We refer to generating such simultaneous movements as performing 'spatial compositions'. In contrast to temporal compositions that seek to transition from one action to another, spatial compositing requires understanding which body parts are involved in which action, to be able to move them simultaneously. Motivated by the observation that the correspondence between actions and body parts is encoded in powerful language models, we extract this knowledge by prompting GPT-3 with text such as "what are the body parts involved in the action <action name>?", while also providing the parts list and few-shot examples. Given this action-part mapping, we combine body parts from two motions together and establish the first automated method to spatially compose two actions. However, training data with compositional actions is always limited by the combinatorics. Hence, we further create synthetic data with this approach, and use it to train a new state-of-the-art text-to-motion generation model, called SINC ("SImultaneous actioN Compositions for 3D human motions"). In our experiments, that training with such GPT-guided synthetic data improves spatial composition generation over baselines. Our code is publicly available at https://sinc.is.tue.mpg.de/.

  • 4 authors
·
Apr 20, 2023

Order Matters: Unveiling the Hidden Impact of Macro Placement Sequences via Proxy-Guided LLM Evolution

Macro placement is a fundamental step in modern chip physical design, playing a crucial role in determining the solution quality of high-dimensional combinatorial optimization problems. Despite recent advancements in machine learning for spatial coordinate determination, the temporal dimension of placement sequencing remains largely governed by static heuristics. In this work, we demonstrate that the placement sequence is not merely a preprocessing step but a decisive factor in optimization, where suboptimal early decisions trigger irreversible domino effects that constrain the solution space. To harness this unexplored dimension, we propose OrderPlace, a proxy-guided LLM evolution framework for automatically discovering macro placement order strategies. Instead of relying on manually crafted heuristics such as area- or connectivity-based ordering, OrderPlace explores a broader space of code-level policies, ranging from static scoring metrics to dynamic physics-inspired mechanisms. To mitigate the prohibitive cost of evaluating sequences, we introduce a lightweight proxy evaluation mechanism that efficiently filters candidates using a deterministic greedy probe. Experimental results on the standard ISPD 2005 benchmarks demonstrate that OrderPlace discovers novel ordering strategies. Compared with WireMask-EA and the state-of-the-art method EGPlace, OrderPlace reduces wirelength by 34.04\% and 14.08\%, respectively.

  • 4 authors
·
Jun 7

Dandelion: A Spherical Flower for Neural Simulation of Planetary Dynamics

Many dynamical processes unfold on the sphere but the default scientific machine learning architectures are Euclidean. Applying these architectures on a regular lat-lon grid causes problems: Cartesian convolutions become distorted at high latitude; 2D FFTs in Fourier neural operators incorrectly assume double periodicity; Cartesian positional encodings in ViTs distort spherical geodesic distances. Recent work moves towards natively spherical primitives, including spherical convolutions (e.g., DeepSphere or DISCO), Spherical Fourier Neural Operators (SFNOs), and geodesic attention. Here we propose Dandelion, a spherical version of Flower, a warp-based neural PDE solver. Layers of Dandelion predict a tangent-plane displacement and transport features along great circles. We obtain a U-Net-like structure by implementing hierarchical pooling entirely in the spherical-harmonic domain. There are thus no convolutions: spatial mixing is achieved only through spherical coordinate changes, or warps. To compare Dandelion with existing spherical architectures, we release an evolving benchmark suite of challenging, natively-spherical PDE datasets including a modified Galewsky jet, anomalous chained turbulence, Cahn-Hilliard decomposition, spherical Riemann shocks, Held-Suarez dry atmospheric transport and global ocean dynamics. This new benchmark fills the gap in existing spherical datasets which are either too small and stylized, or much too large (ERA5) for model iteration. Dandelion is best or second-best on every dataset, and the gap to non-warp baselines widens with resolution: at 256times 512, Dandelion and Flower2D occupy the top two slots in both single-step prediction and rollout.

