Transformer Architectures

Class activation mapping (CAM) is one of the most widely used visual explanation families in explainable artificial intelligence. Its purpose is intuitive: it converts internal model evidence into a heatmap that highlights the image regions, convolutional channels, tokens, or patches that support a target class or concept. Since the first CAM formulation in 2016, the field has moved far beyond global-average-pooled CNN classifiers. CAM-style methods now include gradient-based post-hoc explanations, gradient-free score and ablation methods, high-resolution upscaling, weakly supervised localization and segmentation, transformer token attribution, causal and debiasing methods, and foundation-model-era approaches that use CLIP, DINO, SAM, or feature-distribution comparisons. This review synthesizes a strict corpus of 57 method-centered papers published from 2016 onward. The paper develops a taxonomy that separates methods by attribution mechanism, architectural dependence, and evaluation objective. It then reviews gradient-based CAMs, recent and hybrid CAM-style methods, and model-based or architecture-aware methods. Across the corpus, the main trend is clear: the field is shifting from explaining one class score in one low-resolution CNN layer toward comparative, multi-layer, probabilistic, token-aware, and foundation-model-aware explanations. At the same time, evaluation remains fragmented. Faithfulness, localization, robustness, computational cost, and human trust are often measured with different protocols. The review therefore emphasizes not only what each method contributes, but also which gap it leaves open and which later methods attempt to close that gap.

Trained transformer models develop privileged bases: coordinate axes whose statistics differ from the rest of the residual stream. But what kind of direction does such a basis select? We investigate the prediction direction, the unembedding direction of the token a model currently predicts, and find that it functions as a content-defined privileged anchor. Measured with respect to this anchor, residual-stream variation is geometrically and behaviorally stratified by proximity to the prediction. The stratification holds in all eighteen models tested (dense and mixture-of-experts, 7B-120B, base and instruction-tuned). A narrow, scale-invariant prediction interface concentrates readout-relevant structure, while the vast prediction-distal complement expands with model scale. Because the prediction direction sits nearly orthogonal to the principal variance axes, variance-based analyses recover this organization only partly, and the shortfall grows with prompt heterogeneity. Anchoring reveals a steep geometric gradient: prediction-proximal regions are highly structured and cluster related prompts, while the complement is flatter and anti-discriminates among prompt groups. The interface is a narrow slice but functionally decisive. Disrupting the variance directions closest to the prediction causes immediate divergence and frequent task-frame shifts; disrupting the next level down delays divergence and preserves framing. The complement is weakly readout-aligned per direction yet causally and temporally load-bearing, and behavior is driven by direction rather than magnitude. These results establish the prediction direction as a privileged anchor distinct from previously described coordinate axes, and give a geometric account of how high-dimensional computation coexists with linear readout.

Background: Accurate segmentation of the Left Anterior Descending (LAD) artery in 3D free-breathing, non-contrast CT is critical for cardiac dose sparing in thoracic radiotherapy. The LAD is extremely small, has poor soft-tissue contrast, and varies substantially across patients; even manual contours show limited inter-observer agreement, underscoring the ambiguity of the vessel boundaries. Purpose: To develop a transformer-based framework that improves LAD delineation in low-contrast, imbalanced CT through local-global context modeling and uncertainty-guided optimization. Methods: We propose NA-UNETR, a 3D transformer-based segmentation model whose Neighborhood Attention (NA) and Dilated NA (DiNA) blocks jointly capture fine structural detail and long-range context. Given the scarcity of annotated LAD data, the model is pretrained on 1,000 CTA volumes of general coronary anatomy and fine-tuned with LoRA-based parameter-efficient adaptation on 20 free-breathing institutional CT scans. A composite Dice-Focal and Hausdorff loss, dynamically balanced via homoscedastic uncertainty, improves overlap and boundary accuracy. Results: NA-UNETR reached 45.64% Dice, 38.16 mm HD95, and 10.01 mm ASD, improving Dice by 3.10 percentage points over nnU-Net and reducing HD95 by 2.96 mm relative to Swin UNETR, with the strongest boundary accuracy among all models and improved centerline stability. On ImageCAS it achieved 79.49% Dice, 8.89 mm HD95, and 1.02 mm ASD. Ablations confirmed that residual blocks, variable kernels, and uncertainty-weighted loss each contributed. Conclusions: NA-UNETR balances local precision and global context for thin, low-contrast LAD structures, offering a computationally efficient framework for substructure-level cardiac segmentation in radiotherapy planning.

Transformer-based methods have achieved strong performance in monocular 3D human pose estimation, but most existing approaches organise spatial and temporal reasoning as separate stages, which may weaken unified spatial-temporal interdependencies inherent in human motion and compress frame-level structural information before temporal modelling. In this paper, we propose HSTGFormer, a graph-enhanced Transformer framework that reformulates spatial-temporal reasoning as localised coupled graph aggregation over joint-time nodes. Specifically, HSTGFormer introduces a Hyper Spatial-Temporal Graph (HSTG), which decomposes global spatial-temporal reasoning into local spatial-temporal receptive fields around individual joint-time nodes by extending per-frame skeleton graphs into temporal neighbourhoods, thereby enabling structure-aware coupled reasoning while preserving local structural motion information. It further incorporates an Adaptive Dual-Scale Temporal Graph (ADSTG) to capture joint-specific temporal dependencies over complementary short- and long-range windows. A lightweight node-wise fusion module further adaptively integrates the two graph representations for each joint-time node. Experiments on Human3.6M and MPI-INF-3DHP show that HSTGFormer achieves strong accuracy with high computational efficiency.

Scaling laws promised cost-effective experiments; six years later, they have yet to fully deliver. Instead, researchers have found them unreliable at small scales (starting at 4M parameters) and concluded that sizable models cannot be avoided. We show this is not the case: the confounding factor is hyperparameters. Small models are highly sensitive, but hyperparameter sensitivity fades with scale. This small-scale sensitivity makes scaling laws easy to miss because they only emerge on the fully tuned frontier, and reaching that frontier requires an extensive search far beyond what most ever run. By ablating the basic scaling law recipe, we show well-tuned hyperparameters matter more than any other ingredient. Further, we reveal why those hyperparameters become easier to find: as scale increases, the hyperparameter loss surface becomes lower dimensional. Nevertheless while scaling laws exist in small models, extrapolation hits statistical limitations. A holistic approach is required. Synthesizing our insights with the recent literature, we develop a new methodology for model-centric research and demonstrate it on a question that once took the field years to settle: where to place normalization layers in the transformer architecture. From small-scale experiments, we recover the large scale result: pre-normalization works better as models grow in size. With the right tools and a better understanding, small-scale experiments can deliver on scaling laws' long-awaited promise.

