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Period ending 2026-09-21

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1,209 papers

Latest in Transformers

Jun 5, 2026cs.LG

The Geometry of Last-Layer Model Stealing

This paper uses geometry to explain how a machine learning model can be stolen using an already existing well-known method. The author has shown the exact conditions required to perfectly copy the final layer of a transformer network. When looking deeper into the hidden layers the author has explained clear limits. The author has also demonstrated that a hidden network cannot be fully reverse engineered just by looking at the final results. The research clearly maps out what can and cannot be stolen from a model.
Snigdha Chandan Khilar
Jun 5, 2026stat.ML

The Effect of Training Task Diversity on In-Context Learning through the Lens of Low-Dimensional Subspaces

The transformer's emergent ability to perform in-context learning (ICL) has sparked a wide range of studies designed to understand its underlying mechanisms. Existing works often study how training task diversity, defined either as the number of ICL training task vectors or as the number of function classes from which the task vectors are drawn, shapes both the learning dynamics and generalization capabilities of ICL. While both definitions have uncovered many interesting phenomena, many observations under the latter definition remain theoretically unexplained. This paper presents a minimal analytical model under which these phenomena provably emerge from the properties of the training data. By modeling the training task vectors as a mixture of low-rank Gaussians, we show how training task diversity, defined by the number of non-overlapping columns between subspaces that parameterize the covariance matrices, improves both the generalization and optimization trajectory of ICL with linear attention. In particular, we show that our model can explain (i) why training with task diversity shortens the ICL plateau and (ii) why ICL appears to achieve out-of-distribution generalization. We conclude by empirically demonstrating how our results extend to nonlinear transformers and nonlinear function classes. Overall, our work presents a tractable framework to unify existing observations.
Soo Min Kwon, Alec S. Xu, Can Yaras +3
Jun 4, 2026physics.flu-dyn

Multiscale POD of Transformer Attention Fields: Scale-Selective Analysis via Morlet Scalogram

We introduce scale-selective Proper Orthogonal Decomposition (POD) for transformer attention fields, inspired by the use of POD for extracting energetically dominant modes from turbulent flow ensembles. The Morlet continuous wavelet transform identifies dominant temporal scales in the attention lag structure across a document ensemble; POD then extracts the energetically dominant modes at each scale from the ensemble of attention fields. The resulting modes reveal layer-dependent scale organisation, with early layers emphasising fine scales and later layers shifting toward coarser scales. We define a spectral concentration index from the POD eigenvalue decay rate and show empirically that it differentiates layers by their attention field complexity. By the classical POD optimality theorem, the extracted modes minimise the average L2 reconstruction error over the ensemble (Theorem 1), giving a data-driven effective rank for each layer. The method requires no architectural modification and no linguistic annotations: dominant attention patterns emerge from ensemble statistics alone. The turbulence analogy is structural rather than physical: we borrow ensemble covariance and modal analysis, not fluid dynamics itself.
Athanasios Zeris
Jun 4, 2026cs.CL

You Only Index Once: Cross-Layer Sparse Attention with Shared Routing

Long-context inference in modern LLMs is increasingly constrained by decoding efficiency, especially in reasoning-heavy settings where models generate long intermediate chains of thought. Existing sparse attention methods often face a practical efficiency-quality trade-off. Structured block sparse methods typically provide stronger acceleration but incur noticeable quality loss, while token sparse methods are usually more accurate yet deliver limited end-to-end speedup because top-k routing over the full cache remains expensive. In this work, we propose cross-layer sparse attention (CLSA), which is built on top of KV-sharing architectures such as YOCO. The core idea is to share not only the KV cache across cross-decoder layers, but also the routing index. A single indexer computes token-level top-k selection once and reuses the resulting index across layers, thereby preserving the fine-grained selectivity of token sparse attention while amortizing the routing overhead. The resulting architecture improves all major inference bottlenecks jointly, including pre-filling, KV-cache storage, and long-context decoding. Experiments across short-context and long-context benchmarks show that CLSA is both accurate and efficient, achieving up to 7.6x decoding speedup and 17.1x overall throughput improvement at 128K context. These results suggest a more complete architectural solution for long-context LLMs that jointly advances model quality and inference efficiency.
Yutao Sun, Yanqi Zhang, Li Dong +2
Jun 4, 2026cs.AI

Vortex: Efficient and Programmable Sparse Attention Serving for AI Agents

Sparse attention is becoming increasingly important for serving large language models (LLMs) as generation lengths continue to grow. However, deploying and evaluating new sparse attention algorithms at scale remains highly engineering-intensive, slowing both human researchers and AI agents in exploring the sparse attention design. To address this challenge, we present Vortex, a system that combines a Python-embedded frontend language atop a page-centric tensor abstraction for expressing a broad range of sparse attention algorithms, with an efficient backend tightly integrated into modern LLM serving stacks. Vortex enables rapid prototyping, deployment, and evaluation of sparse attention algorithms, effectively translating their theoretical efficiency gains into real-world throughput improvements. As a result, Vortex substantially accelerates the design and iteration of sparse attention algorithms. First, AI agents use Vortex to automatically generate and refine diverse algorithms, the best reaching up to 3.46×3.46\times higher throughput than full attention while preserving accuracy. Second, Vortex extends sparse attention to emerging architectures and very large models that are otherwise hard to experiment with, reaching up to 4.7×4.7\times higher throughput on the MLA-based GLM-4.7-Flash and 1.37×1.37\times on the 229B-parameter MiniMax-M2.7 on NVIDIA B200 GPUs.
Zhuoming Chen, Xinrui Zhong, Qilong Feng +5
Jun 4, 2026cs.AI

RedKnot: Efficient Long-Context LLM Serving with Head-Aware KV Reuse and SegPagedAttention

As the input length of large language model (LLM) serving continues to grow, the KV cache has become a dominant bottleneck in AI infrastructure. It limits GPU memory capacity, serving concurrency, cache reuse, and distributed scalability. Multiple important problems, including position-independent KV cache, prefix KV cache compression, hot/cold KV cache separation, and distributed KV cache management, all depend on how the KV cache is represented and managed. However, existing serving systems largely rely on a monolithic KV cache abstraction, where the KV cache is treated as a homogeneous sequence of token-level memory blocks and managed with similar policies across attention heads and serving scenarios. We observe that KV cache utility is highly structured across KV heads: different heads exhibit different functional roles, attention distances, and runtime importance. Therefore, a full KV cache is not always necessary for every head, token range, or serving scenario. We present RedKnot, a head-aware KV cache management system for LLM serving. RedKnot breaks the conventional monolithic KV cache abstraction by decomposing the KV cache along KV heads, whose importance and effective attention ranges vary significantly across serving scenarios. This head-level decomposition turns the KV cache from a monolithic tensor abstraction into a structured memory object, enabling RedKnot to uniformly support position-independent KV reuse, prefix KV compression, hot/cold KV separation, and distributed KV placement while preserving output fidelity and improving resource efficiency, without requiring model retraining or fine-tuning. RedKnot establishes a new foundation for AI infrastructure by transforming the KV cache from a monolithic, passive runtime artifact into a dynamic, model-aware runtime substrate for scalable LLM serving.
Yang Liu, ZhaoKai Luo, HuaYi Jin +5
Jun 4, 2026cs.AI

Where does Absolute Position come from in decoder-only Transformers?

RoPE-trained transformers distinguish absolute position in their attention patterns, even though RoPE encodes only relative offsets in the inner product. We trace this leakage to two architectural components, The causal mask is responsible for the first: its per-query softmax denominator depends on the absolute query position by construction. The residual stream supplies the second. Under causal attention the activation at position 00 attends only to itself and runs as a closed dynamical system from the embedding of the token at that position; downstream attention reads this trajectory through sink-reading heads. Both components appear in all three architectures we study, in architecturally specific balance: NTK scaling suppresses the residual-stream component, sliding-window attention allows it to accumulate with depth, and standard RoPE sits between. Replacing the \texttt{BOS} embedding before the forward pass removes 40%40\% of the residual-stream component at early queries. Attention sinks are token-anchored stabilizers that pass forward a deterministic fingerprint of the token at position 00, constant across inputs when that token is the auto-prepended \texttt{BOS} and varying with it otherwise.
Valeria Ruscio, Umberto Nanni, Fabrizio Silvestri
Jun 4, 2026cs.LG

When Good Enough Is Optimal: Multiplication-Only Matrix Inversion Approximation for Quantized Gated DeltaNet

Matrix inversion in chunk-wise parallel linear attention is a major bottleneck for long-context modeling, particularly on NPUs, where forward-substitution-based methods exhibit limited parallelism and poor hardware utilization. We propose a fast, Matrix Multiplication (MatMul)-based algorithm tailored for strictly lower-triangular matrices arising in chunk-wise linear attention. Motivated by the rapid growth of Neumann-series terms and the diagonal concentration of the inverse matrix, we employ a truncated Neumann expansion with structural masking and parallel residual correction to eliminate sequential dependencies. We further extend our method to low-bits INT by mitigating the dynamic range expansion arising from repeated matrix power operations, and adapt the approximation order and residual step to the chunk size to minimize computational cost while preserving the model's accuracy. Experiments on Qwen3.5-family models demonstrate up to 5×\times kernel-level speedup and a 20% reduction in decode-layer overhead, while preserving accuracy under both floating-point and low-precision inference. Our method offers an efficient and hardware-friendly solution for scalable linear attention.
Luoming Zhang, Yuwei Ren, Kui Zhang +7
Jun 4, 2026cs.CV