  • 3 authors
·
Aug 26

p-adic Bi-Filtrations for Topological Machine Learning on Genomic Sequences

We introduce pVR, a topological machine learning framework for alignment-free genomic sequence classification that combines p-adic numbers with topological data analysis. Each DNA sequence is encoded along two complementary axes: a p-adic distance on k-mer prefixes, which captures hierarchical positional structure, and a compositional L_1 distance on k-mer frequencies, which captures local sequence content. The two distances jointly parameterise a bi-filtered Vietoris--Rips complex, and per-sequence topological summaries from this bi-filtration serve as features for standard machine learning classifiers. We establish theoretical guarantees for the construction: stability under metric perturbations and invariance to the choice of prime, alongside a result that explains why a single p-adic axis is topologically uninformative and why the bi-filtration recovers nontrivial homology. On twelve genomic benchmarks (28 to 500 sequences, 3 to 7 classes), pVR outperforms four established alignment-free baselines on three of six low-sample datasets, with gains of up to 21 percentage points; it underperforms only on a SARS-CoV-2 variant benchmark whose point-mutation divergence violates the hierarchical assumption, and all methods saturate in the large-sample regime. pVR also outperforms zero-shot frozen embeddings from the 500M-parameter Nucleotide Transformer v2 by 6.7 to 11.4 percentage points on three low-sample benchmarks. The pVR codebase is publicly available at https://github.com/MAHI-Group/pVR.

  • 2 authors
·
Jun 4

Distinguishability and linear independence for H-chromatic symmetric functions

We study the H-chromatic symmetric functions X_G^H (introduced in (arXiv:2011.06063) as a generalization of the chromatic symmetric function (CSF) X_G), which track homomorphisms from the graph G to the graph H. We focus first on the case of self-chromatic symmetric functions (self-CSFs) X_G^G, making some progress toward a conjecture from (arXiv:2011.06063) that the self-CSF, like the normal CSF, is always different for different trees. In particular, we show that the self-CSF distinguishes trees from non-trees with just one exception, we check using Sage that it distinguishes all trees on up to 12 vertices, and we show that it determines the number of legs of a spider and the degree sequence of a caterpillar given its spine length. We also show that the self-CSF detects the number of connected components of a forest, again with just one exception. Then we prove some results about the power sum expansions for H-CSFs when H is a complete bipartite graph, in particular proving that the conjecture from (arXiv:2011.06063) about p-monotonicity of ω(X_G^H) for H a star holds as long as H is sufficiently large compared to G. We also show that the self-CSFs of complete multipartite graphs form a basis for the ring Λ of symmetric functions, and we give some construction of bases for the vector space Λ^n of degree n symmetric functions using H-CSFs X_G^H where H is a fixed graph that is not a complete graph, answering a question from (arXiv:2011.06063) about whether such bases exist. However, we show that there generally do not exist such bases with G fixed, even with loops, answering another question from (arXiv:2011.06063). We also define the H-chromatic polynomial as an analogue of the chromatic polynomial, and ask when it is the same for different graphs.

  • 2 authors
·
Nov 11, 2025

Amplitude Encoding of Slater-Type Orbitals via Matrix Product States: Efficient State Preparation and Integral Evaluation on Quantum Hardware

Slater-type orbitals (STOs) provide the physically correct description of atomic wavefunctions but have been largely replaced by Gaussian-type orbitals in computational chemistry due to the lack of closed-form multi-center integrals. We present a systematic study of amplitude encoding of STOs on quantum computers using matrix product states (MPS). For one-dimensional orbital functions of the form p_d(x) e^{-ζx}, we derive analytical MPS constructions with constant bond dimension χ= d + 1, requiring O(n) classical and quantum resources for n-qubit registers with no grid sampling. We demonstrate a complete one-electron integral pipeline -- overlap, kinetic energy, and nuclear attraction -- in one dimension, validating the overlap and kinetic energy on IBM Heron processors at 5~qubits with 0.67\% hardware-induced error using Zero-Noise Extrapolation. In three dimensions, we compute multi-center overlap integrals between 1s and 2s orbitals in Cartesian coordinates with 0.02\% discretization error at 18~qubits. A systematic entanglement analysis reveals that the MPS bond dimension of three-dimensional STOs in Cartesian coordinates saturates with increasing grid resolution -- reaching sim138 for the hydrogen 1s orbital at 12~qubits per coordinate -- establishing bounded encoding complexity rather than the exponential scaling initially expected. The SVD truncation threshold provides a practical resource parameter, reducing the bond dimension to 39 at threshold 10^{-6} with negligible accuracy loss. These results map the entanglement landscape for amplitude encoding of atomic orbitals and establish MPS-based state preparation as a viable path toward exact STO basis sets on quantum computers.