Sign language translation has achieved strong results with Transformer architectures, yet recent improvements largely rely on scaling model capacity at the cost of increased computation. We propose a parameter-efficient alternative that improves expressiveness without increasing model size. Rather than scaling capacity, we focus on enhancing the update dynamics of iterative refinement decoders, where each refinement step corresponds to one internal decoder iteration that progressively improves the latent representation before translation generation. We reinterpret residual refinement updates from an Ordinary Differential Equation (ODE) perspective and replace them with higher-order numerical integration schemes, namely Runge--Kutta methods (RK-2 and RK-4). These methods perform multiple function evaluations within each refinement step to produce more accurate and stable representation updates without adding decoder parameters. To the best of our knowledge, this is the first application of ODE-inspired update dynamics to sign language translation. RK-2 achieves 22.96 BLEU-4 on the PHOENIX-2014-T test set and 19.34 BLEU-4 on the CSL-Daily test set, outperforming the IPSLT baseline on both benchmarks, with fewer decoder layers and refinement iterations on CSL-Daily. These results suggest that stronger refinement dynamics can improve translation performance under parameter-efficient decoder designs, providing a complementary alternative to conventional model scaling.

Reliability estimation of large language models is in many cases as crucial as their accuracy, as reliable models are more trustworthy, robust, and suitable for practical applications. Recent advancements in natural language processing (NLP), particularly those based on transformer architectures, have significantly accelerated progress across various NLP tasks. This study focuses on the reliability of transformer-based question answering (QA) models, specifically BERT models and its variants (RoBERTa, ALBERT, DistilBERT). These encoder-only pretrained transformers have demonstrated remarkable accuracy in QA tasks that can be treated as classification tasks. However, their reliability remains underexplored. This study evaluates the reliability of four BERT-based models by assessing response stability under two conditions: (1) internal model variations induced via Monte Carlo Dropout (MCD) and (2) input perturbations through paraphrasing. Using the SQuAD and QuAC datasets, we investigate how dropout rates affect prediction consistency and whether lexical changes impact answer stability. Our findings reveal that RoBERTa maintains higher reliability, whereas AlBERT and DistilBERT exhibit significant inconsistencies. Statistical analyses confirm that enabling MCD during prediction does not disrupt inference dynamics, validating its effectiveness as a reliability metric. These findings underscore the importance of evaluating both accuracy and stability in QA models to ensure stability in real-world applications.

A transformer's answer lives on one axis: the direction its unembedding reads. Its intermediate states largely do not, and that off-axis position is usually treated as an obstacle to interpretation. We show it is functional. A 12-layer model computes in two phases. Through the first, every sublayer writes into a subspace held near-orthogonal to the read-out, attention 75 to 96 degrees off it at every depth. Moving attention's values onto the read-out is 64 to 84 times more damaging than a matched random rotation, and the damage is entirely in cross-token mixing: the subspace insulates composition from the vocabulary. Beneath it the frame itself turns rigidly with depth. In the second phase the answer arrives on-axis, late, and by addition rather than by turning accumulated content onto the read-out. Pressing every layer onto the read-out instead, as training for early exit does, matches the baseline on perplexity, LAMBADA and BLiMP while cutting the concept-phase workspace from about twenty-five effective dimensions to fourteen, a change none of those benchmarks register. The geometry can also be imposed, though not by asking for it. Prescribing it through the loss is a lottery: six of eight seeds collapse, because a model told to null its read-out projection obeys most cheaply by discarding dimensions. Inserting one fixed rotation at the phase boundary lands it instead, at baseline quality. A sparse rotation the surrounding weights can absorb converges on all nine seeds, against five of nine for ordinary training. Which rotation is immaterial: twenty-five runs across thirteen distinct ones reach the same quality, and two baselines from different seeds hold their concepts in near-orthogonal frames while agreeing on their read-outs. That freedom is usable: a basis drawn at random and prescribed before training is adopted across the concept phase, with quality unchanged.

State Space Models (SSMs), as a mainstream research direction of linear Transformers, aim to achieve higher efficiency than standard Transformers in long-context modeling. However, existing SSMs suffer from limited input adaptivity and constrained memory capacity, leading to information loss when modeling ultra-long sequences. To address these limitations, we propose MixFormer, a novel linear Transformer that integrates a Mixture-of-Memory-Experts (MoE) mechanism. Specifically, the model maintains differentiated memory states through multiple collaborating memory experts and employs a novel Time-Aware Linear Attention (TALA) mechanism, which leverages learnable exponential decay functions and positional biases to dynamically update memory. This design enables the model to selectively reinforce important historical information while effectively mitigating memory dilution, substantially improving long-range dependency modeling. Experiments on long-sequence text and image generation tasks demonstrate that MixFormer not only achieves significant performance gains but also provides a more sustainable computational backbone for the next generation of web infrastructure.

Deep decoder-only Transformers often replace the original Post-Norm architecture with Pre-Norm variants because Post-Norm training is highly sensitive to warmup and learning rate under conventional initialization schemes. Although prior work has identified rank collapse and gradient vanishing as related symptoms, it remains poorly understood how causal attention creates high-similarity representations and why training dynamics fail to repair them. We give a two-stage analysis of Post-Norm rank collapse using token similarity as a scalar state variable. First, at initialization, causal attention acts approximately as a prefix-averaging operator that increases token similarity across depth, while the SwiGLU branch contributes only a smaller damping effect. Second, once training enters a high-similarity regime, growth of pre-normalization residual norms makes the RMSNorm backward factor contractive; under mild conditions, gradients to earlier layers decay geometrically. As a complementary result, we characterize the properties of a collapsed network: its best predictor is frequency distribution with relatively high loss floor, and gradients in collapsed layers vanish at frequency distribution. Experiments on 48-layer decoder-only Transformers trained on C4 dataset match the predicted initialization-time similarity growth and collapse-time gradient contraction, and show that collapsed runs stay near the predicted frequency loss. Together, these results distinguish the forward similarity amplification and backward repair incapacity in Post-Norm collapse, while also characterizing the behavior of collapsed networks.

Autoregressive transformers compute along two axes: horizontally across generated tokens, and vertically through model depth. Dense attention gives each token broad horizontal access to the past, but the vertical feedback channel between decoding steps remains narrow: only the sampled token returns to the bottom of the stack, while the top-layer hidden state is discarded. We introduce the \emph{full-bandwidth transformer}, which widens this channel with \emph{latent feedback}: at each decoding step, the previous top-layer hidden state is fused with the sampled token embedding through a gated linear unit and fed back as the next input. Latent feedback lets non-verbalized computation re-enter the stack with a renewed depth budget, while preserving the standard transformer architecture, KV cache, and language-modeling objective. To train full-bandwidth transformers without losing parallel teacher forcing, we use a scheduled multi-pass objective that introduces latent feedback late in pretraining and mixes a small fraction of deeper feedback passes for stability. We train 1B-parameter full-bandwidth transformers up to 400B tokens and find that latent feedback improves validation loss, 5-shot language-model evaluation, math and coding generation, and instruction-tuned performance. With negligible per-token decoding overhead, full-bandwidth transformers match or approach standard transformers trained with roughly $1.5\times$ more tokens, and manage to produce shorter reasoning traces at equal or better accuracy.