ATT-CR: Adaptive Triangular Transformer for Cloud Removal

Cloud removal aims to accurately reconstruct the ground objects obscured by clouds in remote sensing images. Existing Transformer-based methods utilizing self-attention have shown impressive results by effectively modeling long-range dependencies in cloudy images. However, they suffer from the following issues: 1) the high computational complexity of self-attention limits scalability; 2) treating both cloudy and clean pixels as valid within the attention computation brings disturbances in subsequent layers, leading to suboptimal performance. To address these challenges, we propose the Adaptive Triangular Transformer for Cloud Removal (ATT-CR), a model that effectively reduces computational costs and mitigates interference from cloudy pixels. Specifically, it consists of two core components: Triangular Attention (TAN) and Feature Selected Gating Module (FSGM). TAN employs lower and upper triangular matrices to approximate Softmax attention with O(N) computational complexity, significantly reducing the computational costs. The FSGM, on the other hand, integrates with TAN to adaptively distinguish between cloudy and clean features, which minimizes the introduction of invalid information into subsequent layers. Extensive experiments on cloud removal benchmarks demonstrate that ATT-CR delivers superior performance compared to existing methods.
Yang Wu, Ye Deng, Pengna Li +4
Jun 4, 2026cs.CL

Mechanistic Insights into Functional Sparsity in Multimodal LLMs via CoRe Heads

While Multimodal Large Language Models (MLLMs) demonstrate remarkable proficiency on complex vision-language tasks, the mechanisms by which they extract query-relevant visual features from complex, noisy contexts remain opaque. In this paper, we present an in-depth interpretability study that uncovers a profound structural property within MLLMs: functional sparsity in cross-modal retrieval. Leveraging a token-level metric termed Retrieval Attention Mass (RAM), we identify and characterize a highly specialized subset of attention heads, referred to as Context-aware Retrieval (CoRe) heads. Across diverse visual domains and model scales, we observe a clear functional division: CoRe heads act as dedicated information extractors, while most other heads distribute attention over broader contextual regions. Causal interventions further demonstrate the necessity of these specialized heads. Ablating only the top 5% of CoRe heads causes significant degradation in multimodal reasoning performance, whereas ablating lower-ranked heads has minimal effect. Moreover, acceleration experiments validate the utility of CoRe heads, showing that leveraging this localized sparsity significantly accelerates inference while maintaining robust task performance. Our findings reveal a structural principle of functional sparsity within MLLMs, refining the current understanding of mechanistic interpretability and laying a theoretical foundation that can inspire future architecture design and model optimization.
Ruoxi Sun, Quantong Qiu, Juntao Li +3
Jun 3, 2026cs.LG

Dominant-Layer ZO: A Single Layer Dominates Zeroth-Order Fine-Tuning of LLMs

Zeroth-order (ZO) optimization enables memory-efficient fine-tuning of large language models (LLMs) using only forward passes, but it remains unclear how useful adaptation is distributed across layers. In this work, we reveal a surprising phenomenon: ZO fine-tuning is sharply dominated by a single decoding layer. Across multiple LLM families and downstream tasks, fine-tuning this dominant layer alone consistently matches or even exceeds full-model ZO fine-tuning. We further show that the dominant layer is task-agnostic but model-specific, and can be identified before training through a simple inference-only analysis of activation outliers. Specifically, the dominant layer consistently aligns with the first activation-outlier layer in the pre-trained model. To explain this phenomenon, we analyze how perturbation effects propagate under ZO optimization. We find that the dominant layer combines two key properties: high perturbation sensitivity and early placement in the residual stream, allowing perturbation-induced effects to propagate and accumulate through remaining subsequent decoding layers. As a result, this layer produces disproportionately strong and stable optimization signals under forward-only updates. Extensive experiments on LLaMA2-7B and Qwen3-8B across nine benchmarks show that dominant-layer ZO fine-tuning improves average performance over full-model MeZO and LoRA-based ZO fine-tuning while achieving up to 4.52×\times training speedup.
Wanhao Yu, Ziyan Wang, Zheng Wang +7
Jun 3, 2026cs.LG

Graph Set Transformer

We introduce the Graph Set Transformer (GST), a neural network architecture for learning on sets of graphs, designed for tasks in which per-element predictions depend on set-wide context as well as local structure. Existing architectures, including DeepSets and SetTransformer, require pre-encoded graph embeddings from a separate GNN, creating a bottleneck between feature extraction and set-level contextualisation. In contrast, GST interleaves node-level feature propagation and cross-graph contextual modelling at every layer, fusing the two levels of information through a gating mechanism. We evaluate GST on a controlled synthetic suite designed to isolate set-conditional structural reasoning and on three real-data benchmarks spanning per-atom reaction-centre identification, reaction yield prediction, and image classification. Under matched parameter budgets, GST performs better than the baselines across these settings. An architectural ablation strongly suggests that the interleaving of local and set context contributes substantially to this advantage.
Jose E. Escrig Molina, Baoquan Chen, Daniel Probst
Jun 3, 2026cs.CL

Fast & Faithful Function Vectors

Function vectors (FVs) are task representations elicited during in-context learning that can be used to steer Large Language Models (LLMs). However, design choices in their formulation remain underexplored. In this work, we study the impact of varying FV definitions for instructions along two degrees of freedom: attention head selection and steering. For head selection, using gradient-based attributions with Layer-wise Relevance Propagation (LRP) substantially improves efficiency as well as accuracy. For FV steering, applying it in a distributed manner yields a higher accuracy compared to simple aggregation. Our code is publicly available.
Minh An Pham, Anton Segeler, Thomas Wiegand +4
Jun 3, 2026cs.LG

In-Context Graphical Inference

Marginal inference in discrete graphical models forces a choice between exactness and scalability: exact algorithms are intractable for high-treewidth graphs, while iterative approximations (Belief Propagation, variational methods) sacrifice convergence guarantees on frustrated topologies. We argue that this dichotomy stems from a mismatched inductive bias: iterative methods abandon the sequential elimination structure that makes exact inference correct. We introduce In-Context Graphical Inference (ICG-I), an autoregressive Graph Transformer that restores this structure by mimicking Variable Elimination with learned, Tensor- Train-compressed intermediate factors, paired with a Dirichlet output layer and Weighted Conformal Prediction for calibrated, distribution-free coverage guarantees under topological shift. We prove that TT compression errors propagate at most lincarly through the autoregressive chain, that the Dirichlet-Multinomial loss is a proper scoring rule, and that WCP maintains coverage with a quantifiable degradation under estimated density ratios. We conducted intensive experiments to evaluate ICG-I and achieved state-of-the-art performance across all benchmarks. ICG-I reduces MAE from 0.041 (best baseline) to 0.020 on standard instances and achieves 0.048 on N=500 frustrated spin glasses where BP diverges entirely.
Zehua Cheng, Wei Dai, Jiahao Sun
Jun 3, 2026cs.CL

TaDA: Calibrated Probe Gating for Task-Domain LoRA Merging

Combining a task LoRA adapter with a domain LoRA adapter into a single unified model is a practical yet largely unexplored challenge. Existing methods treat both adapters as symmetric peers, applying uniform weights across all layers. We argue that task and domain adapters exhibit a consistent depth-dependent asymmetry across transformer architectures. Domain dominance increases with layer depth, while shallower layers retain stronger task-relevant signals. Motivated by this observation, we propose TaDA\textbf{TaDA} (Ta\textbf{Ta}sk-D\textbf{D}omain LoRA\textbf{A} Merging), a training-free algorithm that exploits this structure through calibrated probe-guided per-layer gating and per-component subspace-aware merging. The gating assigns individual weights per layer and projection type using a probe signal proved invariant to adapter weight magnitude. The merging discards conflicting singular directions before combining the remaining components. TaDA\textbf{TaDA} produces a standard rank-rr LoRA adapter with zero inference overhead. On six scientific QA benchmarks with Llama-2-7B, TaDA achieves an average accuracy of 0.452, outperforming DARE-TIES by +3.6 percentage points and obtaining the best result on all six benchmarks. On six image classification benchmarks with ViT-L/16, TaDA reaches 85.9% average accuracy, improving over the strongest merging baseline while leading in three of the six individual benchmarks.
Huy Quoc To, Fuyi Li, Guangyan Huang +1
Jun 3, 2026cs.LG

Signed Dual Attention: Capturing Signed Dependencies in Time Series Forecasting

Initially developed for natural language processing, Transformer architectures and attention mechanisms are now central to a wide range of deep learning models, including applications in time series forecasting. A standard attention mechanism, however, implicitly assumes homophilic interactions, limiting its ability to model data with positive and negative dependencies, such as time series. In this work, we introduce the Signed Dual Attention, a novel attention formulation that captures both positive and negative relational patterns without additional parameters. By leveraging a dual message-passing scheme inspired by correlation structures, Signed Dual Attention propagates both supportive and contrastive information within a single shared block, effectively achieving the expressiveness of two head attention without additional parameters. This module can be seamlessly integrated into existing architectures and can yield performance gains in certain situations, requiring signed relational modeling. This approach opens a pathway toward more expressive and parameter-efficient transformers.
Balthazar Courvoisier, Tristan Cazenave
Jun 3, 2026cs.LG