  • 1 authors
·
Apr 28

Subgraph Permutation Equivariant Networks

In this work we develop a new method, named Sub-graph Permutation Equivariant Networks (SPEN), which provides a framework for building graph neural networks that operate on sub-graphs, while using a base update function that is permutation equivariant, that are equivariant to a novel choice of automorphism group. Message passing neural networks have been shown to be limited in their expressive power and recent approaches to over come this either lack scalability or require structural information to be encoded into the feature space. The general framework presented here overcomes the scalability issues associated with global permutation equivariance by operating more locally on sub-graphs. In addition, through operating on sub-graphs the expressive power of higher-dimensional global permutation equivariant networks is improved; this is due to fact that two non-distinguishable graphs often contain distinguishable sub-graphs. Furthermore, the proposed framework only requires a choice of k-hops for creating ego-network sub-graphs and a choice of representation space to be used for each layer, which makes the method easily applicable across a range of graph based domains. We experimentally validate the method on a range of graph benchmark classification tasks, demonstrating statistically indistinguishable results from the state-of-the-art on six out of seven benchmarks. Further, we demonstrate that the use of local update functions offers a significant improvement in GPU memory over global methods.

  • 2 authors
·
Nov 23, 2021

Standard Quadratic Formulations of Many NP Problems: A Simplex-Based Compilation Framework for Combinatorial Optimization

The standard quadratic program (StQP) minimizes a quadratic form over nonnegative variables that sum to one. We compose classical graph reductions with regularized Motzkin--Straus clique formulations to express discrete optimization problems in this continuous domain. The graph matrix has diagonal entries τ, zeros on edges, and ones on nonedges. For 0<τ<1, its minimum is τ/ω(G), where ω(G) is the clique number. Its strict local minimizers are precisely the uniform distributions on maximal cliques, and its global minimizers encode maximum cliques. At τ=1/2, integer scaling gives coefficients in {0,1,2} and minimum 1/ω(G), yielding an NP-complete StQP threshold problem with a restricted coefficient alphabet. We give explicit formulations for satisfiability, coloring, Hamiltonian cycles, independent set, vertex cover, set packing, three-dimensional matching, and graph isomorphism. A regularized weighted clique formulation combined with local-state compatibility graphs gives an exact compiler for finite-domain factor models specified by complete local tables, including QUBO, with at most four simplex coordinates per binary pair factor. The catalog covers Karp's 21 problems: twelve use direct graph formulations, and nine use factor-state formulations, including six obtained through binary-linear feasibility. For each route we record dimensions, coefficient structure, and recovery rules. We analyze interaction count, coefficient range, objective separation, perturbation tolerance, support recovery, and decoding overhead. The separation bounds quantify the effects of clique size, factor weights, and offsets. In the complete factor-state construction, every assignment, including each suboptimal assignment, is a strict local minimum.

  • 3 authors
·
Sep 30

Hadronic light-by-light contribution to (g-2)_μ from lattice QCD with SU(3) flavor symmetry

We perform a lattice QCD calculation of the hadronic light-by-light contribution to (g-2)_μ at the SU(3) flavor-symmetric point m_π=m_Ksimeq 420,MeV. The representation used is based on coordinate-space perturbation theory, with all QED elements of the relevant Feynman diagrams implemented in continuum, infinite Euclidean space. As a consequence, the effect of using finite lattices to evaluate the QCD four-point function of the electromagnetic current is exponentially suppressed. Thanks to the SU(3)-flavor symmetry, only two topologies of diagrams contribute, the fully connected and the leading disconnected. We show the equivalence in the continuum limit of two methods of computing the connected contribution, and introduce a sparse-grid technique for computing the disconnected contribution. Thanks to our previous calculation of the pion transition form factor, we are able to correct for the residual finite-size effects and extend the tail of the integrand. We test our understanding of finite-size effects by using gauge ensembles differing only by their volume. After a continuum extrapolation based on four lattice spacings, we obtain a_μ^{rm hlbl} = (65.4pm 4.9 pm 6.6)times 10^{-11}, where the first error results from the uncertainties on the individual gauge ensembles and the second is the systematic error of the continuum extrapolation. Finally, we estimate how this value will change as the light-quark masses are lowered to their physical values.