Transformer-based large language models (LLMs) achieve strong performance across many tasks, but their Key-Value (KV) cache grows linearly with sequence length, creating a severe memory bottleneck for long-context inference. Existing heuristic eviction methods (e.g., H$_2$O and SnapKV) rely on static attention or positional signals that often fail to capture a token's future predictive influence. We propose DistillCache, a reinforcement learning framework that formulates KV-cache eviction as a sequential decision problem. DistillCache learns a lightweight policy network using rich internal model signals (attention statistics, value norms, entropy, and position) and trains it with REINFORCE via a per-step KL-divergence reward to preserve the full-cache output distribution. On a 7B-parameter instruction-tuned Transformer (Mistral-7B-Instruct-v0.3), DistillCache retains 94.2% of full-cache accuracy on LongBench at a 25% cache budget, outperforming both strong heuristic baselines (H$_2$O, SnapKV) by up to 2.7 absolute points and, under our re-implementations, concurrent RL-based methods (ForesightKV, RLKV) by up to 1.4 points on long-context tasks. On reasoning benchmarks, DistillCache is competitive with the best concurrent method and surpasses it under aggressive compression. It also delivers up to 2.1x full-cache throughput while maintaining competitive practical efficiency. These results highlight the effectiveness of learned, distribution-aware policies for memory-efficient long-context LLM inference.

Self-attention models content-dependent interactions between tokens but does not by itself encode token order. Position encoding addresses this limitation by introducing absolute coordinates, relative distances, or position-dependent rotations into Transformer representations and attention scores. This technical survey develops a unified account of sinusoidal and learned absolute position embeddings, Shaw-style relative position representations, Transformer-XL, T5 relative position bias, ALiBi, and Rotary Position Embeddings (RoPE). We derive how RoPE converts absolute position indices into relative phase differences in Query-Key inner products and compare these methods in terms of where position is injected, computational cost, compatibility with KV caching, and length extrapolation. We then examine long-context extensions, including Position Interpolation, RoPE scaling laws, NTK-aware scaling, Dynamic NTK, NTK-by-parts, YaRN, LongRoPE, and LongRoPE2, with emphasis on frequency allocation, attention rescaling, training length, and target context length. We also summarize implementation considerations, evaluation protocols, and position-encoding choices in representative large language models. A central conclusion is that the ability to compute positional features beyond the training length does not imply reliable long-context generalization; context extension must be evaluated through short-context retention, position-wise perplexity, retrieval, reasoning, and long-context code tasks.

The CVPPA@ECCV 2026 BuzzSpot Challenge asks us to detect bees, bumblebees, hoverflies, and moths in 1920x1080 field keyframes. Its annotations carry 2 difficulties: the median box occupies 0.16% of a frame, and bees account for 80% of the labels. To cope with the small boxes, we compare 10 recorded detector configurations on held-out keyframes; plain Co-DINO with a Swin-L backbone has the highest mAP in this comparison, so we select it. Training then addresses the bee dominance in 2 ways: fine-tuning on a crop-mosaic pool in which the combined annotation share of the 3 rare classes rises from 19.9% to 55.1%, and a class-weighted simplex equiangular tight frame (ETF) loss that pulls the projected states of matched decoder queries toward fixed class directions. The full schedule spans 12+3+2 epochs. Without inference-time ensembling or test-time augmentation, we rank first on FinalTest at 0.5062 mAP@[.5:.95].

Spiking Transformers provide a promising paradigm for efficient visual processing with spike-driven computation, yet their Softmax-free Spiking Self-Attention (SSA) struggles to establish spatially localized token interactions. Although existing locality-enhanced SSA methods improve accuracy, it remains unclear whether they consistently induce spatial locality across layers and different Spiking Transformer architectures. Through Mean Attention Distance (MAD) analysis, we reveal that computational locality does not necessarily translate into spatial locality and show that uniformly applying the same locality enhancement overlooks architecture-dependent deployment requirements. Motivated by these observations, we propose Spatially Contiguous Local Attention with Boundary Continuity Pathway (SCLA-BCP). SCLA computes attention within non-overlapping regions of spatially adjacent tokens, while BCP facilitates cross-boundary information exchange through a lightweight convolutional pathway. Furthermore, we develop a hierarchical locality deployment strategy to effectively apply SCLA-BCP across the two major Spiking Transformer architectures. Extensive experiments on seven static and neuromorphic datasets covering classification, detection, and segmentation demonstrate consistent improvements with limited parameter and energy overhead. Notably, our approach improves mAP@50 by up to 9.50% on COCO 2017 and mIoU by up to 3.42% on ADE20K. Visualizations, MAD analysis, and ablation studies further validate its effectiveness.

Transformers have had a profound impact on the world of language processing and computer vision. As efforts to answer the million-dollar question of ``How does a Transformer learn?" have been increasing, existing interpretability studies primarily analyze representations at isolated layers or the network as a whole, while the developmental evolution of individual representations and its manifolds across transformer layers remains underexplored. With this work, we aim at providing a comprehensive analysis of the evolution of representations as the representation point cloud transforms across the layers; thereby attempting to isolate layers or establish a trend which comes closer to justifying how and when raw input representations evolve into task-relevant feature representations. Thus, Transformer Geometry Observatory-TGO-IV introduces a topological framework for analysing the evolution of Transformer representations through the lens of Persistent Homology. Rather than studying local geometric properties alone, TGO-IV constructs Vietoris--Rips simplicial complexes from token-level representation point clouds and investigates the evolution of their persistent topological signatures across Transformer layers. The proposed framework comprises complementary topological observatories including Persistence Diagrams, Barcode Diagrams, Betti Curves, Persistence Landscapes, Bottleneck Distance, and Wasserstein Distance, enabling a comprehensive analysis of how the global topology of representation point clouds develops throughout the forward pass.

Simulating complex fluid flows requires capturing full equilibrium distributions rather than just mean trajectories, yet high-fidelity solvers remain computationally prohibitive. Recent advances, such as Diffusion Graph Networks (DGNs), have combined diffusion models with graph neural networks to sample equilibrium states directly from unstructured meshes, enabling distributional accuracy even from short simulations. However, graph-based diffusion approaches suffer from hand-crafted architectural constraints, limited receptive fields in message passing, and costly multi-scale designs, which restrict scalability to larger and more complex domains. We propose Fluid-DiT, a Graph-Free Diffusion Transformer that replaces graph message passing with attention-based denoising, eliminating explicit graph design while preserving the ability to model distributions of chaotic flows. Our framework introduces a latent-space formulation that disentangles geometric fidelity from distributional learning, reducing high-frequency artifacts and accelerating sampling. By leveraging the transformer's global receptive field, Fluid-DiT naturally captures both local flow structures and long-range correlations without requiring hierarchical graph coarsening. On canonical benchmarks including laminar cylinder wakes, ellipse-flow systems, and turbulent 3D wing experiments, Fluid-DiT consistently outperforms graph-based diffusion baselines in both sample quality and distributional accuracy, achieving higher $R^2$ correlations and lower Wasserstein distances. Moreover, it generalizes robustly from short, incomplete trajectories to unseen Reynolds numbers and geometries, demonstrating strong scalability.