An Empirical Audit of Input Encoders for Multi-Channel Signal Transformers

Transformers consuming multi-channel scalar signals must embed CC simultaneous values into one dmodeld_{\text{model}}-dimensional vector per time step. We audit eight input encoders -- a shared-scalar baseline, per-channel linear projections, an orthogonality regulariser, a nonlinear MLP, block-partitioned concatenation, channel-independent and channel-as-token architectures, and a projected positional encoding -- on a synthetic benchmark where channel identity is informative and on ETTh1, scored by next-step negative log-likelihood. The headline is practical near-equivalence within a wide "top tier": the standard per-channel linear projection matches every alternative up to small, statistically real but practically modest differences. A direct geometric probe attributes this to a spontaneous orthogonalisation of the per-channel projections: they end up near-orthogonal with no explicit regulariser, letting the standard linear recover channel identity from the summed embedding. Two encoders lose decisively: the shared-scalar baseline collapses for information-theoretic reasons we make explicit, and the channel-independent PatchTST-spirit baseline overfits universally on the synthetic benchmark and underperforms on both. Paired tests resolve two small gaps: projecting the sinusoidal positional encoding through a learned linear layer edges the rest at small CC by extending this orthogonality to the positional subspace; a nonlinear MLP stem edges them at the largest CC, with the gap shrinking under more training data. The practical recommendation: use the standard per-channel linear projection by default; reach for something more elaborate only when the task calls for it.
Ossi Lehtinen
Jun 3, 2026cs.LG

Test-Time Compute Scaling for ASR with Depth-Conditioned Looped Transformers

End-to-end ASR systems typically use fixed-depth acoustic encoders at inference, making it difficult to trade additional test-time computation for improved recognition without training a larger model. A natural approach is to reuse a shared Transformer block recurrently, but we find that naive looping does not fully exploit additional recurrent compute. We introduce LARM, a depth-conditioned looped Transformer that turns recurrent encoder depth into a controllable test-time compute axis. LARM combines sparse CTC checkpoints, supervision-clock embeddings, FiLM depth conditioning, and delayed soft-posterior feedback. These components structure the loop into recognition checkpoints separated by latent refinement phases and allow shared weights to specialize across recurrent steps. On LibriSpeech, LARM improves WER as the number of inference loops increases and achieves performance competitive with deeper unshared-parameter baselines. Our results show that test-time compute scaling can extend beyond autoregressive language-model reasoning to continuous non-autoregressive speech recognition.
Yacouba Kaloga, Shashi Kumar, Shakeel A. Sheikh +3
Jun 3, 2026cs.CL

SparDA: Sparse Decoupled Attention for Efficient Long-Context LLM Inference

Sparse attention reduces compute and memory bandwidth for long-context LLM inference. However, two key challenges remain: (1) KV cache capacity still grows with sequence length, and offloading to CPU memory introduces a PCIe transfer bottleneck; (2) the sparse selection step itself retains O(T2)O(T^2) complexity and can dominate attention cost at long contexts. We propose SparDA, a decoupled sparse attention architecture that introduces a fourth per-layer projection, the Forecast, alongside Query, Key, and Value. The Forecast predicts the KV blocks needed by the next layer, enabling lookahead selection that overlaps CPU-to-GPU prefetch with current-layer execution. Because Forecast is decoupled from the attention query, our GQA implementation uses one Forecast head per GQA group, reducing selection overhead versus the original multi-head selector. SparDA adds <<0.5% parameters and trains only the Forecast projections by matching the original selector's attention distribution. On two sparse-pretrained 8B models, SparDA matches or slightly improves accuracy and delivers up to 1.25×\times prefill speedup and 1.7×\times decode speedup over the sparse-attention offload baseline. By enabling larger feasible batch sizes on a single GPU, SparDA further reaches up to 5.3×\times higher decode throughput than the non-offload sparse baseline. Our source code is available at https://github.com/NVlabs/SparDA.
Yaosheng Fu, Guangxuan Xiao, Xin Dong +2
Jun 3, 2026cs.LG

ChessMimic: Per-Rating Transformer Models for Human Move, Clock, and Outcome Prediction in Online Blitz Chess

We present ChessMimic, a system of three small encoder-only transformers - for move, thinking-time, and outcome prediction - conditioned on the position, recent move history, player rating, and clock state. We fit a separate instance of each model per 100-Elo rating band, trading parameter efficiency for sharper per-skill calibration. On a held-out month-wide slice of Lichess Rated Blitz games ChessMimic's human move prediction accuracy outperforms Maia-2 in every Elo band. Compared to Maia-3, our 9M parameter model's accuracy sits between Maia-3-5M and Maia-3-23M without the additional complexity of Geometric Attention Bias. In addition to the move matching model, we also train a game outcome model that conditions not only on the position, but also player ratings, time control, and remaining clock times. The outcome model achieves an AUC of 0.78 out of sample, beating Maia-2 as well as logistic regressions based on material, ratings, and clock time. Finally, we train a clock model that predicts human thinking times. The clock model provides a usable but non-SOTA per-ply think-time signal under ALLIE-style filters (Pearson r = 0.41, Spearman rho = 0.50, MAE 4.10 s, against ALLIE's reported r = 0.70), with the residual gap concentrated in per-position bucket sharpness rather than bucket-marginal calibration. A public demo is at 1e4.ai and we release code, per-band weights, and the C++ data-filter pipeline code in GitHub.
Thomas Johnson
Jun 3, 2026cs.LG

Low-Rank Decay for Grokking in Scale-Invariant Transformers: A Spectral-Geometric View

Modern Transformer architectures frequently employ normalization mechanisms such as RMSNorm and Query-Key Normalization, making parts of the model approximately scale-invariant with respect to weight magnitudes. In this regime, standard Frobenius-norm weight decay acts purely along the radial direction of the weight space and cannot directly simplify the function represented by the normalized layer. We study grokking in small algorithmic tasks through this lens and propose \emph{Low-Rank Decay} (LRD), a nuclear-norm-like spectral regularizer whose subgradient -- the polar factor UV⊤UV^\top -- retains a tangential component even in the scale-invariant setting. This distinction has a concrete dynamical consequence: after the model memorizes the training set and task gradients vanish, L2 decay can no longer reshape the weight spectrum, whereas LRD continues to compress singular values in an ℓ1\ell_1-like fashion. On modular arithmetic tasks, we find that LRD induces rapid effective-rank collapse in Query/Key matrices and expands the data-fraction boundary at which delayed generalization (grokking) occurs. We further provide a spectral-geometric interpretation through the ``needle-to-fan'' expansion of the nuclear-norm subdifferential near low-rank strata.
Mingyu Li
Jun 3, 2026cs.LG

MeshTok: Efficient Multi-Scale Tokenization for Scalable PDE Transformers

Conventional patchified Transformers operate on uniform spatial partitions, distributing computational effort evenly across the domain irrespective of local features. This inflexible tokenization scheme is inherently limited in its ability to efficiently represent and process solutions to complex PDEs. To address this, we propose MeshTok, an adaptive mesh refinement (AMR)-inspired tokenization and sequence modeling framework. This method selectively refines spatial regions exhibiting sharp gradients, transient features, or multiscale structures, generating a heterogeneous set of multiscale tokens defined on a fixed simulation grid. These tokens are processed within a unified Transformer sequence, enabling the model to simultaneously capture coarse-grained global context and fine-grained local details without requiring specialized architectural components. Although adaptive refinement moderately increases token count, it promotes a more targeted allocation of computational resources to physically informative regions, which we view as a practical inductive bias rather than a formal optimality guarantee. Experimental evaluations across multiple PDE families and benchmark datasets demonstrate that MeshTok consistently improves the efficiency-accuracy trade-off compared to uniform-grid baselines. This suggests adaptive multiscale tokenization as a scalable and generalizable design principle for neural PDE modeling. Code is available at https://github.com/SCAILab-USTC/MeshTok.
Yanshun Zhao, Xiaoyu Peng, Jiamin Jiang +2
Jun 3, 2026cs.NI

Generalizable Multi-Task Learning for Wireless Networks Using Prompt Decision Transformers

Future wireless networks demand rapid adaptation to highly heterogeneous environments and dynamic task configurations, necessitating a shift from conventional rule-based and optimization-driven radio resource management (RRM) toward artificial intelligence (AI)-driven RRM. AI-driven approaches can learn complex nonlinear relationships, generalize across diverse network conditions and enable real-time, scalable and autonomous decision-making. Among RRM techniques, coordinated multipoint (CoMP) transmission is pivotal for mitigating inter-cell interference and enhancing cell-edge performance, thereby improving quality of experience (QoE) in dense deployments. However, optimal multi-cell selection remains a complex combinatorial challenge as it requires jointly optimizing over many possible serving-cell combinations under dynamic traffic and channel conditions. Despite their success, conventional deep reinforcement learning (DRL) methods such as proximal policy optimization (PPO) suffer from poor sample efficiency, limited generalization, and costly retraining when state and action spaces change. To address these bottlenecks, we propose a Prompt Decision Transformer (PromptDT) based multi-task learning framework capable of learning across diverse network configurations and reformulating multi-cell selection as a sequence modeling problem. By leveraging offline trajectories and task-specific prompts, PromptDT enables scalable learning across diverse network configurations, including varying base stations and user equipment counts, and scheduler policies. Experimental results demonstrate that PromptDT improves QoE by up to 49% in multi-task settings compared to baselines, with performance scaling positively alongside model capacity. Moreover, PromptDT generalizes effectively to unseen tasks, achieving robust few-shot adaptation to new network configurations without retraining or fine-tuning.
Fatih Temiz, Shavbo Salehi, Melike Erol-Kantarci
Jun 3, 2026cs.CL

