Transformer Architectures

Multi-head attention enables Transformers to capture diverse representations, but all attention heads are typically activated for every input, regardless of task complexity. For coarse-grained tasks such as text classification, where relevant information is often global, this fixed allocation can introduce unnecessary computation. We propose BudgetFormer, a Transformer architecture that dynamically allocates attention heads on a per-input basis. The model learns both a head budget and a relevance distribution to select the most informative heads. To support effective head selection, we introduce a training strategy that balances exploration and exploitation. Experiments on text classification tasks show that BudgetFormer reduces FLOPs and memory usage while matching or surpassing the performance of standard multi-head attention. These results highlight adaptive head allocation as an effective approach to improving Transformer efficiency and performance.

Recent advances in deep learning have enabled the generation of videos from textual descriptions as well as the prediction of future sequences from input videos. Similarly, in human motion modeling, motions can be generated from text or predicted from a single person's motion sequence. However, these approaches primarily focus on single-agent motion generation. In contrast, this study addresses the problem of generating the motion of one person based on the motion of another in interaction scenarios, where the two motions are mutually dependent. We construct a dataset of paired action-reaction motion sequences extracted from boxing match videos and investigate the effectiveness of Transformer-based models for this task. Specifically, we implement and compare three models: a simple Transformer, iTransformer, and Crossformer. In addition, we introduce a person ID embedding to explicitly distinguish between individuals, enabling the model to maintain structural consistency and better capture interaction dynamics. Experimental results show that the simple Transformer can generate plausible interaction-aware motions without suffering from posture collapse, while iTransformer and Crossformer accumulate errors over time, leading to unstable motion generation. Furthermore, the proposed person ID embedding contributes to preventing structural collapse and improving motion consistency. These results highlight the importance of explicitly modeling individual identity in interaction-aware motion generation.

When trained on tasks requiring an understanding of hierarchical structure, transformers have been found to represent this hierarchy in distinct ways: in the geometry of the residual stream, and in stack-like attention patterns maintaining a last-in, first-out ordering. However, it remains unclear whether these representations are causally used or merely decodable. We examine this gap in transformers trained on the Dyck language (a formal language of balanced bracket sequences), where the hierarchical ground truth is explicit. By probing and intervening on the residual stream and attention patterns, we find that depth, distance, and top-of-stack signals are all decodable, yet their causal roles diverge. Specifically, masking attention to the true top-of-stack position causes a sharp drop in long-distance accuracy, while ablating low-dimensional residual stream subspaces has comparatively little effect. These results, which extend to a templated natural language setting, suggest that even in a controlled setting where the relevant hierarchical variables are known, decodability alone does not imply causal use.

We study learned memory tokens as a computational scratchpad for a single-block Universal Transformer with Adaptive Computation Time (ACT) on Sudoku-Extreme, a combinatorial reasoning benchmark. Memory tokens are empirically necessary: no configuration without them reaches non-trivial performance. The optimal count has a sharp lower threshold (T=0 always fails, T=8 reliably succeeds) followed by a stable plateau (T=8-32, 57.4% +/- 0.7% exact-match) and a dilution boundary at T=64. Under halt-side pressure (lambda warmup), mean halt drops monotonically with memory size across the plateau (from 11.6 at T=8 to 8.3 at T=64), showing that memory tokens and ponder depth substitute as resources at fixed accuracy. We also identify a router initialization trap that causes the majority of training runs to fail: both default zero-bias and Graves' recommended positive bias settle into a shallow halt equilibrium the model cannot escape. Inverting the bias to -3 ("deep start") eliminates the failure mode, and ablation shows the trap is inherent to ACT initialization rather than an artifact of our architecture. With reliable training, ACT yields an order of magnitude lower seed variance than fixed-depth processing (+/-0.7 vs +/-9.3 pp); lambda warmup recovers 34% of compute at matched accuracy; and attention heads specialize into memory readers, constraint propagators, and integrators across recursive depth. Code: https://github.com/che-shr-cat/utm-jax.

We investigate the ability of decoder-only transformer models to perform abstract symbolic reasoning; specifically solving propositional logic reasoning problems given in-context. Previous work demonstrated that models fail to generalize to problems involving variable names that were not observed during training, and it was shown that one reason behind this is the difficulty of copying (or generating) unseen tokens. We show both theoretically and empirically that a particular representational collapse also has a crucial role: the unembeddings (last-layer weights) of unseen tokens collapse to nearly the same vector during training. The collapse makes distinguishing multiple unseen variables difficult for the model (especially when the embedding and unembedding parameters are shared), and provides a mechanistic explanation for the effectiveness of existing heuristic interventions like "active forgetting", which periodically reset the token (un)embeddings. Based on these observations, we devise a combination of techniques, involving a small architecture change facilitating copying, data diversity, and freezing or resetting (un)embeddings, that achieves generalization to unseen tokens. We support our claims with extensive controlled experiments on propositional logic reasoning problems. Beyond synthetic experiments, we also observe evidence of (un)embedding collapse in the open-weight models in the Gemma 3 family, which includes 99 unused tokens reserved for downstream use. Empirically we find that the correlated embeddings of these tokens are a poor initialization for finetuning applications.

Recent breakthroughs in 3D generative modeling have yielded remarkable progress in static shape synthesis, yet high-fidelity dynamic 4D generation remains elusive, hindered by temporal artifacts and prohibitive computational demand. We present Sculpt4D, a native 4D generative framework that seamlessly integrates efficient temporal modeling into a pretrained 3D Diffusion Transformer (Hunyuan3D 2.1), thereby mitigating the scarcity of 4D training data. At its core lies a Block Sparse Attention mechanism that preserves object identity by anchoring to the initial frame while capturing rich motion dynamics via a time-decaying sparse mask. This design faithfully models complex spatiotemporal dependencies with high fidelity, while sidestepping the quadratic overhead of full attention and reducing network total computation by 56%. Consequently, Sculpt4D establishes a new state-of-the-art in temporally coherent 4D synthesis and charts a path toward efficient and scalable 4D generation.

Edge points on 3D point clouds can clearly convey 3D geometry and surface characteristics, therefore, edge detection is widely used in many vision applications with high industrial and commercial demands. However, the fine-grained edge features are difficult to detect effectively as they are generally densely distributed or exhibit small-scale surface gradients. To address this issue, we present a learning-based edge detection network, named EdgeFormer, which mainly consists of two stages. Based on the observation that spatially neighboring points tend to exhibit high correlation, forming the local underlying surface, we convert the edge detection of the entire point cloud into a point classification based on local patches. Therefore, in the first stage, we construct local patch feature descriptors that describe the local neighborhood around each point. In the second stage, we classify each point by analyzing the local patch feature descriptors generated in the first stage. Due to the conversion of the point cloud into local patches, the proposed method can effectively extract the finer details. The experimental results show that our model demonstrates competitive performance compared to six baselines.

Brain tumors represent one of the most critical neurological conditions, where early and accurate diagnosis is directly correlated with patient survival rates. Manual interpretation of Magnetic Resonance Imaging (MRI) scans is time-intensive, subject to inter-observer variability, and demands significant specialist expertise. This paper proposes a deep learning framework for automated four-class brain tumor classification distinguishing glioma, meningioma, pituitary tumor, and healthy brain tissue from a dataset of 7,023 MRI scans. The proposed system employs a Vision Transformer (ViT-B/16) pretrained on ImageNet-21k as the backbone, augmented with a clinically motivated preprocessing and training pipeline. Contrast Limited Adaptive Histogram Equalization (CLAHE) is applied to enhance local contrast and accentuate tumor boundaries invisible to standard normalization. A two-stage fine-tuning strategy is adopted: the classification head is warmed up with the backbone frozen, followed by full fine-tuning with discriminative learning rates. MixUp and CutMix augmentation is applied per batch to improve generalization. Exponential Moving Average (EMA) of weights and Test-Time Augmentation (TTA) further stabilize and boost performance. Attention Rollout visualization provides clinically interpretable heatmaps of the brain regions driving each prediction. The proposed model achieves a test accuracy of 99.29%, macro F1-score of 99.25%, and perfect recall on both healthy and meningioma classes, outperforming all CNN-based baselines

LLM architecture research generally aims to maximize model quality subject to fixed compute/latency budgets. However, many applications of interest such as edge and on-device deployment are further constrained by the model's memory footprint, thus motivating parameter-efficient architectures for language modeling. This paper describes a simple architecture that improves the parameter-efficiency of LLMs. Our architecture makes use of looped Transformers as a core primitive, which reuse Transformer layers across depth and are thus more parameter-efficient than ordinary (depth-matched) Transformers. We organize the looped Transformer into three blocks--begin, middle, and end blocks--where each block itself consists of multiple Transformer layers, and only the middle block is applied recurrently across depth. We augment the looped middle block with hyper-connections (Xie et al., 2026), which expand the residual stream into matrix-valued residual streams. Hyper-connections are applied only after each loop, and therefore add minimal new parameters and compute cost. Across various model scales, we find that our Hyper-Connected Looped Transformer (Hyperloop Transformer) is able to perform well compared to depth-matched Transformer and mHC Transformer baselines despite using approximately 50% fewer parameters. This performance persists through post-training weight quantization, thus positioning Hyperloop Transformers as an attractive architecture for memory-efficient language modeling.