The Tower of Hanoi is a simple planning puzzle that in prior work has proven challenging for large reasoning models (LRMs). Current models solve the standard formulation of the puzzle, but still struggle with the flat-to-flat variant (where initial and goal states are not restricted to have all rings on a single peg). This paper presents an in-depth study of how both small, in-house Transformers and large, third-party LRMs solve this task. To understand the failures mechanistically, we first train small Transformers from scratch on precomputed solution traces. Using a variety of interpretability techniques, we show that these Transformers develop an emergent world model: a linearly decodable, geometrically faithful representation of the puzzle's state space (the Sierpinski triangle), that is causally involved in solving the puzzles. Second, we return to the large LLMs and apply our techniques to two frontier reasoning models, Qwen3.6-27B and DeepSeek-R1-Distill-Qwen-32B, that attempt to solve the task through extended chain-of-thought. Surprisingly, we find that both models encode the Sierpinski world model near-perfectly at the end of the prompt, and yet fail at the majority of tasks when there are more than 3 rings. We locate the source of this failure in the decaying representation of the world model. We probe for the representation at different stages during planning, and establish causality by showing that performance can be improved by injecting the prompt-time representation at inference. The failure of the models is thus one of maintenance of the required representations, not their absence, and performance is at least partially recoverable. These results thus reframe the reported collapse in performance from prior work: current Large Reasoning Models build a world model, and then lose it.

We test whether a parameterized quantum circuit (PQC) improves a hybrid quantum-classical model's performance on classical datasets, using an interface-matched classical map as the control while holding all other components fixed. Our architecture, Quantum-Embedded Attention (QEA), uses a learnable projector to compress backbone features into an $n_q$-dimensional angle vector, a shallow PQC to map those angles to one- and two-qubit Pauli expectations, and a classical attention decoder to produce class logits. We hypothesized the PQC would improve accuracy or seed-to-seed stability over a classical map with matched input/output dimensions. We test this with an interface-matched $2\times2$ factorial on Breast Cancer Wisconsin at $n_q\in\{4,8\}$, independently swapping the PQC for a classical map and the attention decoder for a linear head, across five paired seeds per cell. Three of four paired quantum-minus-classical $95\%$ confidence intervals include zero; the fourth, a $+1.63$ percentage-point contrast for the attention decoder at $n_q=4$, reverses sign at $n_q=8$ and does not survive correction across the four contrasts. The experiment thus shows no consistent PQC contribution and cannot establish equivalence. A five-dataset cross-modality grid shows comparable accuracy on AG~News, Breast Cancer Wisconsin, and BirdCLEF but a large deficit on CIFAR-10; these cells are not interface-matched and are interpreted descriptively. We report all planned canonical runs, distinguish current Pauli-readout results from legacy probability-readout experiments, and analyze bottleneck, simulation, finite-shot, and noise limitations. The results do not establish a quantum advantage; they demonstrate why controlled component attribution is necessary before crediting a hybrid model's performance to its quantum layer.

Transformers provide a powerful architecture for global content-based matching, but reasoning problems may benefit from a stronger inductive bias toward iterative traversal of latent relations. We introduce Graph Machine, an architecture with two explicit edge-based mechanisms: Edge-augmented attention, in which edges modulate attention between nodes, and edge-centric referral, in which nodes exchange addresses to update their edges. Conceptually, this enables the model to dynamically and differentiably construct and revise relational graphs across layers. We study this inductive bias using Sudoku under controlled settings and find that Graph Machine outperforms Transformer baselines, with ablation studies and mechanistic analysis attributing the gains to the edge mechanisms. Surprisingly, we found that the model discovers a compact edge-based construction for Sudoku geometry. Our results support explicit edge mechanisms as a promising architectural design, motivating broader evaluation.

In a feature-tokenized transformer (arXiv:2106.11959) such as BiomeGPT (doi:10.64898/2026.01.05.697599), each input token is built by fusing a fixed identity with a sample-specific measurement: a fixed species and a variable abundance, T = S + A. To interpret downstream classification in such models, prior work inspects the attention weights of the special [CLS] token (arXiv:2106.11959, arXiv:1810.04805, BiomeGPT) to rank sample tokens by importance. These weights have two critical limitations: they are nonnegative, so they cannot separate disease-supporting from health-supporting evidence (arXiv:2201.12114), and they act after token fusion, obscuring how the input sources S and A each affect the output. To address this we use Integrated Gradients (arXiv:1703.01365), a signed, fusion-aware attribution method, and propose a source-derived baseline T' = S + A_0 for feature-tokenized models such as BiomeGPT, which preserves species identity as a fixed biological coordinate while isolating the effect of abundance variation. Applied to a disease-versus-health decision margin, it yields polarity that explicitly separates pathogenic from protective microbial signals. We show that this gradient-based approach uncovers species-abundance directional relationships and sensitivity diagnostics entirely obscured by unsigned [CLS] attention weights. We further recommend second-order Integrated Hessians (arXiv:2002.04138) to expose microbiome community interaction rules: how a perturbation in one member alters the model's sensitivity to another, and which other species drive ambiguous cases toward disease or health at a given abundance level. This provides a principled approach to explainability in BiomeGPT that generalizes to other smooth and differentiable feature-tokenized transformers. Code is available at https://github.com/nohren/token-source-attribution

Inspired by recent evidence that transformer architectures benefit from Self-PreTraining (SPT) on long-context benchmarks, we investigate whether similar gains extend to multimodal, multivariate, and even simple univariate medical time series. Our objective is to assess the impact of SPT on the performance and scalability of transformer-based models across diverse medical applications, particularly under limited data conditions. We evaluate transformer architectures on three representative medical time-series tasks: rehabilitation robotics (Camargo dataset), stress detection (Non-EEG Stress), and Parkinson's disease detection (Gait Parkinson's Disease). Models are trained either from scratch or through SPT using four masking-based objectives designed to promote temporal and cross-modal representation learning, and we systematically vary model depth to examine how capacity interacts with pre-training benefits. Across datasets and configurations, SPT consistently improves classification accuracy by 0-6 percentage points depending on masking strategy, dataset and architecture, with gains observed not only in multivariate settings but also when models are restricted to simple univariate inputs. The improvements increase for deeper models that can better exploit the enriched temporal representations learned during pre-training. These findings indicate that SPT is a simple and general strategy that enhances transformer performance on medical time-series tasks without requiring task-specific architectural changes, supporting its potential to improve robustness and accuracy in data-limited clinical settings.