Parameter-Efficient Fine-Tuning with Learnable Rank

Low-Rank Adaptation (LoRA) is a popular parameter-efficient fine-tuning (PEFT) method that restricts weight updates to low-rank adapters, introducing a fixed low-rank inductive bias by optimizing in a low-dimensional subspace. In this work, we question whether a fixed-rank constraint is the most effective inductive bias for parameter-efficient fine-tuning. We introduce Learnable Rank LoRA (LR-LoRA), a PEFT method in which the adapter rank is learned during the training process. Instead of prescribing a uniform rank for all adapter layers, LR-LoRA allows the optimizer to determine the appropriate rank for each layer. Using this approach, we find substantial layer-wise variation in the learned ranks, with the attention and MLP layers in the transformer models exhibiting systematically different rank preferences. Across a range of language understanding and commonsense reasoning benchmarks, LR-LoRA achieves state-of-the-art performance in most settings and consistently outperforms strong PEFT baselines, demonstrating that a learnable rank provides a more flexible and effective inductive bias than fixed-rank adaptations.
Arpit Garg, Simon Lucey, Hemanth Saratchandran
Jun 2, 2026cs.AR

P-Cast Precision in FP8 Attention: Sink-Induced Collapse and the Optimality of S=2^8

FP8 (E4M3) acceleration for attention computation offers significant throughput gains, but the 3-bit mantissa introduces precision challenges when the softmax probability matrix~PP is cast to FP8 before the P⋅VP \cdot V matrix multiplication. We analyze two implementation choices that affect output precision under the \emph{Attention Sink} phenomenon: (1)~the KV block iteration order, and (2) the static scaling factor applied to PP before casting. We show that forward KV iteration causes \emph{P-collapse} -- to leading order a fraction Φ(Δ+δk−6.93−ln⁡S)Φ(Δ+ δ_k - 6.93 - \ln S) of non-sink PP values underflow to zero, where the small shift δk≈1δ_k \approx 1 (for ksink=4k_{\text{sink}}{=}4) is the expected within-sink-block score maximum -- and that reverse iteration removes it, with a zero-underflow guarantee when reverse is combined with S=256S{=}256. We further give a constructive characterization of S=256=28S = 256 = 2^8 as the static scale that simultaneously satisfies (i)~bit-exact IEEE 754 scaling, (ii) the lower envelope of a sawtooth function dp(S)dp(S) over the E4M3 number line (dp=2−4dp = 2^{-4}, the minimum worst-case quantization step), and (iii)~the maximum normal-range coverage \emph{among bit-exact (2k2^k) scales} (a non-bit-exact scale such as 448448 attains slightly higher coverage; sec.5}). Both optimizations are already deployed in FlashAttention-3/4 on engineering grounds; our contribution is a quantitative account of \emph{why} these choices are good and a closed-form threshold Δc=6.93+ln⁡S−δkΔ_c = 6.93 + \ln S - δ_k for predicting kernel-level precision loss. Kernel-faithful experiments (Q,K,VQ, K, V in FP32 to isolate the P-cast effect) show 33-10×10\times MSE improvement at moderate sink strengths, and paired tests confirm both fixes saturate to the same precision floor when combined -- which motivated updating the hpc-ops kernel from S=1S{=}1 to S=256S{=}256.
Reed Lau
Jun 2, 2026cs.LG

Value-Aware Stochastic KV Cache Eviction for Reasoning Models

Reasoning models improve accuracy through extended chains of thought, but their long outputs create a memory and compute bottleneck. KV cache eviction methods reduce this cost by evicting unimportant key-value pairs from the cache, yet they often yield worse accuracy than selection-based sparse attention alternatives, which keep the full KV cache. We identify key factors crucial to KV cache eviction accuracy. First, a small fraction of value states have abnormally large magnitudes, and evicting them causes catastrophic failure where models enter repetitive reasoning loops. Second, introducing stochasticity during eviction improves accuracy by increasing cache diversity. Based on these findings, we propose Value-aware Stochastic KV Cache Eviction (VaSE), a training-free recipe that protects large-magnitude value states and promotes diverse eviction decisions. Across six reasoning tasks, Qwen3 models using VaSE with 4x KV cache compression yield higher average accuracies than SOTA selection method at the same sparsity, while outperforming the strongest eviction method by more than 4%. Overall, VaSE bridges the gap between efficiency and accuracy, supporting FlashAttention2 and enabling a static memory footprint for reasoning models.
Ting-Yun Chang, Harvey Yiyun Fu, Deqing Fu +3
Jun 2, 2026cs.LG

Dynamic Short Convolutions Improve Transformers

Transformers have become the dominant architecture for large language models, largely due to the scalability and flexibility of attention, feed-forward layers, residual connections, and normalization. This paper introduces dynamic short convolutions as an additional neural network primitive for improving Transformers. Unlike static short convolutions, dynamic convolutions use input-dependent filters, which preserves the locality bias of convolution while increasing expressivity. Motivating experiments show that applying dynamic short convolutions to key, query, and value representations improves performance on challenging associative recall tasks compared with static convolutional variants. Across language-modeling experiments ranging from 150M to 2B parameters, dynamic convolutions consistently outperform standard Transformers and Transformers augmented with static short convolutions. Fitting scaling laws indicates a 1.33×\times compute advantage over compute-matched Transformers when dynamic convolutions are applied to the key, query, and value vectors, and a 1.60×\times advantage when adding dynamic convolutions after every linear layer. Dynamic convolutions also offer improvements on linear RNNs (Mamba-2/Gated DeltaNet) and mixture-of-experts architectures. We make these gains practical with custom Triton kernels that enable efficient training with a manageable end-to-end slowdown. These results suggest that dynamic short convolutions are a scalable, hardware-efficient, and expressive primitive for advancing Transformer-based language models.
Oliver Sieberling, Bharat Runwal, Rameswar Panda +1
Jun 2, 2026cs.CV

UtVAA: Ultra-tiny Vision Transformer with Affix Attention for Mobile Image Classification

Vision Transformers (ViTs) have demonstrated strong representation capability in image classification. However, their quadratic self-attention complexity and large parameter counts limit deployment on resource-constrained mobile and edge devices. This paper introduces UtVAA, an ultra-tiny Vision Transformer architecture designed for efficient visual recognition under strict computational budgets. It incorporates a novel Affix Attention block that combines depthwise-pointwise local feature extraction, linear self-attention, coordinate attention for spatial dependency modelling, and a lightweight ternary fusion strategy to integrate local and global representations. In addition, Dilated Bottleneck blocks expand the receptive field using dilated depthwise separable convolutions while maintaining low FLOPs and stable optimisation through residual connections. UtVAA is implemented in scalable Tiny, Medium, and Large variants, with the smallest model containing 204.67K parameters and 53.95M FLOPs. Experimental results on CIFAR-10, CIFAR-100, PlantVillage-Tomato and SLIF-Tomato datasets show that UtVAA achieves competitive accuracy within a sub-million-parameter regime. Overall, the results demonstrate that transformer-based vision models can be redesigned into ultra-tiny architectures without significant loss in discriminative performance, making UtVAA suitable for mobile and edge deployment. Code is available at https://github.com/romiyal/UtVAA
Romiyal George, Sathiyamohan Nishankar, Selvarajah Thuseethan +1
Jun 2, 2026cs.CV

TrAction: Action Recognition with Sparse Trajectories

Modern action recognition models operate on memory- and compute-intensive dense RGB video volumes and frequently exploit appearance and background shortcuts, for example, predicting actions from objects or scenes instead of characteristic motion. We investigate an efficient alternative input modality that is largely free of such biases by construction: sparse point trajectories. To this end, we develop a simple transformer architecture for 2.5D trajectory-based recognition together with a masked-trajectory pretraining, which we show to substantially improve downstream action recognition accuracy. Despite using only a fraction of the dense RGB input, our method reaches 45% top-1 on Something-Something V2 and 54% on EPIC-Kitchens-100, and surpasses V-JEPA on time-reversal sensitivity. More importantly, we find trajectory features to be complementary to state-of-the-art appearance-based features. Fusing our pretrained model with DINOv2 and V-JEPA 2 improves top-1 accuracy on Something-Something V2 by 8.7 and 1.6 points, respectively. Code: https://github.com/ecker-lab/TrAction
Jan F. Meier, Felix B. Mueller, Alexander Ecker +1
Jun 2, 2026cs.NE

PrimeSVT: An Automated Memory-aware Pruning Framework with Prioritized Compression Policy for Spiking Vision Transformers

The large sizes of Spiking Vision Transformers (SViTs) still hinder their embedded implementation, highlighting the need for model compression. State-of-the-art works compress SViT models through unstructured pruning, which needs specialized hardware accelerators for their specific sparsity patterns to maximize efficiency gains. Moreover, their manual approach requires a huge design time to find an appropriate pruning setting for each network, thus making this approach not scalable. To address this limitation, we propose PrimeSVT, a novel framework that performs automated memory-aware structured pruning on pre-trained SViT models, thereby maximizing their efficiency gains during inference amenable to widely-used computing architectures. To achieve this, PrimeSVT first sorts the SViT layers based on their sizes (i.e., number of parameters), identifies the targeted pruning layers based on their robustness under different pruning rates, then leverages this order for compressing the model layer-by-layer sequentially from the largest one to the smallest one (i.e., so-called prioritized compression policy), while considering the user-defined constraints (i.e., acceptable accuracy and memory saving). In each layer, PrimeSVT employs channel-wise filter pruning based on their L2-norm values to structurally remove the non-significant weights. Experimental results show that PrimeSVT saves 26.68% memory through automated single-shot pruning, while preserving accuracy within 3% (70.3% without fine-tuning and 72.9% with fine-tuning) from the original unpruned SViT model (73.3%), thus meeting the accuracy and memory constraints. These show that our PrimeSVT framework enables design automation for SViTs and their embedded implementation.
Rachmad Vidya Wicaksana Putra, Achyuta Muthuvelan, Alberto Marchisio +1
Jun 2, 2026cs.CL