  • 5 authors
·
Jul 12, 2020

Equivariant Neural Primal-Dual Assignment for Maximum Common Edge Subgraphs

Maximum common edge subgraph (MCES) matching finds a partial vertex correspondence between two labeled graphs that preserves as many labeled edges as possible. Molecular similarity search requires matching many graph pairs, making the cost of repeated queries important. The strongest baseline attains accurate MCES solutions but trains a separate network for each pair. We introduce Equivariant Neural Primal-Dual Assignment (ENPDA), which learns a shared matching policy and applies it to new pairs without further training, answering queries roughly three orders of magnitude faster and recovering its training cost after a few dozen queries. The policy recomputes exact objective marginals for candidate matches and learns corrections and step sizes that update their scores. Target prices respond to competition when several source vertices favor the same target. Four update rounds and a Hungarian projection produce a partial one-to-one matching. We prove per-pair guarantees that hold for any network parameters. In exact arithmetic, reordering either graph permutes the assignment and price states, the projected matching is one-to-one, and repaired prices give a valid MCES upper bound. Subtracting the preserved-edge count bounds the optimality gap; combined with structural caps, these certificates prove global optimality for 60 of 291 native test pairs. On three molecular benchmarks with disjoint train/validation/test splits, ENPDA improves over an analytic counterpart with the same update and projection budget by 7.4-8.6 accuracy points; after one second of refinement search, 2.5-3 points of the gain remain. Transferred without fine-tuning to edge-deletion tasks from social and protein graphs, the policy gains 9.1-17.6 points over the analytic counterpart. When output matchings must keep aromatic rings intact, ENPDA recovers more reference bonds than the baselines on all three datasets.

  • 6 authors
·
Sep 25

The Impossibility of Inverse Permutation Learning in Transformer Models

In this technical note, we study the problem of inverse permutation learning in decoder-only transformers. Given a permutation and a string to which that permutation has been applied, the model is tasked with producing the original (``canonical'') string. We argue that this task models a natural robustness property across a variety of reasoning tasks, including long-context retrieval, multiple choice QA and in-context learning. Our primary contribution is an impossibility result: we show that an arbitrary depth, decoder-only transformer cannot learn this task. This result concerns the expressive capacity of decoder-only transformer models and is agnostic to training dynamics or sample complexity. We give a pair of alternative constructions under which inverse permutation learning is feasible. The first of these highlights the fundamental role of the causal attention mask, and reveals a gap between the expressivity of encoder-decoder transformers and the more popular decoder-only architecture. The latter result is more surprising: we show that simply padding the input with ``scratch tokens" yields a construction under which inverse permutation learning is possible. We conjecture that this may suggest an alternative mechanism by which chain-of-thought prompting or, more generally, intermediate ``thinking'' tokens can enable reasoning in large language models, even when these tokens encode no meaningful semantic information (e.g., the results of intermediate computations).

  • 4 authors
·
Sep 28, 2025

One-connection rule for structural equation models

Linear structural equation models are multivariate statistical models encoded by mixed graphs. In particular, the set of covariance matrices for distributions belonging to a linear structural equation model for a fixed mixed graph G=(V, D,B) is parameterized by a rational function with parameters for each vertex and edge in G. This rational parametrization naturally allows for the study of these models from an algebraic and combinatorial point of view. Indeed, this point of view has led to a collection of results in the literature, mainly focusing on questions related to identifiability and determining relationships between covariances (i.e., finding polynomials in the Gaussian vanishing ideal). So far, a large proportion of these results has focused on the case when D, the directed part of the mixed graph G, is acyclic. This is due to the fact that in the acyclic case, the parametrization becomes polynomial and there is a description of the entries of the covariance matrices in terms of a finite sum. We move beyond the acyclic case and give a closed form expression for the entries of the covariance matrices in terms of the one-connections in a graph obtained from D through some small operations. This closed form expression then allows us to show that if G is simple, then the parametrization map is generically finite-to-one. Finally, having a closed form expression for the covariance matrices allows for the development of an algorithm for systematically exploring possible polynomials in the Gaussian vanishing ideal.

  • 4 authors
·
Oct 1, 2022

Space-time tradeoffs of lenses and optics via higher category theory

Optics and lenses are abstract categorical gadgets that model systems with bidirectional data flow. In this paper we observe that the denotational definition of optics - identifying two optics as equivalent by observing their behaviour from the outside - is not suitable for operational, software oriented approaches where optics are not merely observed, but built with their internal setups in mind. We identify operational differences between denotationally isomorphic categories of cartesian optics and lenses: their different composition rule and corresponding space-time tradeoffs, positioning them at two opposite ends of a spectrum. With these motivations we lift the existing categorical constructions and their relationships to the 2-categorical level, showing that the relevant operational concerns become visible. We define the 2-category 2-Optic(C) whose 2-cells explicitly track optics' internal configuration. We show that the 1-category Optic(C) arises by locally quotienting out the connected components of this 2-category. We show that the embedding of lenses into cartesian optics gets weakened from a functor to an oplax functor whose oplaxator now detects the different composition rule. We determine the difficulties in showing this functor forms a part of an adjunction in any of the standard 2-categories. We establish a conjecture that the well-known isomorphism between cartesian lenses and optics arises out of the lax 2-adjunction between their double-categorical counterparts. In addition to presenting new research, this paper is also meant to be an accessible introduction to the topic.