Positional embeddings (PE) in Transformers encode token distance and order but are largely agnostic to \textit{syntactic structure}. We introduce \textbf{S}yntax-\textbf{i}nformed \textbf{P}ositional \textbf{E}mbeddings (\textbf{SiPE}), which learns a lightweight syntactic prior from dependency parses during pretraining and injects it across all three dominant PE families (absolute, relative, rotary), for both encoders and decoders, leaving self-attention and the rest of the architecture untouched. We isolate \emph{where} and \emph{how} the prior should enter the model, and find it depends on the architecture: for autoregressive decoders that use relative PE, the prior is strongest when coupled multiplicatively with the relative-position term of the attention score, outperforming injection into the input embeddings, into self-attention, or into the positional and attention terms jointly---while for encoders it is best added directly to the input embeddings, composing with each encoder's native positional mechanism. We find that models pre-trained with SiPE improve on the SyntaxGym benchmark by up to $10.3\%$ while simultaneously reducing perplexity by $9.0\%$ over a base model with no syntactic supervision---a metric nearly every existing syntax-injection method instead degrades. Crucially, these gains extend beyond syntactic generalization: SiPE also improves real-world language understanding, raising scores on the GLUE benchmark by up to $8.2\%$ over a model trained without it. Unlike existing syntactic language models that marginalize over many parses at inference or discard syntax at runtime, SiPE conditions on a single parse, establishing a new Pareto frontier between syntactic supervision and inference cost.

Structured input files such as JSON, DOT, OBJ, INI, S-expression, and TinyC are widely used in software systems, but small corruptions can cause parsers to reject otherwise useful data. Repairing such inputs is important because malformed configuration, program, and data files can interrupt testing, analysis, deployment, and downstream automation even when most of the original content remains intact. Existing repair techniques can produce structurally valid inputs, but they often rely on deletion or repeated search, which may lose original content and result in semantic incorrectness. This paper presents RepairFormer, a transformer-based framework for structured input repair. The approach formulates repair as a supervised sequence generation task and uses format tags, oracle validation, and boundary-localized repair to generate valid outputs while preserving content. The boundary workflow focuses generation on the detected fault region, reducing the input size, and supporting repair of longer files. In evaluation, RepairFormer achieves a 88% in repair and 94% in recovery, showing strongest content preservation when repairs are successful. Additional experiments on our benchmark shows RepairFormer repairs 97.57% and recovers 94.29% with 5x faster runtime compared to state of the art.

Vision Transformers (ViTs) increasingly rely on input-adaptive inference, such as token pruning and early halting, to meet energy and latency budgets. This survey examines a recent class of adversarial efficiency degradation attacks that target these mechanisms to increase computation without necessarily degrading accuracy. We unify and compare two representative attacks, SlowFormer (a universal adversarial patch) and DeSparsify (per-image perturbations), across three popular token-pruning frameworks: A-ViT, ATS, and AdaViT. We standardize reporting using GFLOPs, accuracy loss, and an Attack Success (AS) metric that measures how much of the model's compute savings the attack takes away. Understanding these attacks is crucial for designing countermeasures that not only mitigate risk but also remain lightweight, since deployment often occurs in low-power settings such as mobile or embedded devices. To organize our analysis, we focus on three questions: how input-adaptive optimizations (e.g., token pruning and early halting) create attack surfaces for efficiency degradation; how such attacks operate in practice and which optimizations are most vulnerable; and which defenses exist today and whether they meaningfully restore efficiency under attack.

Existing studies on self-supervised learning for white-box networks typically decouple the derivation of white-box networks via optimization algorithms from self-supervised learning paradigms. In this work, we instead revisit the two components from a joint perspective. The LeJEPA-based self-supervised framework assumes an isotropic Gaussian distribution as the optimal embedding distribution for downstream tasks, which is conceptually equivalent to the expansion term $R(Z)$ in the sparse rate reduction objective guiding white-box Transformer optimization. Building on this observation, we use the LeJEPA self-supervised paradigm to optimize $R(Z)$, and derive the remaining terms $R^{c}(Z\mid U_{[K]})+λ\lVert Z\rVert_{0}$ via the alternating direction method of multipliers (ADMM) into an attention-only Transformer that dispenses with the ISTA structure or MLP layers of the original design. Experimental results demonstrate that our attention-only white-box Transformer achieves classification accuracies of $88.88\%$ on CIFAR-10 and $63.54\%$ on CIFAR-100 at the Base scale under the LeJEPA self-supervised paradigm, while the original white-box Transformer CRATE achieves classification accuracies of $89.18\%$ on CIFAR-10 and $63.56\%$ on CIFAR-100. Our model achieves competitive performance while reducing the parameter count by roughly $31\%$. Beyond the white-box setting, we further investigate standard ViTs and find that replacing all MLP blocks with ReLU activations under knowledge distillation removes approximately 66% of the parameters while preserving competitive accuracy, motivating further investigation into the potential redundancy of MLP modules in standard ViT architectures.

Engineered Skeletal Muscle Tissues (ESMs) have become a key structure for biomedical disease modeling and pharmacological screening, yet their functional characterization often relies on simplistic metrics like peak force, discarding critical kinetic information. This is partially due to the high level of mathematical complexity which mechanistic models introduce to capture these dynamics. Hence, exactly the complexity prevents scalable application and widespread adaptation in the field. Here we present a Physics-Flavored Neural Network (PFNN) that automates the kinetic phenotyping of ESMs. Our architecture integrates a stretched-exponential physical model into a CNN-Transformer, enabling the extraction of physically meaningful parameters directly from force-time profiles. To address the scarcity of labeled biological data, we employ a hybrid training paradigm: the model develops a "physical intuition" on synthetic data before undergoing unsupervised self-alignment on unlabeled real-world measurements. Our results demonstrate that this physics-flavored approach achieves high-fidelity parameterization across diverse contractile phenotypes and cell lines, including Duchenne Muscular Dystrophy models. Our scalable, self-improving pipeline bridges the gap between idealized biophysics and noisy \emph{in vitro} data, providing a robust tool for high-throughput biophysical research.