Causal Evidence of Stack Representations in Modeling Counter Languages Using Transformers

Formal languages have proven to be effective conduits to understand the inner mechanisms of transformers. Past work has shown that transformers trained on next token prediction over counter languages learn representations consistent with an underlying stack structure. Beyond representational analysis, this paper investigates the causal role of these representations. Linear probes are trained to predict the stack depth at each token from the model's hidden states, and a principal representation direction is extracted from the probe. Ablation of this direction from the model causes sequential accuracy to collapse to near 0%, providing strong empirical evidence that the stack representation is not just learned, but is causally necessary for model performance.
Nishit Singh
Jun 2, 2026cs.CV

BA-T: An Iterative Transformer for Two-View Bundle Adjustment

Feed-forward models for 3D reconstruction have achieved strong performance using deep cross-view attention to exchange information across images. However, these approaches often depend on heavy decoder stacks and lack a structured mechanism for geometry refinement, resulting in poor multi-view consistency. We address this by drawing inspiration from classical bundle adjustment (BA), which can be viewed as an iterative information propagation process between poses and local geometry. Inspired by BA, we propose BA-T, an iterative Transformer that implements BA-style structured updates as a repeatable layer in implicit token space. Instead of relying on deep attention stacks, BA-T refines predictions based on latent residual by a single lightweight layer. Experiments demonstrate that BA-T progressively improves pose and reconstruction accuracy across iterations, achieves stronger cross-view consistency than conventional decoders, and matches or surpasses substantially larger models while using only 16% of their decoder parameters. BA-T provides a compact, efficient, and structural alternative to depth-heavy attention, enabling accurate 3D reconstruction within a lightweight architecture. The code will be made publicly at https://github.com/zhangganlin/BA-T.
Ganlin Zhang, Weirong Chen, Daniel Cremers +1
Jun 2, 2026cs.NE

PSViT: A Methodology for Structurally Pruning Spiking Vision Transformers

Spiking Vision Transformer (SViT) models are promising low-power ViT models for solving vision-based tasks with state-of-the-art performance. However, their large sizes limit their deployments for resource-constrained embedded platforms, underscoring the needs of model compression. One of prominent compression techniques is pruning, and the state-of-the-art works employ unstructured pruning techniques to compress SViT models. Such techniques require specialized hardware architectures tailored for the sparsity patterns to maximize their efficiency benefits, making this approach not scalable. To address this, we propose PSViT, a novel methodology to perform structured pruning on SViT models, hence making it possible to efficiently accelerate their inference using the existing and widely-used computing architectures. To do this, PSViT employs several key steps: uniform channel-wise filter pruning to structurally eliminate the non-significant weights, sensitivity analysis to evaluate the impact of channel-wise pruning of individual layer on accuracy and network size, as well as fine-grained channel-wise pruning based on the sensitivity analysis and the given network architecture. Experimental results show that PSViT effectively obtains 22.4% memory saving through single-shot pruning, while maintaining high accuracy within 3% (70.3% without fine-tuning and 72.8% with fine-tuning) from the original non-pruned SViT model (73.3%) on the ImageNet-1K. These results also show that the PSViT methodology advances the effort in enabling efficient SViT deployments on resource-constrained applications.
Rachmad Vidya Wicaksana Putra, Achyuta Muthuvelan, Alberto Marchisio +1
Jun 2, 2026cs.SD

A Training-Efficient Transformer-Based Anti-Spoofing Network for Logical Access in ASVspoof 5

Synthetic and manipulated speech can reduce the reliability of automatic speaker verification systems, so anti-spoofing methods need to be both accurate and efficient in training and inference. This paper focuses on the ASVspoof 5 Track 1 closed condition, where standard cross-entropy training may not give enough attention to hard trials and is not directly aligned with ranking- and threshold-based evaluation metrics. We propose TFPARN, a Transformer-based focal-pairwise attentive ranking network. The system extracts log-Mel features from speech, uses a Transformer encoder to model frame-level information, applies attention pooling to obtain utterance-level representations, and is trained with a combination of focal classification loss and pairwise ranking loss. RawBoost augmentation is used during training, and test-time augmentation is applied during evaluation to improve robustness. Compared with re-implemented AASIST and RawNet2 baselines under the same protocol, TFPARN achieves the best results, with a minDCF of 0.2430 and an EER of 12.52%. Ablation experiments further show that the pairwise loss, focal loss, and attention pooling all improve performance. TFPARN also uses the lowest inference memory among the compared systems, at 1.4 GB, runs at about 0.79 ms per utterance, and reaches its best checkpoint in less training time than AASIST. These results show that TFPARN provides a good balance between detection accuracy and computational cost for logical access anti-spoofing.
Sidan Yin, Bo Zhao
Jun 1, 2026cs.AR

Multi-Segment Attention: Enabling Efficient KV-Cache Management for Faster Large Language Model Serving

Large Language Model (LLM) inference relies on key-value (KV) caches to avoid redundant attention computation. While approximate KV cache retention techniques reduce memory usage by sacrificing model accuracy, lossless approaches instead evict KV cache blocks from GPU memory and reconstruct them on demand to preserve exact outputs. Existing lossless KV cache management systems primarily base eviction decisions on access frequency or positional heuristics, without considering how different KV cache blocks affect the execution efficiency of GPU attention kernels. In this paper, we propose AsymCache, a computation-latency-aware KV cache management system for LLM inference that explicitly aligns cache residency decisions with GPU attention kernel performance, including three key components: Multi-Segment Attention (MSA) for efficient non-contiguous KV context processing, a cache eviction policy that jointly optimizes hit rate and position-aware recomputation cost, and an adaptive chunking scheduler for high hardware utilization. Experiments show that AsymCache reduces TTFT by up to 1.90-2.03x and time-per-output-token (TPOT) by 1.62-1.71x over latest baselines, confirming the effectiveness of the method in common workloads and validating its design goal of balancing computational efficiency with cache hit rate. Moreover, the low-level design of AsymCache allows seamless integration into agent serving systems such as Continuum, where it further reduces average job latency by up to 18.1%.
Chunan Shi, Yilei Chen, Yilin Chen +2
Jun 1, 2026astro-ph.IM

Data-Driven Forecasting of three-Component Seismograms Using Transformer Architectures

Forecasting seismic waveforms beyond observed data remains challenging due to the nonlinear, dispersive, and multi-scale nature of seismic wave propagation. In this work, we introduce \textsc{SeismoGPT}, a transformer-based autoregressive model designed to forecast three-component seismic waveforms directly in the time domain. Forecasting is formulated as a physically constrained continuation problem in which the model receives waveform context beginning at the P-wave arrival and extending a defined time beyond the S-wave arrival, after which future motion is generated recursively without access to ground-truth samples. Evaluation is performed on synthetic seismograms spanning source depths of 5--100,km, epicentral distances of 10--90∘^\circ, and magnitudes 3≤Mw≤73 \leq M_w \leq 7. To disentangle the effects of context length and prediction horizon, we define three evaluation configurations using a distance-normalized context ratio and fixed prediction horizons of 120 and 240,s. Across all configurations, the model achieves a median normalized cross correlation of 0.93 or higher. Analysis of representative forecasts shows that successful predictions preserve both phase coherence and spectral energy distribution. Where failure cases arise, this is primarily due to gradual phase drift during autoregressive rollout rather than unphysical signal generation. These results demonstrate that transformer-based sequence models can learn stable dynamical continuation of seismic wavefields, highlighting the potential of foundation-model approaches for physics-driven time-series forecasting. There are potential applications of this methodology in seismic warning and hazard mitigation, particularly for next-generation gravitational-wave observatories, such as the Einstein Telescope.
Waleed Esmail, Stuart Russell, Jana Klinge +2
Jun 1, 2026cs.LG

Do Transformers Need Three Projections? Systematic Study of QKV Variants

Transformers have become the standard solution for various AI tasks, with the query, key, and value (QKV) attention formulation playing a central role. However, the individual contribution of these three projections and the impact of omitting some remain poorly understood. We systematically evaluate three projection sharing constraints: a) Q-K=V (shared key-value), b) Q=K-V (shared query-key), and c) Q=K=V (single projection). The last two variants produce symmetric attention maps; to address this, we also explore asymmetric attention via 2D positional encodings. Through experiments spanning synthetic tasks, vision (MNIST, CIFAR, TinyImageNet, anomaly), and language modeling (300M and 1.2B parameter models on 10B tokens), we discovered that our transformers perform on par or occasionally better than the QKV transformer. In language modeling, Q-K=V projection sharing achieves 50% KV cache reduction with only 3.1% perplexity degradation. Crucially, projection sharing is complementary to head sharing (GQA/MQA): combining Q-K=V with GQA-4 yields 87.5% cache reduction, while Q-K=V + MQA achieves 96.9%, enabling practical on-device inference. We show that Q-K=V preserves quality because keys and values can occupy similar representational spaces and attention operates in a low-rank regime, whereas Q=K-V breaks attention directionality. Our results systematically characterize projection sharing as an underexplored instance of weight tying in attention, with direct, quantifiable inference memory benefits, particularly valuable for edge deployment. The code is publicly available at https://github.com/Brainchip-Inc/Do-Transformers-Need-3-Projections
Ali Kayyam, Anusha Madan Gopal, M Anthony Lewis
Jun 1, 2026cs.AI

Evaluating Transformer and LSTM Frameworks for Prediction in Ungauged Basins

Watershed networks exhibit convergent topologies in which multiple tributaries merge into downstream channels,integrating diverse upstream hydrological processes. In ungauged basins, the absence of direct observations increases uncertainty and limits the ability to anticipate extreme events. This study evaluates whether an encoder-only Transformer provides an advantage over an LSTM for upstream streamflow inference under limited hydrologic information, using retrospective simulations from the NOAA National Water Model (NWM). Across both upstream-only and combined configurations, the LSTM showed stronger overall performance than the Transformer model across the two configurations. Incorporating downstream information further boosted performance for all models, increasing median NNSE by more than 60%. Rather than treating this as a leaderboard-style comparison, we interpret the experiments as a test of architectural inductive bias for hydrologic sequence inference. The results indicate that recurrent memory remains better aligned with this upstream reconstruction task than an encoder-only Transformer, while downstream hydrologic context provides a strong auxiliary constraint that substantially improves prediction skill across architectures
Taye Akinrele, James Halgren, Noorbakhsh Amiri Golilarz +2
Jun 1, 2026cs.CL

Do Value Vectors in Deep Layers Need Context from the Residual Stream?