Transformers process tokens in parallel but are temporally shallow: at position $t$, each layer attends to key-value pairs computed based on the previous layer, yielding a depth capped by the number of layers. Recurrent models offer unbounded temporal depth but suffer from optimization instability and historically underutilize modern accelerators. We introduce the Recurrent Transformer, a simple architectural change where each layer attends to key-value pairs computed off its own activations, yielding layerwise recurrent memory while preserving standard autoregressive decoding cost. We show that the architecture can emulate both (i) a conventional Transformer and (ii) token-to-token recurrent updates under mild assumptions, while avoiding optimization instability. Naively, prefill/training appears bandwidth-bound with effective arithmetic intensity near $1$ because keys and values are revealed sequentially; we give an exact tiling-based algorithm that preserves the mathematical computation while reducing HBM traffic from $Θ(N^2)$ to $Θ(N\log N)$, increasing effective arithmetic intensity to $Θ(N/\log N)$ for sequence length $N$. On 150M and 300M parameter C4 pretraining, Recurrent Transformers improve cross-entropy over a parameter-matched Transformer baseline and achieve the improvement with fewer layers (fixed parameters), suggesting that recurrence can trade depth for width, thus reducing KV cache memory footprint and inference latency.

Accurate representation of moist convective sub-grid-scale processes remains a major challenge in global climate models, as traditional parameterization schemes are both computationally expensive and difficult to scale. Neural network (NN) emulators offer a promising alternative by learning efficient mappings between atmospheric states and convective tendencies while retaining fidelity to the underlying physics. However, most existing NN-based parameterizations are memory-less and rely only on instantaneous inputs, even though convection evolves over time and depends on prior atmospheric states. Recent studies have begun to incorporate convective memory, but they often treat past states as independent features rather than modeling temporal dependencies explicitly. In this work, we develop a temporal memory-aware Transformer emulator for the Emanuel convective parameterization and evaluate it in a single-column climate model (SCM) under both offline and online configurations. The Transformer captures temporal correlations and nonlinear interactions across consecutive atmospheric states. Compared with baseline emulators, including a memory-less multilayer perceptron and a recurrent long short-term memory model, the Transformer achieves lower offline errors. Sensitivity analysis indicates that a memory length of approximately 100 minutes yields the best performance, whereas longer memory degrades performance. We further test the emulator in long-term coupled simulations and show that it remains stable over 10 years. Overall, this study demonstrates the importance of explicit temporal modeling for NN-based parameterizations.

We investigate the integration of human-like working memory constraints into the Transformer architecture and implement several cognitively inspired attention variants, including fixed-width windows based and temporal decay based attention mechanisms. Our modified GPT-2 models are trained from scratch on developmentally plausible datasets (10M and 100M words). Performance is evaluated on grammatical judgment tasks (BLiMP) and alignment with human reading time data. Our results indicate that these cognitively-inspired constraints, particularly fixed-width attention, can significantly improve grammatical accuracy especially when training data is scarce. These constrained models also tend to show a stronger alignment with human processing metrics. The findings suggest that such constraints may serve as a beneficial inductive bias, guiding models towards more robust linguistic representations, especially in data-limited settings.

Dropout is a widely used regularization technique in deep learning, but its effects are typically realized through stochastic masking rather than explicit optimization objectives. We propose a deterministic formulation that expresses dropout as an additive regularizer directly incorporated into the training loss. The framework derives explicit regularization terms for Transformer architectures, covering attention query, key, value, and feed-forward components with independently controllable strengths. This formulation removes reliance on stochastic perturbations while providing clearer and fine-grained control over regularization strength. Experiments across image classification, temporal action detection, and audio classification show that explicit dropout matches or outperforms conventional implicit methods, with consistent gains when applied to attention and feed-forward network layers. Ablation studies demonstrate stable performance and controllable regularization through regularization coefficients and dropout rates. Overall, explicit dropout offers a practical and interpretable alternative to stochastic regularization while maintaining architectural flexibility across diverse tasks.

The quadratic complexity of softmax attention presents a major obstacle for scaling Transformers to high-resolution vision tasks. Existing linear attention variants often replace the softmax with Gaussian kernels to reduce complexity, but such approximations lack theoretical grounding and tend to oversuppress mid-range token interactions. We propose LaplacianFormer, a Transformer variant that employs a Laplacian kernel as a principled alternative to softmax, motivated by empirical observations and theoretical analysis. To address expressiveness degradation under low-rank approximations, we introduce a provably injective feature map that retains fine-grained token information. For efficient computation, we adopt a Nyström approximation of the kernel matrix and solve the resulting system using Newton--Schulz iteration, avoiding costly matrix inversion and SVD. We further develop custom CUDA implementations for both the kernel and solver, enabling high-throughput forward and backward passes suitable for edge deployment. Experiments on ImageNet show that LaplacianFormer achieves strong performance-efficiency trade-offs while improving attention expressiveness.

Vision Transformers (ViTs) have achieved remarkable success across vision tasks, yet recent studies show they remain vulnerable to backdoor attacks. Existing patch-wise attacks typically assume a single fixed trigger location during inference to maximize trigger attention. However, they overlook the self-attention mechanism in ViTs, which captures long-range dependencies across patches. In this work, we observe that a patch-wise trigger can achieve high attack effectiveness when activating backdoors across neighboring patches, a phenomenon we term the Trigger Radiating Effect (TRE). We further find that inter-patch trigger insertion during training can synergistically enhance TRE compared to single-patch insertion. Prior ViT-specific attacks that maximize trigger attention often sacrifice visual and attention stealthiness, making them detectable. Based on these insights, we propose PASTA, a twofold stealthy patch-wise backdoor attack in both pixel and attention domains. PASTA enables backdoor activation when the trigger is placed at arbitrary patches during inference. To achieve this, we introduce a multi-location trigger insertion strategy to enhance TRE. However, preserving stealthiness while maintaining strong TRE is challenging, as TRE is weakened under stealthy constraints. We therefore formulate a bi-level optimization problem and propose an adaptive backdoor learning framework, where the model and trigger iteratively adapt to each other to avoid local optima. Extensive experiments show that PASTA achieves 99.13% attack success rate across arbitrary patches on average, while significantly improving visual and attention stealthiness (144.43x and 18.68x) and robustness (2.79x) against state-of-the-art ViT defenses across four datasets, outperforming CNN- and ViT-based baselines.

Despite the remarkable success of Vision Transformers (ViTs) across a wide range of vision tasks, recent studies have revealed that they remain vulnerable to adversarial examples, much like Convolutional Neural Networks (CNNs). A common empirical defense strategy is adversarial training, yet the theoretical underpinnings of its robustness in ViTs remain largely unexplored. In this work, we present the first theoretical analysis of adversarial training under simplified ViT architectures. We show that, when trained under a signal-to-noise ratio that satisfies a certain condition and within a moderate perturbation budget, adversarial training enables ViTs to achieve nearly zero robust training loss and robust generalization error under certain regimes. Remarkably, this leads to strong generalization even in the presence of overfitting, a phenomenon known as \emph{benign overfitting}, previously only observed in CNNs (with adversarial training). Experiments on both synthetic and real-world datasets further validate our theoretical findings.