We reinterpret Transformer inference by developing a functionally equivalent mechanical-structural description of its functional architecture. Parameterized transformations of token representations, or transforming concepts, are identified with simple neural networks organized through output-input and output-weight interconnections. This redescription makes explicit an organizational feature that is not equally salient in the standard matrix description: during inference, the outputs of some networks determine the weights, and hence the transformations, of others. These output-weight interconnections generate prompt-dependent dynamic transformations and give rise to Sequence-level Interactive Dynamic Parallel Processing (SIDPP). We show that the number of dynamic parameters grows linearly with prompt length and may become comparable to, or exceed, the number of static parameters fixed through training, a phenomenon we call strong prompt sensitivity. Philosophically, this shifts the conceptual picture of the Transformer from one centered on the static structure acquired through training to one that also treats the prompt-dependent transformations dynamically constructed during inference as constitutive features of its operation. GPT-4.5's recent Turing test results provide a behavioral illustration of this phenomenon. Finally, we identify biological mechanisms morphologically and functionally correspondent to output-weight interconnections, supporting the in-principle neural realizability of SIDPP and motivating Conjecture T: human neural systems may realize a functional architecture relevantly similar to that of the Transformer.

Humans recognize a musical passage even when it is shifted in time or transposed in pitch, indicating a notion of equivariance in the representation space. Our analysis, however, shows that standard music transformers map such time-shifted or pitch-transposed inputs onto uncorrelated representations: these models become progressively less equivariant as they scale in size or train longer. This suggests that in standard music transformers, additional model capacity is allocated to memorizing absolute patterns rather than capturing shared musical structures. In this paper, we propose the Equivariant Music Transformer (EMT), which enforces equivariance through self-distillation by jointly optimizing a next-token-prediction and an auxiliary equivariance regularization loss. We find that the additional equivariance loss acts as a beneficial regularizer, simultaneously improving next-token prediction and producing equivariant latent representations. Through both objective and subjective evaluations, EMT demonstrates superior equivariance and generative capability compared to data augmentation, feature engineering, and state-of-the-art (SOTA) baselines. More broadly, our findings reveal that standard language modeling methods alone do not capture music's translational symmetries, and dedicated inductive biases are required to produce better music representations. The code, weights and demos are available online.

Dense pretrained transformers do not naturally expose interpretable units for circuit extraction. Existing approaches obtain such units by learning auxiliary sparse representations or training sparse models, incurring substantial additional computation while potentially introducing a fidelity gap between the representation being analyzed and the original pretrained model. We propose Sparse Weight Decomposition (SWD), which reparameterizes pretrained linear projections by factorizing each weight matrix into two sparse factors whose shared intermediate coordinates serve as individually addressable circuit units. Without training a separate replacement network, this parametric representation supports the same scoring, selection, and ablation circuit extraction workflow used for methods that learn sparse features. Across single-matrix replacements, SWD matches the held-out fidelity achieved by Transcoder and other strong baselines while using less than 1% of the data that those baselines use to train their replacements. For matched replacement fidelity, SWD reaches the same circuit sufficiency and necessity targets with fewer active read/write edges and selected units across tasks on GPT-2, Qwen2.5, and Qwen3.5-27B. We further show that SWD remains effective for full-model replacement of all attention and MLP weight matrices after fine-tuning the nonzero factor values. Finally, SWD also features a zero-data variant, allowing broader use of mechanistic interpretability analysis (e.g., per-step analysis).

Looped transformers have emerged as a parameter-efficient alternative to scaling depth for strong reasoning. By reusing one stack of layers across $T$ iterations, they attain the effective depth and reasoning capabilities of larger models at a fixed parameter count. Yet existing approaches suffer from latent overthinking and undifferentiated computation, largely because intermediate representations receive no guidance across loops. Multi-token prediction (MTP) supplies exactly the dense, forward-looking supervision the loop is missing. We propose \textsc{LoopMTP}, which links the two through a structural correspondence in latent space: a model that loops $T$ times can anticipate $T$ future tokens. \textsc{LoopMTP} realizes this by softly aligning the hidden state of loop $t$ with the embedding of the token $t$ steps ahead, while a lightweight gate preserves useful information across iterations. \textsc{LoopMTP} improves average accuracy by up to 8.1% (relative) over the non-looped baseline, with training remaining stable for up to 15 loops.

When a transformer learns an irregular morphological pattern, what has it learned? Our test case is the Spanish \emph{L-shaped morphome}, a complex irregular pattern in which the verb's stem alternates in exactly the first-person singular indicative and all subjunctive forms, and whose membership no phonological, semantic, or syntactic feature predicts. Prior studies have shown that character-level transformers can reproduce this pattern, but that evidence describes what models produce, not what they represent. Probing five architectures, twelve trained models each, under lemma-disjoint cross-validation with controls and surface baselines, we show that the models encode the L-shaped class itself, not just its visible alternations. It is decodable above every surface baseline, survives instances in which every form shows the same stem, and probes trained on alternating instances still classify non-alternating ones. The encoding is localized where the stem choice is made, at the stem-final consonant position of the middle decoder, before the alternant is read. And it is item-specific: which verbs a model learned matters far more than which architecture it is. The models store the morphome as an item-specific lexical abstraction, sufficient to reproduce the pattern but not to generalize it as humans do.

We introduce the Infinite SLAM Transformer (SLAMFormer-$\infty$), the first geometric transformer capable of supporting both long-range frontend and backend processing without an explicit distance bound. Instead of relying on a first-frame-anchored formulation, SLAMFormer-$\infty$ employs memory conditions to define flexible coordinate systems and scales for input frames, enabling more expressive structural conditioning. Built upon this formulation, the frontend preserves efficient local computation, while the backend jointly optimizes long-range trajectories and scene geometry in a globally consistent manner. Experimental results demonstrate that SLAMFormer-$\infty$ achieves superior or highly competitive performance in both trajectory estimation and scene reconstruction across large-scale datasets. Notably, SLAMFormer-$\infty$ generalizes to extremely long trajectories, successfully operating on sequences exceeding $17\mathrm{km}$.

Transformer-based architectures have dominated sequence modeling, largely due to the expressive power of attention mechanisms. However, for a class of deterministic state tracking tasks---such as parity checking, modular counting, and parenthesis matching---attention may be overkill. In this paper, we show that \textbf{state propagation alone is sufficient}. We propose the \textbf{Complex State Propagator (CSP)}, a minimalistic recurrent architecture that \textbf{only propagates hidden states} across layers without output projections at intermediate steps. The state is represented as a complex-valued vector, updated via input-dependent rotations in the complex domain. To enable deep propagation without gradient vanishing or degradation, we introduce a \textbf{block-level skip connection} alongside element-wise complex normalization and SiLU activation at sequence boundaries. Applied with Focal Loss, CSP achieves \textbf{100% accuracy} with perfect F1 scores across canonical tasks.