The success of the transformer architecture as the backbone of modern LLMs is in large part due to its use of attention layers. An attention layer follows the standard neural network paradigm: it takes the residual stream as input and thereby produces context-dependent query, key, and value vectors. However, we find that model performance meaningfully improves when deeper layers learn only a context-free value vector to preserve the original token information, without drawing on any context from the residual stream. When the model has access to this context-free value vector, adding back the context-dependent component provides little additional benefit for aggregate benchmark performance. Such context-free value vectors can be stored as sparse model parameters, eliminating the need to recompute or persistently cache these values. Through systematic ablations on the key design choices for such context-free value vectors, we propose Bank of Values (BoV), a new way of computing value vectors in attention by learning a lookup table of token-specific value vectors for each of the last third of layers. Across 135M and 780M models, BoV improves validation loss over standard attention and, at 780M, the average score across 21 benchmarks, matching the previous best method that adds token information to the value vector with less compute and memory.
Muyu He, Yuchen Liu, Qingya Huang +1
Jun 1, 2026cs.CV

Edge Prediction for Roof Wireframe Reconstruction with Transformers

This paper presents a competitive solution to the S23DR Challenge 2026, which aims to reconstruct 3D house roof wireframe models from sparse SfM point clouds and ground-level semantic segmentations and depth maps. Our proposed method utilizes an end-to-end Transformer encoder-decoder architecture inspired by DETR. To effectively process the geometric and semantic data, the sparse SfM point cloud input is dynamically subsampled based on semantic priority and augmented with Gestalt and ADE20k class features. To further increase segmentation context, we fuse the point features with additional Gestalt feature encodings which are obtained by projecting the points into latent feature maps produced by a frozen autoencoder. Learned query embeddings are then decoded directly into 3D wireframe edges via cross-attention mechanisms. Evaluated on the "HoHo 22k" dataset, our approach significantly outperforms both handcrafted and learned baselines, achieving a Hybrid Structure Score (HSS) of 0.6476 and securing the second-highest position on the challenge's private leaderboard.
Gustav Hanning, Ludvig Dillén, Jonathan Astermark +2
Jun 1, 2026cs.AI

Forget Attention: Importance-Aware Attention Is All You Need

Combining attention's global retrieval with the sequential importance signal of state space models (SSMs) is the open challenge of hybrid language modeling. Transformers see everywhere but cannot prioritize; SSMs know what matters but cannot revisit. Existing hybrids -- Jamba (block level) and Hymba (head level) -- place the two in separate compartments, so neither informs the other during the attention computation itself. We propose SISA (SSM-Informed Softmax Attention), which adds an SSM-derived importance term directly inside the attention score and realizes the full operation as a single SDPA call on augmented query/key vectors -- no recurrent state, no custom kernel. At 152M / 5B tokens, SISA reaches LAMBADA-greedy 17.3% (vs. Transformer 13.9 and Mamba-3 15.5) and attains NIAH 100% from step 1K, 7x faster than Transformer's retrieval convergence; at 369M, Mamba-3 leads LAMBADA while SISA preserves perfect NIAH and stock-SDPA execution. SISA thus defines a third design axis for SSM-attention hybrids -- score-level fusion -- beyond the block-level and head-level paradigms that have dominated the field.
Suhyeong Shin, Yeongwook Yang
Jun 1, 2026cs.LG

Riemannian Gradient Descent for Low-Rank Architectures

We explore Riemannian optimization techniques for rank-factored matrix parameters, targeting contemporary deep learning applications. We examine ten points in the algorithm design space: two geometries for rank-rr matrices, three geometries for rank-rr partial isometries, and block-matrix variants of these five, where factors are shared across block-rows and block-columns. We apply our methods to the multihead attention parameters in small language models. After tuning learning rates, our methods do not conclusively outperform an AdamW baseline. Our implementations are available online.
Nicholas Knight
Jun 1, 2026cs.CL

LayerRoute: Input-Conditioned Adaptive Layer Skipping via LoRA Fine-Tuning for Agentic Language Models

Agentic language model systems alternate between two structurally distinct step types: structured tool calls (short, deterministic, low perplexity) and open-ended planning/reasoning steps (long, complex, high perplexity). Despite this heterogeneity, current inference systems apply identical compute to every step. We introduce LayerRoute, a lightweight adapter that learns to selectively skip transformer blocks on a per-input basis. LayerRoute augments each of the 24 transformer blocks in Qwen2.5-0.5B-Instruct with: (1) a per-layer router (~897 parameters, Linear(896,1)) that outputs a hard binary gate via the straight-through estimator, and (2) LoRA adapters (rank 8, ~1.08M parameters) on the Q/K/V/O attention projections. The backbone weights remain frozen. A single end-to-end training pass on agentic data (Hermes, Glaive, GSM8K, Turing) with a gate regularisation term forces the system to discover which blocks are skippable per input type. After 3,000 steps (6.4 minutes on an A100 40GB), LayerRoute achieves a 12.91% skip differential: tool calls skip 15.25% of FLOPs while planning steps skip only 2.34%, using only 1.10M trainable parameters (0.22% of the 494M backbone). Quality improves over the base model due to LoRA adaptation, with perplexity delta of -1.29 on tool calls and -1.30 on planning.
Prateek Kumar Sikdar
Jun 1, 2026cs.CV

VG2\text{VG}^2GT: Voxel-Gaussian Splatting Visual Geometry Grounded Transformer

Gaussian splatting has shown strong potential for 3D reconstruction and novel view synthesis. However, most existing methods require accurate camera parameters and per-scene optimization, while feed-forward methods with pixel-aligned Gaussian primitives often suffer from artifacts and non-uniform primitives. In this paper, we propose VG2\text{VG}^2GT, a Voxel-Gaussian Splatting Visual Geometry-Grounded Transformer. VG2\text{VG}^2GT leverages a frozen pretrained visual foundation model (VFM), incorporates a multi-scale differentiable voxel module to enhance geometric understanding, and directly splits and regresses Gaussian primitive parameters from voxel features. During training, depth maps are supervised through stochastic solid volume rendering, enabling geometrically accurate Gaussian scene reconstruction while keeping the visual foundation model fully frozen. This design enables VG2\text{VG}^2GT to be seamlessly plugged into any patch-feature-based VFM, while substantially reducing the required training cost. VG2\text{VG}^2GT outperforms current state-of-the-art methods on widely used DTU, Replica, TAT, and ScanNet datasets.
Yibin Zhao, Yihan Pan, Jun Nan +3
Jun 1, 2026cs.LG

Rethinking the Role of Positional Encoding: Sliding-Window Transformers without PE Remain Turing Complete

Positional encoding (PE) is widely viewed as necessary for transformers to process ordered sequences: without them, the next-token map appears permutation-invariant in its context tokens. This intuition underlies all prior universality results, which rely on positional information to prove that transformers with chain-of-thought can perform arbitrary computation, i.e., they are Turing complete. We revisit this belief in the regime most relevant to long-form reasoning, where generation proceeds through a finite sliding context window. Our opening perception is that the window mechanism itself (mildly) breaks the permutation symmetry. To distill and precisely capture the degree of this added expressiveness, we introduce an abstract autoregressive model, the HIST model, in which each update depends only on constant-size internal state and the token-count histogram within the current window. We prove that this HIST model is Turing complete by showing that the evolution of the window can reveal the token that has just left the window, which suffices to simulate Turing-complete Post machines. We then construct a sliding-window transformer over a constant-size token alphabet, without PE, and show that it can simulate the HIST model. Our result demonstrates that positional encodings are not indispensable for transformers to perform universal computation: The window sliding itself already breaks permutation symmetry and captures sufficient positional information.
Qian Li, Xinyu Mao, Shang-Hua Teng
May 31, 2026cs.DC

Move the Query, Not the Cache: Characterizing Cross-Instance Latent Attention Redistribution Across GPU Fabrics

Frontier LLMs increasingly decide what a query attends to with a sparse-attention indexer that picks a few KV-cache blocks per query: attention's unit is now a small, reusable chunk. Agentic workloads hammer it: many sub-agents query one large codebase, reusing the same blocks. When that corpus outgrows one GPU it is partitioned across instances, so a query and the blocks it selects often sit on different GPUs: answering it means attention across instances. The reflex of prior cross-instance KV systems is to move the cache: pull the selected blocks to the requester. Multi-head Latent Attention inverts the arithmetic, compressing each token's key and value into one narrow vector, so a routed query row is only ~1 KB, smaller than the chunk it attends; routing the query is then often cheaper than moving the cache. Which primitive wins, over which fabric and request shape, is uncharted, least of all on device-initiated RDMA that makes per-request cross-node transfers cheap. We characterize cross-instance MLA attention on a real multi-node H100 cluster, distilling two reusable artifacts: a topology-aware cost model (probe / transfer / compute / return / merge) and a closed-form route/fetch/local predicate, whose constants we measure on real IBGDA, where the model tracks batched round-trips to within ~7%. At decode it routes the query, trading the cost of moving the cache (a ~3 ms re-adaptation splice for a contiguous chunk, or a scattered gather under selection) for a tens-of-microsecond round trip, and picks the fabric by probe latency, not peak bandwidth. We instantiate the cost model and predicate for MLA, but neither is MLA-specific: they apply wherever compression or sparse selection shrinks attention to small chunks (DeepSeek-V3.2, V4, and GLM-5.1 today). Extending them to a new architecture requires measuring just two coefficients: the routed payload and fetch's move-the-cache cost.
Bole Ma, Jan Eitzinger, Harald Köstler +1
May 31, 2026cs.LG