Reconstructing physically plausible 3D human-scene interactions (HSI) from a single image currently presents a trade-off: optimization based methods offer accurate contact but are slow (~20s), while feed-forward approaches are fast yet lack explicit interaction reasoning, producing floating and interpenetration artifacts. Our key insight is that geometry-based human--scene fitting can be amortized into fast feed-forward inference. We present GRAFT (Geometric Refinement And Fitting Transformer), a learned HSI prior that predicts Interaction Gradients: corrective parameter updates that iteratively refine human meshes by reasoning about their 3D relationship to the surrounding scene. GRAFT encodes the interaction state into compact body-anchored tokens, each grounded in the scene geometry via Geometric Probes that capture spatial relationships with nearby surfaces. A lightweight transformer recurrently updates human meshes and re-probes the scene, ensuring the final pose aligns with both learned priors and observed geometry. GRAFT operates either as an end-to-end reconstructor using image features, or with geometry alone as a transferable plug-and-play HSI prior that improves feed-forward methods without retraining. Experiments show GRAFT improves interaction quality by up to 122% over state-of-the-art feed-forward methods and matches optimization-based interaction quality at ${\sim}100{\times}$ lower runtime, while generalizing seamlessly to in-the-wild multi-person scenes and being preferred in 64.8% of three-way user study. Project page: https://pradyumnaym.github.io/graft .

Metal-organic frameworks (MOFs) are a major target of machine-learning-based property prediction, yet most models assume that a single framework representation maps to a single property value. This assumption becomes problematic for experimental MOFs, where samples reported as the same framework can exhibit different properties because of differences in crystallinity, phase purity, defects, and other sample-dependent factors. Here we introduce Experimental X-ray Diffraction Integrated Transformer (EXIT), a multimodal transformer for sample-aware prediction of MOF properties that combines MOFid with X-ray diffraction (XRD). In EXIT, MOFid encodes MOF identity, whereas XRD provides complementary information about the experimentally realized sample state. EXIT is pre-trained on one million hypothetical MOFs with simulated XRD to learn transferable representations, leading to improved downstream performance relative to existing approaches. EXIT is fine-tuned on literature-derived experimental datasets for surface area and pore volume prediction. Incorporating experimental XRD improves predictive performance relative to models without experimental XRD, and attention analysis and sample-level case studies further show that EXIT assigns different predictions to samples sharing the same MOF identity when their XRD patterns differ. These results establish a practical step from framework-aware to sample-aware MOF property prediction and highlight the value of incorporating experimental characterization into porous materials informatics.

Multi-view crowd tracking estimates each person's tracking trajectories on the ground of the scene. Recent research works mainly rely on CNNs-based multi-view crowd tracking architectures, and most of them are evaluated and compared on relatively small datasets, such as Wildtrack and MultiviewX. Since these two datasets are collected in small scenes and only contain tens of frames in the evaluation stage, it is difficult for the current methods to be applied to real-world applications where scene size and occlusion are more complicated. In this paper, we propose a Transformer-based multi-view crowd tracking model, \textit{MVTrackTrans}, which adopts interactions between camera views and the ground plane for enhanced multi-view tracking performance. Besides, for better evaluation, we collect and label two large real-world multi-view tracking datasets, MVCrowdTrack and CityTrack, which contain a much larger scene size over a longer time period. Compared with existing methods on the two large and new datasets, the proposed MVTrackTrans model achieves better performance, demonstrating the advantages of the model design in dealing with large scenes. We believe the proposed datasets and model will push the frontiers of the task to more practical scenarios, and the datasets and code are available at: https://github.com/zqyq/MVTrackTrans.

Goal-conditioned navigation models for ground robots trained using supervised learning show promising zero-shot transfer, but their collision-avoidance capability nevertheless degrades under distribution shift, i.e. environmental, robot or sensor configuration changes. We propose ViLiNT a multimodal, attention-based policy for goal navigation, trained on heterogeneous data from multiple platforms and environments, which improves robustness with two key features. First, we fuse RGB images, 3D LiDAR point clouds, a goal embedding and a robot's embodiment descriptor with a transformer architecture to capture complementary geometry and appearance cues. The transformer's output is used to condition a diffusion model that generates navigable trajectories. Second, using automatically generated offline labels, we train a path clearance prediction head for scoring and ranking trajectories produced by the diffusion model. The diffusion conditioning as well as the trajectory ranking head depend on a robot's embodiment token that allows our model to generate and select trajectories with respect to the robot's dimensions. Across three simulated environments, ViLiNT improves Success Rate on average by 166% over equivalent state-of-the-art vision-only baseline (NoMaD). This increase in performance is confirmed through real-world deployments of a rover navigating in obstacle fields. These results highlight that combining multimodal fusion with our collision prediction mechanism leads to improved off-road navigation robustness.

Hyperspectral image (HSI) classification remains challenging due to high spectral dimensionality, redundancy, and limited labeled data. Although convolutional neural networks (CNNs) and Vision Transformers (ViTs) achieve strong performance by exploiting spectral-spatial information and long-range dependencies, they often incur high computational cost and large model size, limiting practical use. To address these limitations, a unified hybrid framework, termed ConvVitMamba, is proposed for efficient HSI classification. The architecture integrates three components: a multiscale convolutional feature extractor to capture local spectral, spatial, and joint patterns; a Vision Transformer based tokenization and encoding stage to model global contextual relationships; and a lightweight Mamba inspired gated sequence mixing module for efficient content-aware refinement without quadratic self-attention. Principal Component Analysis (PCA) is used as preprocessing to reduce redundancy and improve efficiency. Experiments on four benchmark datasets, including Houston and three UAV borne QUH datasets (Pingan, Qingyun, and Tangdaowan), demonstrate that ConvVitMamba consistently outperforms CNN, Transformer, and Mamba based methods while maintaining a favorable balance between accuracy, model size, and inference efficiency. Ablation studies confirm the complementary contributions of all components. The results indicate that the proposed framework provides an effective and efficient solution for HSI classification in diverse scenarios. The source code is publicly available at https://github.com/mqalkhatib/ConvVitMamba

Looped transformers scale computational depth without increasing parameter count by repeatedly applying a shared transformer block and can be used for iterative refinement, where each loop rewrites a full fixed-size prediction in parallel. On difficult problems, such as those that require search-like computation, reaching a highly structured solution starting from noise can require long refinement trajectories. Learning such trajectories is challenging when training specifies only the target solution and provides no supervision over the intermediate refinement path. Diffusion models tackle this issue by corrupting data with varying magnitudes of noise and training the model to reverse it in a \textit{single step}. However, this process misaligns training and testing behaviour. We introduce Denoising Recursion Models, a method that similarly corrupts data with noise but trains the model to reverse the corruption over \textit{multiple} recursive steps. This strategy provides a tractable curriculum of intermediate states, while better aligning training with testing and incentivizing non-greedy, forward-looking generation. Through extensive experiments, we show this approach outperforms the Tiny Recursion Model (TRM) on ARC-AGI, where it recently achieved breakthrough performance.

Large Language Models (LLMs) remain vulnerable to optimization-based jailbreak attacks that exploit internal gradient structure. While Sparse Autoencoders (SAEs) are widely used for interpretability, their robustness implications remain underexplored. We present a study of integrating pretrained SAEs into transformer residual streams at inference time, without modifying model weights or blocking gradients. Across four model families (Gemma, LLaMA, Mistral, Qwen) and two strong white-box attacks (GCG, BEAST) plus three black-box benchmarks, SAE-augmented models achieve up to a 5x reduction in jailbreak success rate relative to the undefended baseline and reduce cross-model attack transferability. Parametric ablations reveal (i) a monotonic dose-response relationship between L0 sparsity and attack success rate, and (ii) a layer-dependent defense-utility tradeoff, where intermediate layers balance robustness and clean performance. These findings are consistent with a representational bottleneck hypothesis: sparse projection reshapes the optimization geometry exploited by jailbreak attacks.