  • 1 authors
·
Sep 19, 2022

Bipartite Carrier Compression and Machine-Certified Bounds in Schönhage Trilinear Multiplication Tensors

Under the conditional framework breaking the longstanding O(n log n) integer multiplication barrier (originating from OpenAI Preprint #109), the asymptotic time complexity exponent T(n) = O(n (log n)^{1-κ}) is governed by bounding the second moment E[X^2] < 1 of recursive branching processes over trilinear tensor carrier graphs. In this work, we present a constructive combinatorial optimization over the alternating carrier bipartite matching graphs of the Schönhage trilinear tensor decomposition at dimensions h=23 and h=25. Through an alternating augmenting path search, we uncover a non-trivial cluster-unlocking cascade that eliminates 185 carrier roles (95 roles in h=23 and 90 roles in h=25), reducing the global physical wire width by 377,890 wires from the reviewed baseline W = 177,284,805 down to W = 176,906,915. Evaluated over the exact 10^{-14} rational grid, this wire reduction certifies an improved second-moment coefficient AB = 5,164,059 / 125,000,000,000 and establishes the sharpened conditional exponent κ= 826,215,307 / 20,000,000,000,000 \approx 4.131076535 \times 10^{-5}, strictly surpassing the preceding record on this architecture (κ\approx 4.123864 \times 10^{-5}). All 47 polynomial constraints and 7 rational security margins are audited in exact Q-arithmetic with zero floating-point error, and the fundamental wire reduction identity is formally verified in the Lean 4 interactive theorem prover without unproven axioms.

  • 3 authors
·
Oct 8

Shortcut Partitions in Minor-Free Graphs: Steiner Point Removal, Distance Oracles, Tree Covers, and More

The notion of shortcut partition, introduced recently by Chang, Conroy, Le, Milenkovi\'c, Solomon, and Than [CCLMST23], is a new type of graph partition into low-diameter clusters. Roughly speaking, the shortcut partition guarantees that for every two vertices u and v in the graph, there exists a path between u and v that intersects only a few clusters. They proved that any planar graph admits a shortcut partition and gave several applications, including a construction of tree cover for arbitrary planar graphs with stretch 1+varepsilon and O(1) many trees for any fixed varepsilon in (0,1). However, the construction heavily exploits planarity in multiple steps, and is thus inherently limited to planar graphs. In this work, we breach the "planarity barrier" to construct a shortcut partition for K_r-minor-free graphs for any r. To this end, we take a completely different approach -- our key contribution is a novel deterministic variant of the cop decomposition in minor-free graphs [And86, AGG14]. Our shortcut partition for K_r-minor-free graphs yields several direct applications. Most notably, we construct the first optimal distance oracle for K_r-minor-free graphs, with 1+varepsilon stretch, linear space, and constant query time for any fixed varepsilon in (0,1). The previous best distance oracle [AG06] uses O(nlog n) space and O(log n) query time, and its construction relies on Robertson-Seymour structural theorem and other sophisticated tools. We also obtain the first tree cover of O(1) size for minor-free graphs with stretch 1+varepsilon, while the previous best (1+varepsilon)-tree cover has size O(log^2 n) [BFN19].

  • 6 authors
·
Jul 31, 2023

Kinematical correlations via κ-Poincaré coproducts

We study a kinematical consequence of the Hopf-algebraic momentum composition law in κ-Minkowski spacetime. The same curved momentum space can be described in different coordinates. In the bicrossproduct basis the ordered-plane-wave labels are the translation-generator eigenvalues, so the relevant map is one-to-one. In the classical basis, instead, the translation eigenvalues P_μ are nonlinearly related to the ordered-plane-wave labels p_μ. This relation can fail to be globally one-to-one in a high-momentum region. When a given classical-basis four-momentum admits more than one real auxiliary preimage, the branch-sensitive quantity P_+equiv P_0+P_4=κe^{p_0/κ} enters the coproduct and resolves the branches in two-particle states. Imposing the vanishing total-momentum constraint therefore gives branch-dependent κ-deformed back-to-back momentum correlations. In a single-branch regime this is just a deformed correlated product, while in a multibranch regime a state specified only by P_μ can be expanded into distinct auxiliary branches. If P_μ are taken as the directly meaningful momenta, the physical content is the resulting deformed correlation pattern. If the auxiliary variables p_μ are assigned operational meaning, the same constrained state can be interpreted as a superposition over different auxiliary branches. We also compare this structure with standard regular self-adjoint nonrelativistic minimal-length models and find no analogous smooth local two-real-branch inversion on their physical domains.

  • 2 authors
·
Jun 1