Local feature matching is a fundamental component of photogrammetry, enabling accurate image correspondence critical for tasks such as 3D reconstruction, stereo mapping, and visual localization. While recent detector-free matching methods, like LoFTR, have advanced the field, the global features obtained by leveraging the global-range modeling capacity of the unconstrained attention mechanism compromise the model's attention to the salient structures in certain scenarios. This limitation leads to a phenomenon we define as attention divergence, wherein a portion of high-confidence matches are distributed outside the valid matching region (overlapping region), especially in scenes with large viewpoint variations. This occurs because similar features in irrelevant regions may receive equal weighting and consideration within the standard Transformer, limiting matching reliability in challenging photogrammetric environments. To address this issue in feature matching, we propose SGFormer (Structure-Guided Transformer), a novel structure-aware matching network that adaptively updates attention on features near salient structure in overlapping regions. SGFormer employs a semi-dense coarse-to-fine pipeline and incorporates the proposed Triple-Structure-Attention (TSA) module into the backbone net for extracting distinctive features. The TSA module utilizes shallow local features from early network layers to enhance the representation around salient structure, guiding subsequent transformer stages to intensify the model's focus on regions with salient structure across the global scope. SGFormer, thereby reinforcing attention to visually consistent areas while mitigating the influence of non-overlapping regions. Extensive experiments show that SGFormer significantly mitigates attention divergence and improves matching accuracy.

Model families are typically trained size by size, each from scratch. Can apretrained large model instead be converted into a smaller sibling? Wecharacterize the 1.4B->410M conversion in the Pythia family end to end.Representations align strongly across sizes (ridge R^2=0.84) while parametersalign weakly. Dense weight projection is functionally destructive, and abit-exact reconstruction control shows this is not an assembly artifact: basismixing breaks rotary, per-head, GELU, and LayerNorm structure. After the best-fitlinear operator, weight residuals are statistically indistinguishable from noiseunder shuffle controls. Conversion value therefore lives in initialization. Inmatched-budget continued pre-training we decompose conversion into twoindependent levers: least-squares compensation (a function lever, best zero-shot)and variance-preserving rescale (a dynamics lever, best endpoints). Compensationis a token-efficient, low-budget win rather than a universal one. At 30M tokens itbeats the strongest subcloning variant on both a width-reduced pair (84.0 +/- 1.8vs. 89.7 +/- 3.7, 3/3 seeds) and a held-out depth-reduced pair (109.3 vs. 117.9,3/3 seeds), reaching a given quality with fewer tokens. At a 33x larger budget thetwo converge to parity (40.0 vs. 40.0), both far ahead of from-scratch, whichtransfer initialization always beats: by up to 18x at low budget, with the marginnarrowing at convergence and at the largest scale. We also map the method'sboundary. At about 5x the donor scale (6.9B->1.4B) stacking both leversover-corrects, consistent with ill-conditioning of the compensation solve at largewidth, which points to dimension-aware regularization as a fix. At matched budgetour initialization also beats structured pruning with distillation, the standardpipeline for this task, and improves further when combined with it. Code,checkpoints, and the frozen evaluation corpus are released.

Feed-forward networks (FFNs) account for a large fraction of Transformer parameters, yet their hidden width is usually constant across depth. We ask whether this capacity can instead be allocated from a forward-pass measurement of layer behavior. We view each FFN as transporting a cloud of token representations and quantify the induced geometric change using correspondence-preserving shift, Gromov-Wasserstein distortion, and degree-one persistent homology under raw and scale-normalized metrics. A layerwise approximation surrogate yields an exact fixed-budget optimizer. Across seven pretrained language models, raw Euclidean work largely tracks residual-norm growth, whereas normalized work is predominantly front-loaded. Gromov-Wasserstein work is more consistently associated with perturbation-based layer sensitivity than the finite-sample topological estimate. In paired 128M and 256M training runs, several normalized-work schedules reduce mean validation loss relative to both uniform width and a hand-designed cosine taper. With the amplified paired differences at 440M, the best geometry-based allocations improve over uniform substantially larger than the cosine taper, while the anti-topological raw control is worse than uniform.

Automated Sign Language Recognition for under-represented languages remains a largely unsolved problem. Central African Sign Language (CASL) exemplifies this gap: the only available bench-mark, CASL-W60, has a best reported accuracy of 69.93%, and we show that the common heuristic of fine-tuning high-resource models fails to close it. This failure stems from two compounding factors: the limited scale of available CASL data and the significant lexical and visual domain gap between CASL and large-scale corpora such as WLASL, which renders pre-trained representations largely uninformative. To address this, we propose TransSLR, a lightweight Temporal Transformer Encoder trained from scratch on 64-frame normalized pose sequences, with average pooling and a classification head. By operating on geometric keypoint representations rather than raw RGB, TransSLR achieves signer-independent generalization without relying on visual appearance. On the CASL-W60 benchmark, TransSLR establishes a new state-of-the-art accuracy of 80.39%, surpassing the prior best by +10.46%. Beyond accuracy, our encoder-only design significantly reduces computational overhead, making deployment feasible in resource-constrained environments. We conduct extensive experiments on the CASL-W60 benchmark, comparing against RGB-based and multimodal baselines, and demonstrate that TransSLR achieves state-of-the-art performance.

Transformer models are most often understood through what they do: their benchmark performance, generation quality, or behavior on downstream tasks. Yet frozen transformer input-embedding spaces may also be examined through their responses to a controlled deterministic probe before contextual computation or task-specific adaptation. Guided by this response-based view, we introduce \emph{ChaosProbe}, a deterministic neurochaos-inspired method for constructing response-based fingerprints of frozen transformer input-embedding spaces. For each prompt-level embedding matrix, ChaosProbe applies a chaotic trajectory-based transformation and summarizes its Firing Rate and Entropy channel responses with complementary representation-level measures, producing a fixed-length signature for each model. In a bounded proof-of-concept study of $80$ neutral prompts and four pretrained models---GPT-2, DistilGPT2, BERT-base-uncased, and RoBERTa-base---Pearson correlation, Spearman correlation, and cosine similarity each recover all four same-family nearest-neighbor assignments and both expected mutual family pairs. Euclidean distance recovers three of the four assignments and one of the two mutual family pairs. Paired bootstrap resampling supports the stability of the Pearson and Spearman pairings over the observed prompt set, and signature-validity checks show that constant or collapsed responses do not dominate the reported fingerprints. These results provide a cohort-dependent proof of concept that deterministic neurochaotic response signatures can expose broad structure among frozen transformer input-embedding spaces.

Personalized neoantigen prediction is challenging due to the scarcity of positive samples, the noise of the experimental data, the severe class imbalance trait and the complex of immunogenicity features. Prior arts, such as linear regression and XGBoost fail to model long-range dependencies and contextual relationships within peptide features, therefore the performance of neoantigen positive recall rate is limited. In this paper, we present a novel deep learning framework based on Transformer, coined as TransNRank. By leveraging the self-attention mechanism, our model captures both local and global feature contexts, enabling more accurate recognition of immunogenic neoantigens. A positive-aware training objective is utilized to handle the class imbalance problem, assigning more weights to those few positive samples. Extensive experiments are performed on NCI, TESLA and HiTIDE datasets. Notably, our TransNRank can push the upper bound top 20 recall rate of neoantigen prediction from 46.9% (45 from 96) to 53.1% (51 from 96), while reducing the training epochs from 200 epochs to 20 epochs. Furthermore, we analyze the features contribution based on TransNRank and find that the mutation at anchor and TCGA expression level play an unexpected important role in neoantigen prediction, and removing insignificant features to reduce the input dimensionality of peptides does not drastically impair the overall performance of the model. Our paradigm not only streamlines the prediction pipeline but also sets a new state-of-the-art for neoantigen discovery, with broad implications for accurate immuno-oncology.