Transformer-based embedding models suffer from quadratic computational and linear memory complexity, limiting their utility for long sequences. We propose recurrent architectures as an efficient alternative, introducing a vertically chunked inference strategy that enables fast embedding generation with memory usage that becomes constant in the input length once it exceeds the vertical chunk size. By fine-tuning Mamba2 models, we demonstrate their viability as general-purpose text embedders, achieving competitive performance across a range of benchmarks while maintaining a substantially smaller memory footprint compared to transformer-based counterparts. We empirically validate the applicability of our inference strategy to Mamba2, RWKV, and xLSTM models, confirming consistent runtime-memory trade-offs across architectures and establishing recurrent models as a compelling alternative to transformers for efficient embedding generation.

The key-value (KV) cache is the dominant memory bottleneck during Transformer inference, yet little is known theoretically about how aggressively it can be compressed before multi-step reasoning degrades. We study this through $k$-hop pointer chasing on $n$ tokens under a shared KV cache of size $s$, attention dimension $m$, $H$ heads, $p$-bit precision, and a locality-respecting cache controller (satisfied by all standard KV-compression methods). We give three results. (1) Product depth lower bound (conjectured). We conjecture that any such Transformer ($n \geq 4k$, $s \leq \sqrt{n}/4$) requires depth $L = Ω(\lceil k/s \rceil \cdot \lceil \log_2 n/(Hmp) \rceil)$, and isolate the sole remaining gap as a probabilistic step on the joint distribution of cache trace and pointer chain. Unconditionally, we prove a matching upper bound $L = O(\min(k, \lceil k/s \rceil \log s) \cdot \log n/(mp))$ via windowed pointer doubling, and a max-bound $L = Ω(\max(\lceil k/s \rceil, \log n/(Hmp)))$. Closing the conjecture amounts to upgrading max to product. (2) Bandwidth barrier. The product bound binds only when $Hmp \lesssim \log n$. Any lower bound provable via per-window distinguishability counting -- including reachability, bandwidth, and combinations -- cannot exceed $\lceil k/s \rceil$ once $Hmp \geq \log_2 n$. Breaking this requires lifting unconditional communication-complexity bounds for pointer chasing to Cache-Transformer depth. (3) Adaptive vs oblivious error scaling. Under random cache over $T = \lceil \log_2 k \rceil$ doubling stages, oblivious caches give $\Pr[\mathcal{E}] \leq (s/(n-T))^T + 2T^3/n$ (exponential in $T$), while adaptive locality-respecting caches achieve $\Pr[\mathcal{E}] = s/n$ exactly, independent of $T$. The $Ω((n/s)^{T-1})$ separation explains why heavy-hitter eviction empirically dominates random eviction for multi-hop reasoning.

In today's day and age, we face a challenge in detecting deepfake images because of the fast evolution of modern generative models and the poor generalization capability of existing methods. In this paper, we use an ensemble of fine-tuned vision transformers like DINOv2, AIMv2 and OpenCLIP's ViT-L/14 to create generalizable method to detect deepfakes. We use the DF-Wild dataset released as part of the IEEE SP Cup 2025, because it uses a challenging and diverse set of manipulations and generation techniques. We started our experiments with CNN classifiers trained on spatial features. Experimental results show that our ensemble outperforms individual models and strong CNN baselines, achieving an AUC of 96.77% and an Equal Error Rate (EER) of just 9% on the DF-Wild test set, beating the state-of-the-art deepfake detection algorithm Effort by 7.05% and 8% in AUC and EER respectively. This was the winning solution for SP Cup, presented at ICASSP 2025.

Path planning is usually solved by addressing either the (high-level) route planning problem (waypoint sequencing to achieve the final goal) or the (low-level) path planning problem (trajectory prediction between two waypoints avoiding collisions). However, real-world problems usually require simultaneous solutions to the route and path planning subproblems with a holistic and efficient approach. In this paper, we introduce NaviFormer, a deep reinforcement learning model based on a Transformer architecture that solves the global navigation problem by predicting both high-level routes and low-level trajectories. To evaluate NaviFormer, several experiments have been conducted, including comparisons with other algorithms. Results show competitive accuracy from NaviFormer since it can understand the constraints and difficulties of each subproblem and act consequently to improve performance. Moreover, its superior computation speed proves its suitability for real-time missions.

Standard transformer architectures apply the same number of layers to every token regardless of contextual difficulty. We present Token-Selective Attention (TSA), a learned per-token gate on residual updates between consecutive transformer blocks. Each gate is a lightweight two-layer multi-layer perceptron (MLP) that produces a continuous halting probability, making the mechanism end-to-end differentiable with 1.7% parameter overhead and no changes to the base architecture. Notably, TSA learns difficulty-proportional routing without any explicit depth pressure: even at $λ=0$ (no depth regularisation), the task-loss gradient alone drives the router to skip 20% of token-layer operations. On character-level language modeling, TSA saved 14-23% of token-layer operations (TLOps) across Tiny-Shakespeare and enwik8 at <0.5% quality loss. At matched efficiency, TSA achieved 0.7% lower validation loss than early exit, and the learned routing transfers directly to inference-time sparse execution for real wall-clock speedup.

Modeling single-cell gene expression across diverse biological and technical conditions is crucial for characterizing cellular states and simulating unseen scenarios. Existing methods often treat genes as independent tokens, overlooking their high-level biological relationships and leading to poor performance. We introduce SAVE, a unified generative framework based on conditional Transformers for multi-condition single-cell modeling. SAVE leverages a coarse-grained representation by grouping semantically related genes into blocks, capturing higher-order dependencies among gene modules. A Flow Matching mechanism and condition-masking strategy further enhance flexible simulation and enable generalization to unseen condition combinations. We evaluate SAVE on a range of benchmarks, including conditional generation, batch effect correction, and perturbation prediction. SAVE consistently outperforms state-of-the-art methods in generation fidelity and extrapolative generalization, especially in low-resource or combinatorially held-out settings. Overall, SAVE offers a scalable and generalizable solution for modeling complex single-cell data, with broad utility in virtual cell synthesis and biological interpretation. Our code is publicly available at https://github.com/fdu-wangfeilab/sc-save

Spiking transformers achieve competitive accuracy with conventional transformers while offering $38$-$57\times$ energy efficiency on neuromorphic hardware, yet no theoretical framework guides their design. This paper establishes the first comprehensive expressivity theory for spiking self-attention. We prove that spiking attention with Leaky Integrate-and-Fire neurons is a universal approximator of continuous permutation-equivariant functions, providing explicit spike circuit constructions including a novel lateral inhibition network for softmax normalization with proven $O(1/\sqrt{T})$ convergence. We derive tight spike-count lower bounds via rate-distortion theory: $\varepsilon$-approximation requires $Ω(L_f^2 nd/\varepsilon^2)$ spikes, with rigorous information-theoretic derivation. Our key insight is input-dependent bounds using measured effective dimensions ($d_{\text{eff}}=47$--$89$ for CIFAR/ImageNet), explaining why $T=4$ timesteps suffice despite worst-case $T \geq 10{,}000$ predictions. We provide concrete design rules with calibrated constants ($C=2.3$, 95% CI: $[1.9, 2.7]$). Experiments on Spikformer, QKFormer, and SpikingResformer across vision and language benchmarks validate predictions with $R^2=0.97$ ($p<0.001$). Our framework provides the first principled foundation for neuromorphic transformer design.

Looped transformers promise test-time compute scaling by spending more iterations on harder problems, but it remains unclear which architectural choices let them extrapolate to harder problems at test time rather than memorize training-specific solutions. We introduce a fixed-point based framework for analyzing looped architectures along three axes of stability -- reachability, input-dependence, and geometry -- and use it to characterize when fixed-point iteration yields meaningful predictions. Theoretically, we prove that looped networks without recall have countable fixed points and cannot achieve strong input-dependence at any spectral regime, while recall combined with outer normalization reliably produces a regime in which fixed points are simultaneously reachable, locally smooth in the input, and supported by stable backpropagation. Empirically, we train single-layer looped transformers on chess, sudoku, and prefix-sums and find that downstream performance tracks the framework's predictions across tasks and architectural configurations. We additionally introduce internal recall, a novel recall placement variant, and show that it becomes competitive with -- and on sudoku, substantially better than -- standard recall placement once outer normalization is applied.