CART: Context-Anchored Recurrent Transformer -- A Parameter-Efficient Architecture with Learned Stability

We present CART (Context-Anchored Recurrent Transformer), a parameter-efficient language model that reuses a single shared core block R times across depth. Unlike prior looped transformers that recompute key-value tensors at every iteration, CART computes K and V once from a multi-layer prelude and has the recurrent core cross-attend to those frozen tensors via multi-head latent attention. A learned Linear Time-Invariant (LTI) gate keeps the recurrence stable: its spectral radius settles in a narrow band (rho in [0.79, 0.83]) across all 36 fully-trained configurations. We evaluate CART on single consumer GPUs in two stages: a 64-configuration screen at 3,000 steps, then 36 configurations (P=6, R in {6,8,10}, three seeds) trained for 30,500 steps (~1B tokens). Two patterns hold across widths d in {256,512,768,1024}: prelude depth P dominates loop count R, and the Stage-1 ranking of R reverses at full training (R=6 becomes best at d>=512). At the binding d=1024 parameter-parity test, CART does not beat a parameter-matched dense baseline, losing by 1-2% at stored-parameter parity and by ~10% at effective-parameter parity. Diagnostic ablations split the effective-parameter gap into ~5% from weight sharing and a residual ~5% from the heterogeneous prelude/anchor/core/coda framing; the recurrent-core machinery (hyper-connections, LTI gate, loop-index embedding) is individually vestigial. Variable-R inference degrades on both sides of the trained R, a negative result for test-time depth scaling under this recipe.
Chad A. Capps
May 31, 2026cs.CV

Interpolation between Convolution and Attention via K-Nearest Neighbors

The shift from Convolutional Neural Networks to Transformers has reshaped computer vision, yet these two architectural families are typically viewed as fundamentally distinct. Convolutional Neural Networks are defined by spatially local convolution operations, while Transformers rely on global self-attention. We argue that convolution and self-attention, despite their apparent differences, can be unified within a single k-nearest neighbor aggregation framework. The critical insight is that both operations are special cases of neighbor selection and weighted aggregation. Convolution selects neighbors by spatial proximity while self-attention selects by feature similarity, revealing that they lie on a continuous spectrum rather than representing categorically different computations. We introduce Convolutional Nearest Neighbors (ConvNN), a unified framework that formalizes this connection. ConvNN exactly recovers standard and depthwise convolution by restricting neighbor selection to normalized spatial coordinates, and exactly recovers self-attention and its sparse variants, including KVT-attention, by replacing spatial proximity with scaled dot-product similarity. Beyond these special cases, ConvNN serves as a drop-in replacement for both convolution and attention layers, enabling systematic exploration of the intermediate spectrum between local and global aggregation through configurable similarity functions, neighbor selection strategies, positional encodings, and aggregation kernels.
Mingi Kang
May 31, 2026cs.LG

Leaf Spectral Reflectance Prediction Using Multi-Head Attention Neural Networks

Accurate modeling of leaf spectral reflectance from physiological and biochemical traits is essential for advancing remote sensing applications in plant science and precision agriculture. Widely used radiative transfer models, such as PROSPECT-PRO, rely on generalized trait-reflectance relationships developed from a wide range of species, which may not fully capture the spectral behavior of specific crops like grapevines. In this study, we developed a trait-to-spectra prediction model using a multi-head attention neural network trained on a grapevine-specific dataset that includes 16 leaf traits measured across multiple varieties, growth stages, and years. The model was evaluated using stratified 5-fold cross-validation and achieved an average coefficient of determination (R^2) of 0.84 and normalized root mean squared error (NRMSE) of 1.52 percent, demonstrating high accuracy and generalizability. When compared to PROSPECT-PRO in forward mode, the neural network exhibited lower mean absolute error (MAE), especially in the near-infrared (NIR) and shortwave-infrared (SWIR) regions. These results emphasize the importance of species-specific modeling approaches and show that integrating biochemical and structural traits into data-driven architectures can significantly improve spectral prediction. The proposed model provides a robust framework for generating accurate leaf-level reflectance data, with potential applications in canopy trait retrieval, vineyard monitoring, and remote sensing-driven crop management.
Parastoo Farajpoor, Alireza Pourreza, Mohammadreza Narimani +2
May 31, 2026cs.LG

Blurry Window Attention

The Softmax Attention operation in Transformer language models has a quadratic complexity in the sequence length and a growing state size in the form of KV cache, which becomes a bottleneck in long context scenarios. To overcome this limitation, alternative architectures with linear complexity and finite state size have been introduced, such as State-Space Models (SSMs), Linear Attention (LA), and Attention with Bounded-memory Control (ABC). Though linear models achieve similar language perplexity as Transformers, they are still behind in tasks which require retrieval or recall of specific information. In this work, we introduce Blurry Window Attention (BLA) a novel ABC method inspired by SSMs. BLA stores a frequency window from which a blurry KV history is reconstructed via interpolation using Dirichlet kernels. BLA can be understood as a generalization of Sliding Window Attention (SWA) depending on the Dirichlet kernels resolution or as a special case of the Gated Slot Attention (GSA), where the decay factor is implemented with Dirichlet kernels. We describe in details the theory and efficient implementation of BLA. On the Multi-Query Associate Recall (MQAR) synthetic task, we show that the state efficiency of BLA is 8×\times better than SWA and is competitive with popular linear attention models, and in the RegBench synthetic task, only BLA and SWA improve their performance as the state size grows among the linear models we tested.
Axel Laborieux, Christos Sourmpis, Juan Gabriel Kostelec +1
May 31, 2026cs.LG

FAiT: Frequency-Aware Inverted Transformer for Multivariate Time Series Forecasting

While Transformer-based architectures have established themselves as a dominant paradigm in Multivariate Time Series Forecasting (MTSF), their core self-attention mechanism inherently functions as a low-pass filter, systematically smoothing out high-frequency signals vital for sharp local changes. Recent advancements have increasingly incorporated frequency-domain operations to address this bias, however, most existing designs rely on fixed spectral bases and apply sequence-wise (uniform) modulation, implicitly assuming a time-invariant frequency response. This overlooks a key property of real-world series that their spectral characteristics often evolve over time, making uniform modulation insufficient for capturing fine-grained temporal dynamics. To tackle these limitations, we propose FAiT, a Frequency-Aware inverted Transformer. Specifically, FAiT rectifies the spectral bias internally through Inverted Attention, which interprets the attention map as a learnable low-pass operator and constructs a dedicated complementary high-pass branch by inverting the attention matrix to recover attenuated transient signals. Furthermore, FAiT introduces Dynamic Temporal-Frequency Modulation (DTFM), which synthesizes instance-conditioned weights to adaptively re-calibrate the energy of spectral sub-bands, enabling fine-grained control over evolving multi-scale patterns. Extensive experiments on widely used benchmarks demonstrate that FAiT consistently outperforms state-of-the-art Transformer-based and frequency-enhanced baselines, while maintaining computational efficiency.
Peng He, Yao Liu, Yanglei Gan +3
May 31, 2026cs.CL

Don't Read Everything: A Curvature-Conditioned Query for Linear Attention

Linear attention reduces the quadratic cost of softmax attention by maintaining a recurrent fast-weight state, but it consistently lags on in-context retrieval and long-context tasks. Existing remedies act on the write side of memory through gating, delta updates, or kernel feature maps, but the read step is left unchanged: every past key contributes additively to the output, so useful targets are diluted by the bulk of stored vectors. We borrow one specific piece of softmax's geometry to construct a cheap read-time contraction of the query. A second-order Taylor expansion of the softmax log-partition at the isotropic-attention point gives a local quadratic model whose curvature coincides with the running key covariance, a quantity that can be maintained with the same recurrent/chunkwise mechanism as the linear-attention state. The associated linear operator contracts the query along the high-variance directions of memory before it reads the state. We call this mechanism Curvature-Conditioned Query (CCQ). CCQ modifies only the read step and is composable with any linear-attention backbone. Attached to GLA and Gated DeltaNet, it improves perplexity, zero-shot downstream accuracy, S-NIAH retrieval at and beyond the training context, length-extrapolation perplexity from 4K to 20K, and LongBench accuracy.
Dong Le, Thong Nguyen, Cong-Duy Nguyen +1
May 31, 2026cs.AI