When do transformers commit to a decision, and what prevents them from correcting it? We introduce \textbf{prolepsis}: a transformer commits early, task-specific attention heads sustain the commitment, and no layer corrects it. Replicating \citeauthor{lindsey2025biology}'s (\citeyear{lindsey2025biology}) planning-site finding on open models (Gemma2 2B, Llama3.2 1B), we ask five questions. (Q1)~Planning is invisible to six residual-stream methods; CLTs are necessary. (Q2)~The planning-site spike replicates with identical geometry. (Q3)~Specific attention heads route the decision to the output, filling a gap flagged as invisible to attribution graphs. (Q4)~Search requires ${\leq}16$ layers; commitment requires more. (Q5)~Factual recall shows the same motif at a different network depth, with zero overlap between recurring planning heads and the factual top-10. Prolepsis is architectural: the template is shared, the routing substrates differ. All experiments run on a single consumer GPU (16,GB VRAM).

To quantify the geometric expressivity of transformers, we introduce a tropical geometry framework to characterize their exact spatial partitioning capabilities. By modeling self-attention as a vector-valued tropical rational map, we prove it evaluates exactly to a Power Voronoi Diagram in the zero-temperature limit. Building on this equivalence, we establish a combinatorial rationale for Multi-Head Self-Attention (MHSA): via the Minkowski sum of Newton polytopes, multi-head aggregation expands the polyhedral complexity to $\mathcal{O}(N^H)$, overcoming the $\mathcal{O}(N)$ bottleneck of single heads. Extending this to deep architectures, we derive the first tight asymptotic bounds on the number of linear regions in transformers ($Θ(N^{d_{\text{model}}L})$), demonstrating a combinatorial explosion driven intrinsically by sequence length $N$, ambient embedding dimension $d_{\text{model}}$, and network depth $L$. Importantly, we guarantee that this idealized polyhedral skeleton is geometrically stable: finite-temperature soft attention preserves these topological partitions via exponentially tight differential approximation bounds.

Existing single-modal RGB trackers often face performance bottlenecks in complex dynamic scenes, while the introduction of event sensors offers new potential for enhancing tracking capabilities. However, most current RGB-event fusion methods, primarily designed in the spatial domain using convolutional, Transformer, or Mamba architectures, fail to fully exploit the unique temporal response and high-frequency characteristics of event data. To address this, we1 propose FreqTrack, a frequency-aware RGBE tracking framework that establishes complementary inter-modal correlations through frequency-domain transformations for more robust feature fusion. We design a Spectral Enhancement Transformer (SET) layer that incorporates multi-head dynamic Fourier filtering to adaptively enhance and select frequency-domain features. Additionally, we develop a Wavelet Edge Refinement (WER) module, which leverages learnable wavelet transforms to explicitly extract multi-scale edge structures from event data, effectively improving modeling capability in high-speed and low-light scenarios. Extensive experiments on the COESOT and FE108 datasets demonstrate that FreqTrack achieves highly competitive performance, particularly attaining leading precision of 76.6% on the COESOT benchmark, validating the effectiveness of frequency-domain modeling for RGBE tracking.

Mixture-of-Experts (MoE) models substantially improve performance by increasing the capacity of dense architectures. However, directly training MoE models requires considerable computational resources and introduces extra overhead in parameter storage and deployment. Therefore, it is critical to develop an approach that leverages the multi-expert capability of MoE to enhance performance while incurring minimal additional cost. To this end, we propose a novel pre-training approach, termed ExFusion, which improves the efficiency of Transformer training through multi-expert fusion. Specifically, during the initialization phase, ExFusion upcycles the feed-forward network (FFN) of the Transformer into a multi-expert configuration, where each expert is assigned a weight for later parameter fusion. During training, these weights allow multiple experts to be fused into a single unified expert equivalent to the original FFN, which is subsequently used for forward computation. As a result, ExFusion introduces multi-expert characteristics into the training process while incurring only marginal computational cost compared to standard dense training. After training, the learned weights are used to integrate multi-experts into a single unified expert, thereby eliminating additional overhead in storage and deployment. Extensive experiments on a variety of computer vision and natural language processing tasks demonstrate the effectiveness of the proposed method.

Converting a pretrained Transformer into a more efficient hybrid model through distillation offers a promising approach to reducing inference costs. However, achieving high-quality generation in distilled models requires careful joint design of both the student architecture and the distillation process. Many prior distillation works evaluate downstream multiple-choice benchmarks by ranking candidate answers with log-likelihood rather than requiring autoregressive generation, which can obscure important differences in model quality. For example, on overlapping benchmarks, we show that a 7B distilled model that nearly matches its teacher to within 0.2 pp under log-likelihood scoring falls behind by 20.8 pp when it must generate answers autoregressively. We investigate this phenomenon with GenDistill, a multi-stage pipeline we designed for distilling a pretrained Transformer into an efficient Hybrid Kimi Delta Attention (Hybrid-KDA) student. Using it as a controlled testbed on Qwen3-0.6B, we systematically ablate six design axes (training objective, loss masking, training duration, dataset selection, parameter freezing, and architecture choice) and evaluate every choice under both log-likelihood and generation-based protocols. We find that log-likelihood-based evaluation consistently underestimates the gap between teacher and student, and can in some cases reverse the ranking of design choices, so conclusions drawn from perplexity-only evaluation may be misleading. Among the factors we study, dataset selection, completion-only masking, and freezing attention layers during post-training have the largest impact on generation quality. Our best distillation recipe, using a Hybrid-KDA model as the student, retains 86-90% of teacher accuracy on knowledge benchmarks while reducing KV cache memory by up to 75% and improving time-to-first-token by 2-4x at 128K-token contexts.

Transformers have shown inconsistent success in AI planning tasks, and theoretical understanding of when generalization should be expected has been limited. We take important steps towards addressing this gap by analyzing the ability of decoder-only models to verify whether a given plan correctly solves a given planning instance. To analyse the general setting where the number of objects -- and thus the effective input alphabet -- grows at test time, we introduce C*-RASP, an extension of C-RASP designed to establish length generalization guarantees for transformers under the simultaneous growth in sequence length and vocabulary size. Our results identify a large class of classical planning domains for which transformers can provably learn to verify long plans, and structural properties that significantly affects the learnability of length generalizable solutions. Empirical experiments corroborate our theory.

Vision foundation models trained with self-supervised objectives achieve strong performance across diverse tasks and exhibit emergent object segmentation properties. However, their alignment with human object perception remains poorly understood. Here, we introduce a behavioral benchmark in which participants make same/different object judgments for dot pairs on naturalistic scenes, scaling up a classical psychophysics paradigm to over 1000 trials. We test a diverse set of vision models using a simple readout from their representations to predict subjects' reaction times. We observe a steady improvement across model generations, with both architecture and training objective contributing to alignment, and transformer-based models trained with the DINO self-supervised objective showing the strongest performance. To investigate the source of this improvement, we propose a novel metric to quantify the object-centric component of representations by measuring patch similarity within and between objects. Across models, stronger object-centric structure predicts human segmentation behavior more accurately. We further show that matching the Gram matrix of supervised transformer models, capturing similarity structure across image patches, with that of a self-supervised model through distillation improves their alignment with human behavior, converging with the prior finding that Gram anchoring improves DINOv3's feature quality. Together, these results demonstrate that self-supervised vision models capture object structure in a behaviorally human-like manner, and that Gram matrix structure plays a role in driving perceptual alignment.