Emergent Ordinal Geometry in Transformers Trained on Local Comparisons

Transitive inference is the challenge of inferring that A < C from knowing only adjacent relations (A < B, B < C). It is solved by humans and animals not through logical chaining but via an analogue mental number line, whose signature is the symbolic distance effect: distant comparisons are easier than nearby ones. We ask whether Transformers acquire the same primitive, training small models exclusively on adjacent comparisons from a hidden total order and evaluating generalization to unseen distant pairs. We find that out-of-distribution generalization emerges alongside a striking geometric reorganization: entity embeddings collapse onto a one-dimensional manifold whose principal axis recovers the hidden rank order with near-perfect fidelity, and this structure is sensitive to optimization in ways that produce grokking-like transient dynamics. Critically, even when accuracy is at ceiling, decision confidence and geometric separation both scale monotonically with rank distance, directly mirroring the symbolic distance effect observed across decades of behavioural experiments on humans, primates, and rodents. We further show the same rank-aligned geometry in a pretrained large language model, where it tracks the topology of each ordinal relation: linear for sizes and digits, cyclic for months. These results ground a 50-year-old behavioural regularity in the geometry of learned representations, offering a mechanistic account of transitive inference that bridges cognitive science and modern neural networks.
Nishit Singh
May 31, 2026cs.LG

Beyond Sinusoids: A Morlet Wavelet Framework for Transformer Positional Encoding

Standard positional encodings for transformers - sinusoidal and rotary (RoPE) - treat every position as equally local: they encode where a token is, but not how far its positional influence should extend. We propose that the Morlet wavelet, which simultaneously minimises uncertainty in position and frequency, is the natural basis for positional encoding, and introduce Morlet Positional Encoding (MoPE): each embedding dimension learns its own frequency and locality bandwidth from data. The main theoretical result is a unification: sinusoidal PE and the RoPE correlation kernel both emerge as limiting cases of MoPE when locality is switched off (sigma_i -> infinity). The phase of MoPE recovers the RoPE rotation angle exactly; the amplitude adds a learned Gaussian locality kernel that standard encodings lack. Empirically, MoPE combined with Energy-Gated Attention achieves +0.119 improvement over standard attention on TinyShakespeare, outperforming either component alone. Analysis of the learned parameters reveals that all 128 frequency-bandwidth pairs converge to the wavelet admissibility boundary - an empirical observation consistent with a companion result on energy gating, suggesting a reproducible property of character-level language signals that warrants further investigation.
Athanasios Zeris
May 31, 2026cs.AI

TriLens: Per-Layer Logit-Lens Entropy for White-Box Hallucination Detection

When a language model hallucinates, the final answer is wrong, but the mistake is not necessarily invisible inside the model. Different internal pathways may remain uncertain, disagree in how quickly they sharpen, or commit to competing continuations before the output is produced. We introduce TriLens, a white-box detector that turns this intuition into a compact representation: at every layer, it reads the multi-head self-attention output, the feed-forward output, and the residual stream through the model's own logit lens, then records only the entropy of each readout. The resulting 3L-dimensional trajectory describes how certainty forms across depth and across modules, without storing high-dimensional hidden states or sampling multiple generations. This simple signal yields a strong detector across instruction-tuned LLMs and QA benchmarks, and our analyses show that the three module-wise entropy trajectories provide complementary evidence. TriLens suggests that hallucination detection can benefit from tracking how internal computation settles, not only what the final layer predicts.
Bohan Yang, Yijun Gong, Zhi Zhang +3
May 31, 2026eess.SP

Efficient Temporal Modeling for Mobile Sleep Staging via Lightweight Random Attention

Mobile sleep staging serves as a foundational infrastructure for in-home sleep monitoring and closed-loop modulation. But existing sequential models such as RNNs and Transformers are computationally expensive for mobile deployment. In this paper, we propose Random Attention (RA), a lightweight temporal modeling module based on fixed random projections, which replaces learnable sequence modeling with similarity-based aggregation. RA introduces little additional parameters beyond the epoch encoder while enabling effective temporal smoothing. We further provide a theoretical interpretation via the Random Attention Prior Kernel (RAPK), which decomposes RA into a global smoothing term and a feature similarity term, offering an interpretable view of temporal sleep structure. Experiments on Sleep-EDF-20 and Sleep-EDF-78 show that RA consistently improves epoch-wise baselines by 1-3% in accuracy and F1 score, while achieving competitive performance compared with LSTM, GRU, and Transformer models. RA also demonstrates strong generalization across different backbone encoders and improved robustness over conventional temporal smoothing methods. These results indicate that efficient sleep staging can be achieved through lightweight similarity-based temporal aggregation, making RA suitable for real-time wearable applications.
Guisong Liu, Pengfei Wei, Jainsong Zhang +1
May 30, 2026cs.LG

Refit the Probe: Single-Direction Ablation Is Not a Necessity Test

Probes are routinely paired with an intervention: ablate the direction the probe found, run the model, and read the change in task accuracy, taking a large drop as evidence that the computation depends on what the probe read and a near-zero drop as evidence that it does not. Either inference requires that the ablation have removed the target from the layer. We find that the ablation does not remove what it targets. A probe refitted on the ablated activations recovers its original accuracy in every cell we test, and keeps recovering when the probe's entire row space is deleted rather than a single axis, because the quantity survives in the orthogonal complement. Because a refitted probe recovers, neither a large task drop nor a near-zero one establishes whether the model needed the target, and one probe fit detects this. Replacing the ablation with iterative nullspace projection, scored against random subspaces of matched dimension, reverses the conclusion: representations that looked causally inert carry most of the task. The correction also separates where a variable is most readable from where deleting it does most damage, and those are not the same layer in any pretrained model we study. The erasure is defined by a linear probe family, so removing a nonlinearly encoded quantity remains open.
Yuhang Jiang
May 30, 2026cs.AI

Mitigating Hallucinations in Large Language Models Via Decoder Layer Skipping

Large Language Models (LLMs) have achieved strong performance across diverse natural language tasks, yet their outputs often suffer from hallucinations -- content that is misaligned with factual information. In this work, we conduct a comprehensive layer-wise analysis of the decoding process and reveal that hallucinations tend to originate from deeper decoder layers. To address this issue, we introduce \textbf{DeLask} (\textbf{De}coder \textbf{La}yer \textbf{Sk}ipping), a novel decoding framework that dynamically skips layers prone to producing hallucinations. DeLask leverages the theoretical insight that the forward computation of an LL-layer Transformer is conditionally equivalent to LL steps of gradient descent. We define a \emph{driftance value} by computing the cosine similarity between gradients derived from consecutive decoder steps, identifying problematic layers when the descent direction reverses. Rather than discarding such layers entirely, DeLask partially aggregates their hidden states with preceding layers, thereby preserving consistency while suppressing erroneous signals. Extensive experiments across diverse LLMs and benchmarks demonstrate that DeLask consistently mitigates hallucinations and enhances overall reliability, providing a lightweight and generalizable decoding framework for improving the robustness of large-scale language models.
Hanze Li, Jinhao You, Yichen Guo +3
May 30, 2026cs.CV

GIRL-DETR: Gradient-Isolated Reinforcement Learning for Video Moment Retrieval

Video Moment Retrieval (VMR) task requires accurately localizing temporal boundaries aligned with natural language queries, but many models suffer from a misalignment between continuous surrogate losses and non-differentiable metrics, leading to optimization stagnation during the late stages of training and trapping boundary predictions in suboptimal solutions. Although Reinforcement Learning (RL) post-training successfully optimizes localization results for large models, applying it directly to lightweight networks easily disrupts the fragile feature representations established during the supervised phase. To overcome this optimization bottleneck, we propose Gradient-Isolated Reinforcement Learning for DETR (GIRL-DETR), introducing RL post-training into a lightweight temporal localization framework for the first time. The input video and text features first establish early alignment through Cross-Modal Interaction (CMI) before entering the transformer encoder. Subsequently, a Text-Guided Gating (TGG) mechanism dynamically injects semantic priors into the queries before the transformer decoder generates candidate proposals, providing high signal-to-noise ratio inputs for temporal prediction. After the supervised training reaches convergence, the backbone network is frozen to protect the feature manifold, while the detection head directly optimizes the non-differentiable evaluation metric tIoU to enhance localization accuracy through a Three-stage Progressive Reinforcement Learning (TPRL) strategy. This approach achieves an orthogonal decoupling of state representation and metric optimization. Experiments on Charades-STA, QVHighlights, and TACoS demonstrate that GIRL-DETR effectively resolves surrogate loss degradation and achieves substantial accuracy improvements with minimal parameter updates, providing a robust new pathway for RL applications in lightweight VMR models.
Shihang Zhang, Mingjin Kuai, Ye Wei +2
May 30, 2026cs.LG

Prior-Guided Multi-Omic Transformers for Single-Cell Gene Regulatory Network Inference

Gene regulatory networks (GRNs) capture transcription factor-target interactions and are central to understanding cell-state regulation and disease. Reconstructing GRNs from paired single-cell transcriptomic and chromatin accessibility data is promising but challenging: scATAC is extremely sparse, and most methods rely on fixed peak-to-gene links and weak supervision. We present EpiAwareNet, a prior-guided multi-omic Transformer framework that reconstructs GRNs from paired single-cell data using only lightweight biological priors. In Stage 1, EpiAwareNet learns joint gene-peak representations with a gene-peak cross-attention module, enabling data-driven, gene-specific aggregation of accessibility signals rather than hard-coded peak-to-gene assignments. In Stage 2, EpiAwareNet incorporates a bulk-derived GRN prior as noisy positive edges to provide weak supervision under label scarcity, refining regulatory scores while remaining robust to prior noise. In our experiments, EpiAwareNet improves GRN reconstruction over representative single- and multi-omic baselines and yields GRNs with greater biological plausibility, such as improved recovery of known regulatory interactions, suggesting that lightweight biological priors from bulk data can effectively guide single-cell GRN inference when combined with adaptive cross-modal representation learning. Code and data will be available at https://github.com/tianyang-x/EpiAwareNet_pub.
Tianyang Xu, Tianci Liu, Niraj Rayamajhi +4