Diffusion Transformers (DiTs) are a dominant backbone for high-fidelity text-to-image generation due to strong scalability and alignment at high resolutions. However, quadratic self-attention over dense spatial tokens leads to high inference latency and limits deployment. We observe that denoising is spatially non-uniform with respect to aesthetic descriptors in the prompt. Regions associated with aesthetic tokens receive concentrated cross-attention and show larger temporal variation, while low-affinity regions evolve smoothly with redundant computation. Based on this insight, we propose AccelAes, a training-free framework that accelerates DiTs through aesthetics-aware spatio-temporal reduction while improving perceptual aesthetics. AccelAes builds AesMask, a one-shot aesthetic focus mask derived from prompt semantics and cross-attention signals. When localized computation is feasible, SkipSparse reallocates computation and guidance to masked regions. We further reduce temporal redundancy using a lightweight step-level prediction cache that periodically replaces full Transformer evaluations. Experiments on representative DiT families show consistent acceleration and improved aesthetics-oriented quality. On Lumina-Next, AccelAes achieves a 2.11$\times$ speedup and improves ImageReward by +11.9% over the dense baseline. Code is available at https://github.com/xuanhuayin/AccelAes.

Vision Transformers require significant computational resources and memory bandwidth, severely limiting their deployment on resource-constraint hardware. Most structured pruning methods reduce theoretical cost effectively, yet they typically operate at a single structural granularity and depend on multi-stage pipelines with importance ranking, auxiliary solvers or post-hoc magnitude thresholding, followed by a separate fine-tuning phase to recover accuracy. We propose Hierarchical Auto-Pruning (HiAP), which casts ViT pruning as a single budget-aware learning problem and jointly allocates sparsity across four granularities in one end-to-end phase. HiAP introduces stochastic Gumbel-Sigmoid gates at macro level (attention heads and FFN blocks) and micro level (intra-head dimensions and FFN neurons), and optimizes them against the task loss together with an analytical MAC cost term. The budget coefficient steers the network to a target compute level while the gates gradually harden into a dense, smaller sub-network at convergence. It does not require importance heuristics, ranking metrics, auxillary solvers or secondary fine-tuning. On ImageNet with DeiT small, HiAP automatically discovers hetergenous architectures, pruning depths, heads, and width by different amount across layers, and reaches competitive accuracies against substantially more complex pruning pipelines at comparable compute from a single training run.

Multimodal Transformers often produce predictions without clarifying how different modalities jointly support a decision. Most existing multimodal explainable AI (MXAI) methods extend unimodal saliency to multimodal backbones, highlighting important tokens or patches within each modality, but they rarely pinpoint which cross-modal feature pairs provide complementary evidence (synergy) or serve as reliable backups (redundancy). We present Feature-level I2MoE (FL-I2MoE), a structured Mixture-of-Experts layer that operates directly on token/patch sequences from frozen pretrained encoders and explicitly separates unique, synergistic, and redundant evidence at the feature level. We further develop an expert-wise explanation pipeline that combines attribution with top-K% masking to assess faithfulness, and we introduce Monte Carlo interaction probes to quantify pairwise behavior: the Shapley Interaction Index (SII) to score synergistic pairs and a redundancy-gap score to capture substitutable (redundant) pairs. Across three benchmarks (MMIMDb, ENRICO, and MMHS150K), FL-I2MoE yields more interactionspecific and concentrated importance patterns than a dense Transformer with the same encoders. Finally, pair-level masking shows that removing pairs ranked by SII or redundancy-gap degrades performance more than masking randomly chosen pairs under the same budget, supporting that the identified interactions are causally relevant. Code is available at https://github.com/dut0817/FL-I2MoE.

Transformers excel at in-context retrieval but suffer from quadratic complexity with sequence length, while State Space Models (SSMs) offer efficient linear-time processing but have limited retrieval capabilities. We investigate whether hybrid architectures combining Transformers and SSMs can achieve the best of both worlds on two synthetic in-context retrieval tasks. The first task, n-gram retrieval, requires the model to reproduce an n-gram that succeeds the query within the input sequence. The second task, position retrieval, presents the model with a query token and requires it to perform a two-hop lookup: first locating the corresponding element in the sequence, and then outputting its positional index. Under controlled conditions, we assess data efficiency, length generalization, robustness to out of domain training examples, and learned representations across Transformers, SSMs, and hybrid architectures. We find that hybrid models outperform SSMs and match or exceed Transformers in terms of data efficiency and extrapolation for tasks that require precise information retrieval from the input context. However, Transformers maintain superiority in position retrieval tasks. Through representation analysis, we discover that SSM-based models develop locality-aware embeddings where tokens representing adjacent positions become neighbors in embedding space, forming interpretable structures. This property is absent in Transformers as causal attention is sufficient for acquiring positional associations, and the introduction of positional encoding amplifies this behavior, leading to improvement in data efficiency. SSMs on the other hand update their internal representations incrementally and without positional encodings, are required to learn these associations. Our findings reveal fundamental differences in how Transformers and SSMs, and hybrid models learn positional associations.

Foundation models must handle multiple generative processes, yet mechanistic interpretability largely studies capabilities in isolation; it remains unclear how a single transformer organizes multiple, potentially conflicting "world models". Previous experiments on Othello playing neural-networks test world-model learning but focus on a single game with a single set of rules. We introduce MetaOthello, a controlled suite of Othello variants with shared syntax but different rules or tokenizations, and train small GPTs on mixed-variant data to study how multiple world models are organized in a shared representation space. We find that transformers trained on mixed-game data do not partition their capacity into isolated sub-models; instead, they converge on a mostly shared board-state representation that transfers causally across variants. Linear probes trained on one variant can intervene on another's internal state with effectiveness approaching that of matched probes. For isomorphic games with token remapping, representations are equivalent up to a single orthogonal rotation that generalizes across layers. When rules partially overlap, early layers maintain game-agnostic representations while a middle layer identifies game identity, and later layers specialize. MetaOthello offers a path toward understanding not just whether transformers learn world models, but how they organize many at once.

Training selects for behavior, not circuitry: many weight configurations can implement the same function. Studying any single trained neural network thus risks describing accidents of one training run rather than the computation itself. This work shifts focus from what transformers happen to do to what they must do by extracting algorithmic cores, compact subspaces that are necessary and sufficient for a task and that recur across independently trained models. Here, Algorithmic Core Extraction (ACE) is introduced to isolate these subspaces, causally validate them, and recover the algorithms they implement across settings ranging from synthetic tasks to large-scale pretrained models. Markov-chain transformers embed three-dimensional cores in nearly orthogonal subspaces yet recover identical transition spectra. Modular-addition transformers form compact cyclic cores at grokking that later inflate under continued regularization, redundantly distributing the same computation across many functionally equivalent modes. This functional redundancy is found to accelerate the transition from memorization to generalization, yielding an inverse scaling law for grokking time. In six language models spanning more than two orders of magnitude in scale (GPT-2 Small/Medium/Large, LLaMA-3.1, Gemma-2, and Qwen2.5), subject-verb agreement is governed by a single, steerable axis that aligns across architectures. Flipping this axis inverts grammatical number throughout open-ended generation. Together these results suggest that beneath the apparent complexity of trained transformers lies a simpler, shared computational structure, and that targeting invariants rather than parameterizations may offer a more tractable path to mechanistic understanding and control. Code: https://github.com/joshseth/cores

Recent work has identified a subset of attention heads in Transformer as retrieval heads, which are responsible for retrieving information from the context. In this work, we first investigate retrieval heads in multilingual contexts. In multilingual language models, we find that retrieval heads are often shared across multiple languages. Expanding the study to cross-lingual setting, we identify Retrieval-Transition heads(RTH), which govern the transition to specific target-language output. Our experiments reveal that RTHs are distinct from retrieval heads and more vital for Chain-of-Thought reasoning in multilingual LLMs. Across four multilingual benchmarks (MMLU-ProX, MGSM, MLQA, and XQuaD) and two model families (Qwen-2.5 and Llama-3.1), we demonstrate that masking RTH induces bigger performance drop than masking Retrieval Heads (RH). Our work advances understanding of multilingual LMs by isolating the attention heads responsible for mapping to target languages.

When a decoder-only transformer is forced to process matched correct and incorrect single-token continuations of a factual query, the two pathways through hidden-state space diverge: displacement vectors from the query-only representation keep near-equal magnitude but rotate apart, with angular separation growing through mid-depth before late layers resolve an asymmetric outcome. A logit-lens preference in the incorrect run falls far below the equal-probability prior (roughly 11.5x more mass on the incorrect token than the correct one). We read this pattern, rotational divergence then late-layer asymmetric commitment, as the geometric signature of the model externally appearing to reject a wrong continuation, while staying explicit that it is observational, not causal: the incorrect run could equally reflect the model conforming to the token it is forced to carry, which only a random-token control can settle. It holds across six decoder-only transformers spanning four architecture families (Llama, Mistral, Gemma, StableLM) from 1B to 13B parameters; a seventh (Qwen2 1.5B) is flat under our protocol, plausibly a tokenizer artefact, leaving an emergence threshold open. Linear probes recover the distinction at intermediate depth, and cross-domain transfer is structurally asymmetric, a financial-medical corridor transferring far better than transport pairs. Where single-layer activation patching is cleanly interpretable (LLaMA-2 13B, Mistral 7B) it yields no layer band of consistent recovery; a third model (StableLM-2 1.6B) recovers uniformly above the ceiling, which we diagnose as a code-path artefact and exclude. Under this scoped null the late-layer asymmetry is not localized to a single component, fitting a distributed-by-trajectory account rather than single-layer localized recall. We document this with forced-completion probing across seven models, three domains, and 300 queries.

This paper studies simple transformers trained on a high-order Markov chain, where the model must incorporate information from multiple past positions, each with different statistical importance. We show that transformers learn the task incrementally, with each stage corresponding to learning how to copy information from a subset of positions via a sparse attention pattern. Notably, the learning dynamics transition from a competitive phase, where all heads focus on the statistically most important positions, to a cooperative phase, where different heads specialize in different patterns. We model these dynamics with simplified differential equations and prove stage-wise convergence of the resulting system. Functionally, these stages correspond to a sequence of increasingly expressive misspecified models, with the full model class reached only at the end. Overall, we give a theoretical account of how structured attention patterns and head specialization emerge in stages without an explicit curriculum, with implications for generalization in sequential tasks.

Motivation: Interpretability is not optional in biology: understanding gene regulation requires models whose learned structure can be directly interrogated, not merely accurate predictors whose internals resist mapping onto regulatory relationships. We ask whether an architecture mirroring the central dogma yields attention and gradient maps that recover known regulatory elements and networks in inspectable form. Results: Central Dogma Transformer II (CDT-II) mirrors the central dogma in its architecture -- DNA self-attention, RNA self-attention, and DNA-to-RNA cross-attention -- requiring only genomic embeddings and raw per-cell expression. On K562 CRISPR interference (CRISPRi) data with five genes held out entirely, CDT-II predicts perturbation effects (per-gene mean r = 0.84), recovers the GFI1B regulatory network (6.6-fold enrichment, P = 3.5 x 10^-17), and concentrates cross-attention on ENCODE regulatory elements including CTCF sites (mean 7.67x across 28 target genes, P < 0.001). Gradient attribution predicts consequences of perturbing therapeutic targets (mean r = 0.82). For TFRC, target of the anti-TfR1 antibody PPMX-T003, it identifies erythrocyte-structure, iron-dependent DNA-synthesis and oxidative-stress genes, matching anemia and ferroptosis reported clinically and preclinically -- without clinical data as input. CDT-II acts as an AI microscope, surfacing clinically relevant regulatory structure from perturbation experiments alone. Availability: Source code is available at https://github.com/nobusama/CDT2. Pre-computed embeddings, training data, and model weights are available at https://huggingface.co/datasets/nobusama17/CDT2-data.

In this paper, we focus on motion discrete tokenization, which converts raw motion into compact discrete tokens--a process proven crucial for efficient motion generation. In this paradigm, increasing the number of tokens is a common approach to improving motion reconstruction quality, but more tokens make it more difficult for generative models to learn. To maintain high reconstruction quality while reducing generation complexity, we propose leveraging language to achieve efficient motion tokenization, which we term Language-Guided Tokenization (LG-Tok). LG-Tok aligns natural language with motion at the tokenization stage, yielding compact, high-level semantic representations. This approach not only strengthens both tokenization and detokenization but also simplifies the learning of generative models. Furthermore, existing tokenizers predominantly adopt convolutional architectures, whose local receptive fields struggle to support global language guidance. To this end, we propose a Transformer-based Tokenizer that leverages attention mechanisms to enable effective alignment between language and motion. Additionally, we design a language-drop scheme, in which language conditions are randomly removed during training, enabling the detokenizer to support language-free guidance during generation. On the HumanML3D and Motion-X generation benchmarks, LG-Tok achieves Top-1 scores of 0.542 and 0.582, outperforming state-of-the-art methods (MARDM: 0.500 and 0.528), and with FID scores of 0.057 and 0.088, respectively, versus 0.114 and 0.147. LG-Tok-mini uses only half the tokens while maintaining competitive performance (Top-1: 0.521/0.588, FID: 0.085/0.071), validating the efficiency of our semantic representations. Code and checkpoints are available at https://eanson023.github.io/LG-Tok/

The architectural shape of dense Transformers has remained remarkably stable: narrow-wide-narrow feed-forward networks (FFNs) consume most non-embedding parameters. Motivated by theoretical and empirical evidences that residual wide-narrow-wide (hourglass) MLPs remain expressive despite bottlenecks, we revisit whether this architectural convention is necessary for dense language models. We study Hourglass Transformers, which replace the conventional FFN with residual stacks of hourglass sub-MLPs and use hourglass attention to decouple residual-stream width from attention width. This exposes a practical depth-width trade-off: compressing the FFN intermediate dimension allows wider hidden states and fewer layers at matched parameter budgets. Across model scales from 113M to 8B parameters, Hourglass Transformers achieve language-modeling and downstream performance comparable to conventional Transformers, while improving training compute efficiency by $8.7\%$ at matched average downstream accuracy across the 906M, 3B, and 8B scales. After long-context extension, the 8B Hourglass model also outperforms its matched conventional baseline across 4k-64k context lengths. At 64k context, the reduced attention layer count lowers both computation and KV-cache requirements, yielding up to $1.93\times$ faster token decoding and $50\%$ lower KV-cache memory at the 1B scale. These results identify hourglass structures as a practical architecture-efficiency alternative for compute- and latency-conscious Transformer design.

We introduce a constrained optimization framework for training transformers that behave like optimization descent algorithms. Specifically, we enforce layerwise descent constraints on the objective function and replace standard empirical risk minimization (ERM) with a primal-dual training scheme. This approach yields models whose intermediate representations decrease the loss monotonically in expectation across layers. We apply our method to both unrolled transformer architectures and conventional pretrained transformers on tasks of video denoising and text classification. Across these settings, we observe constrained transformers achieve stronger robustness to perturbations and maintain higher out-of-distribution generalization, while preserving in-distribution performance.

Single Image Super-Resolution (SISR) is a fundamental computer vision task that aims to reconstruct a high-resolution (HR) image from a low-resolution (LR) input. Transformer-based methods have achieved remarkable performance by modeling long-range dependencies in degraded images. However, their feature-intensive attention computation incurs high computational cost. To improve efficiency, most existing approaches partition images into fixed groups and restrict attention within each group. Such group-wise attention overlooks the inherent asymmetry in token similarities, thereby failing to enable flexible and token-adaptive attention computation. To address this limitation, we propose the Individualized Exploratory Transformer (IET), which introduces a novel Individualized Exploratory Attention (IEA) mechanism that allows each token to adaptively select its own content-aware and independent attention candidates. This token-adaptive and asymmetric design enables more precise information aggregation while maintaining computational efficiency. Extensive experiments on standard SR benchmarks demonstrate that IET achieves state-of-the-art performance under comparable computational complexity.

We present a systematic review of 337 articles evaluating the syntactic abilities of Transformer-based language models (TLMs), reporting on over 3,000 datapoints spanning a wide range of syntactic phenomena, languages, models, and methods. We take the data to collectively show that TLMs encode a non-trivial amount of syntactic knowledge. Behavioral evidence shows strong performance on formal syntactic phenomena, but weaker and more variable performance on phenomena at the syntax-semantics interface. Performance is also consistently lower for languages with less digital support. Probing and mechanistic studies further support the presence of syntactic knowledge in TLMs. Yet, because most work remains observational and methodologically heterogeneous, insight into the detailed computational mechanisms underlying syntactic processing remains limited. At the same time, the literature remains heavily concentrated on English and BERT-like models. We discuss the implications of our results and provide recommendations for future research.

Recent breakthroughs of transformer-based diffusion models, particularly with Multimodal Diffusion Transformers (MMDiT) driven models like FLUX and Qwen Image, have facilitated thrilling experiences in visual generation. However, these models rely only on the interactions between textual conditions and visual features to produce semantically aligned images. Once the interactions fail to reflect the nuanced compositional structure of the prompt, the generated images might be unsatisfactory. Thus, a comprehensive understanding of how different blocks and their interactions with textual conditions is crucial for better understanding the intrinsic attributes and for enhancing their interactions accordingly to strengthen the prompts adherence. In this paper, we first develop a systematic pipeline to comprehensively investigate each block's functionality by \textit{removing}, \textit{disabling}, and \textit{enhancing} textual hidden-states at corresponding blocks. Our analysis reveals that 1) semantic information appears in earlier blocks and finer details are rendered in later blocks, 2) removing specific blocks is usually less disruptive than disabling text conditions, and 3) enhancing textual conditions in selective blocks improves semantic attributes. Building on these observations, we propose \method, a novel inference-time method for tailoring block-wise textual guidance. Our approach not only improves text-image alignment but also enables a range of downstream applications, including precise editing and inference acceleration. Extensive experiments demonstrated that our method outperforms various baselines and remains flexible across text-to-image generation, image editing, and inference acceleration. Our method improves T2I-Combench from 56.92% to 63.00% and GenEval from 66.42% to 71.63% on SD3.5, without sacrificing synthesis quality.

Face super-resolution aims to recover high-quality facial images from severely degraded low-resolution inputs, but remains challenging due to the loss of fine structural details and identity-specific features. This work introduces SwinIFS, a landmark-guided super-resolution framework that integrates structural priors with hierarchical attention mechanisms to achieve identity-preserving reconstruction at both moderate and extreme upscaling factors. The method incorporates dense Gaussian heatmaps of key facial landmarks into the input representation, enabling the network to focus on semantically important facial regions from the earliest stages of processing. A compact Swin Transformer backbone is employed to capture long-range contextual information while preserving local geometry, allowing the model to restore subtle facial textures and maintain global structural consistency. Extensive experiments on the CelebA benchmark demonstrate that SwinIFS achieves superior perceptual quality, sharper reconstructions, and improved identity retention; it consistently produces more photorealistic results and exhibits strong performance even under $8\times$ magnification, where most methods fail to recover meaningful structure. SwinIFS also provides an advantageous balance between reconstruction accuracy and computational efficiency, making it suitable for real-world applications in facial enhancement, surveillance, and digital restoration. Our code, model weights, and results are available at https://github.com/Habiba123-stack/SwinIFS.

We present GeoTransolver, a multiscale geometry-aware physics attention transformer for Computer Aided Engineering (CAE). GeoTransolver extends the Transolver backbone with GALE (Geometry-Aware Latent Embeddings) attention, which pairs physics-aware self-attention on learned state slices with cross-attention to a shared geometry and global context computed via multi-scale ball queries (inspired by Domino) and reused in every block. Implemented and released in NVIDIA PhysicsNeMo, GeoTransolver persistently projects geometry and global parameters, into physical state spaces to anchor computations to domain structure and operating regimes. We benchmark on DrivAerML, SHIFT-SUV, and SHIFT-Wing against Domino, Transolver (PhysicsNeMo implementation), and literature-reported AB-UPT, evaluating drag/lift R2 and relative L1 errors on field variables. As an additional nonlinear structural mechanics application, we also report Transolver and GeoTransolver results on bumper-beam and full-vehicle Body-in-White (BIW) crash-dynamics benchmarks, evaluating relative L2 trajectory error and probe-level kinematic MSE. GeoTransolver delivers improved accuracy, robustness to geometry and regime shifts, and favorable data efficiency; we include DrivAerML ablations and qualitative contour and design-trend results, advancing operator learning for high-fidelity surrogates on complex, irregular, non-linear domains.

We investigate whether graded states of mind form spectrum-like structure in transformer representation spaces. To do so, we construct a dataset of 636 short natural-language sentences annotated with both a continuous score from $-5$ to $5$ and one of seven ordered tiers, ranging from collapsed or scarcity-driven expressions to more coherent, reflective, and integrative ones. We evaluate five frozen transformer representations: four sentence-embedding models and one decoder-only residual-stream representation. Across all representations, simple probes reliably recover both the continuous score and the discrete tier labels, and permutation tests show that performance significantly exceeds shuffled-label baselines. Additional analyses reveal a consistent geometric pattern: UMAP projections show low-to-high organization, confusion matrices concentrate errors between neighboring tiers, and directional ablation identifies a prominent score-aligned component. These results suggest that transformer representations contain statistically significant, spectrum-like organization aligned with the annotated state-of-mind structure. The annotations are used only as an operational framework for representation analysis, not as a clinical or diagnostic measure.

Gravitational-wave data analysis relies on accurate and efficient methods to extract physical information from noisy detector signals, yet the increasing rate and complexity of observations represent a growing challenge. Deep learning provides a powerful alternative to traditional inference, but existing neural models typically lack the flexibility to handle variations in data analysis settings. Such variations accommodate imperfect observations or are required for specialized tests, and could include changes in detector configurations, overall frequency ranges, or localized cuts. We introduce a flexible transformer-based architecture paired with a training strategy that enables adaptation to diverse analysis settings at inference time. Applied to parameter estimation, we demonstrate that a single flexible model, called Dingo-T1, can (i) analyze 48 gravitational-wave events from the third LIGO-Virgo-KAGRA Observing Run under a wide range of analysis configurations, (ii) enable systematic studies of how detector and frequency configurations impact inferred posteriors, and (iii) perform inspiral-merger-ringdown consistency tests probing general relativity. Dingo-T1 also improves median sample efficiency on real events from a baseline of 1.4% to 4.2%. Our approach thus demonstrates flexible and scalable inference with a principled framework for handling missing or incomplete data, key capabilities for current and next-generation observatories.

Language modeling has shown us that transformers can discover latent structure from context, but the dynamics of how they acquire different components of that structure remain poorly understood, leading to assertions that models just remix training data. In this work, we use the Alchemy benchmark in a controlled setting (Wang et al.,2021) to investigate latent structure learning. We train a small decoder-only transformer on three task variants: 1) inferring missing transitions from partial contextual information, 2) composing simple rules to solve multi-transition sequences, and 3) decomposing complex multi-step examples to infer intermediate transitions. By factorizing each task into interpretable components, we show that the model learns the different latent structure components in discrete stages. We also observe an asymmetry: the model composes fundamental transitions robustly, but struggles to decompose complex examples to discover the atomic transitions. Finally, using causal interventions, we identify layer-specific plasticity windows during which freezing substantially delays or prevents stage completion. These findings provide insight into how a transformer model acquires latent structure, offering a detailed view of how capabilities evolve during training.

Until recently, numerical weather prediction (NWP) models have stood rivalless in operational forecasting despite a few limitations. Namely, physically-based models are computationally demanding and struggle at short lead times, reducing their utility for nowcasting. Motivated by these shortcomings, recent work proposes AI-weather prediction (AI-WP) alternatives that emulate analysis data with neural networks. While these data-driven approaches have achieved high skill for medium-range forecasting-applications of AI-WP to precipitation and to nowcasting are less explored. To these ends, this paper discusses \textit{SaTformer}: a video transformer adapted for precipitation nowcasting. To ameliorate some problems related to what is essentially a fat-tailed regression task, we find it prudent to formulate nowcasting as a classification problem and employ a frequency-weighted loss. This straightforward approach scored first on the NeurIPS Weather4Cast 2025 ``Cumulative Rainfall'' challenge. Code and model weights are available: \texttt{\href{github.com/leharris3/w4c-25}{github.com/leharris3/satformer}}.