Handwritten Text Recognition (HTR) is computationally imbalanced in two ways: most image pixels are background, and many width-axis sequence positions are blank-dominated. This creates a mismatch for Spiking Neural Networks (SNNs): handwriting is observed as a static image, whereas spiking computation unfolds over timesteps. We propose Spike-HTR, a hybrid spiking recognizer that controls both the number of spiking steps and the number of width positions processed by the deep sequence mixer. To make a static image suitable for short-horizon spiking inference, InkCoder converts it into a coarse-to-fine input stream, where early steps cover broad stroke regions and later steps emphasize sharper stroke details. To reduce sequence computation, a CTC-guided length reducer keeps likely character or uncertain positions and compresses long blank-dominated stretches before deep mixing. With $T{=}2$, Spike-HTR trains only on target data, decodes without language models or lexicons, and reaches validation/test CERs of 3.5/5.4, 2.3/2.5, and 4.2/3.9 on IAM, LAM, and READ2016. Codes are available at https://github.com/QomolangmaH/SpikeHTR.

Detection transformer models, including DETR and its extensions, learn to output a set of object-level embeddings that can be simultaneously decoded into 2D bounding boxes and class distributions. In this paper, we investigate what pre-trained 2D detection transformers understand about the 3D properties of objects. Specifically, we investigate the extent to which properties including the depth of objects from the camera and the 3D location of objects relative to the camera can be recovered from object-level embeddings using linear and non-linear probes. Across a range of detection transformer models, our results show a surprisingly strong and previously unknown ability of 2D DETR models to represent useful information about the 3D properties of objects, despite the complete lack of 3D supervision during model pre-training.

The emergence of transformer-based deep learning models has brought unprecedented performance across various domains, particularly in natural language processing and computer vision. However, deploying these models, especially on resource-constrained devices, poses significant challenges due to their high computational complexity and large memory size and bandwidth requirements. This complexity has led researchers to use low-bit model weights to reduce memory usage and improve efficiency. In addition to reducing processing and memory demands, quantization introduces another useful property: value locality, where the extremely large number of parameters are restricted to a limited range of values. To fully take advantage of this locality, this paper presents DeVIT, an acceleration method for vision transformers that leverages differential computation to enable multiplier-less matrix multiplication.

Diffusion Transformers (DiTs) have emerged as a core architecture in generative modeling due to their scalability and adaptability to multimodal tasks. DiTs comprise isotropic transformer blocks, and learn representations progressively across depth, where the denoising objective drives later layers to focus on fine-detail reconstruction. This results in degraded representation quality and an imbalanced encoder-decoder behavior. Prior approaches such as representation alignment (REPA) mitigate this by encouraging stronger early representations via training regularization. Alternatively, U-Net-style DiT architectures introduce explicit multi-scale encoder-decoder structures for improved convergence. But they build on standard U-Net wisdom via learnable operators for spatial downsampling, which are not well-suited to transformer architectures, introducing inefficiencies and compatibility issues with components such as cross-attention and representation regularization. In this work, we propose UDT, a U-Net diffusion transformer that combines the representation power of DiTs with the encoding-decoding benefits of U-Nets, through data-adaptive token merging for downsampling and upsampling, while preserving the DiT token dimension. Our baseline UDT architecture outperforms existing U-Net DiTs and achieves performance comparable to REPA across all model sizes. Furthermore, using architectural optimization and REPA, UDT outperforms SiT's 7.9 FID at 1400 epochs (w/o CFG) within 40 epochs (~ 40x faster convergence) for XL model size on 256x256 ImageNet. Finally, it achieves strong image generation performance with CFG, reaching FID of 1.38 (320 epochs) with SD-VAE and 1.35 (500 epochs) with VA-VAE, providing a new backbone for DiTs with strong empirical benefits.

All Transformer-based large language models compute attention via the Euclidean inner product, an architectural choice that Dong et al. (2021) proved causes representational rank to decay doubly exponentially with depth in pure self-attention stacks. We develop a theoretical framework that targets this structural limitation at the mathematical level by replacing the flat Euclidean metric with learned per-token Riemannian metrics. Our contributions are threefold. (1) We prove that Riemannian attention scores with heterogeneous per-token metrics are non-Gram---they cannot be factorized as QK^T with factorization dimension O(d). We are explicit that this is a structural observation, not a proof of rank preservation. (2) We establish that low-rank metric factors render all geometric operations tractable: geodesic distance in O(dr) per token and metric inversion in O(dr^2) via the Woodbury identity---both far below the O(d^3) cost of a general matrix---making Riemannian attention feasible at billion-parameter scale with negligible overhead. (3) We present the Fiber Bundle Transformer, a complete architecture specification in which each token position carries its own Riemannian metric, attention is geodesic distance computation, feed-forward updates use metric-preconditioned steps, and the connection carries explicit curvature and torsion proxies. We derive formal predictions about correctly implemented geometric architectures and identify the central open problem: proving or disproving that heterogeneous Riemannian metrics prevent the rank collapse that row-stochastic attention matrices otherwise cause. This paper presents theoretical analysis and architectural design; empirical validation is the subject of future work.

Transformers do not merely lack data on some Boolean extrapolation tasks; they generalize in a systematically wrong way. Recent work on generalization on the unseen has shown that, despite fitting the observed domain, Transformers often extrapolate according to a simpler minimum-degree interpolator rather than the true target function. These Boolean tasks are not practical applications, but controlled stress tests for understanding Transformer inductive bias. We ask whether this failure mode can be corrected by injecting explicit structural priors into attention. Existing structured-initialization methods alter Transformer inductive bias indirectly, by choosing query and key projections whose similarity scores approximate a desired attention pattern. However, we find that when applied to Boolean extrapolation, these QK-based priors can be rapidly overwritten during training and fail to change the learned extrapolation rule. We propose a simpler alternative: initialize the additive attention mask directly. Unlike standard hard masks used for causality or locality attention, our mask is a finite, learnable attention-logit bias initialized from task-level interaction structure. This separates the structural prior from content-dependent attention scores, allowing it to persist throughout optimization. On Boolean reasoning tasks, mask-based initialization achieves near-perfect extrapolation where vanilla and QK-initialized Transformers remain trapped by the default inductive bias. The same mechanism also improves low-data arithmetic performance and remains competitive on vision and language benchmarks. These results show that attention masks can serve not only as architectural constraints, but as a simple substrate for encoding persistent inductive bias in Transformers.

A dense, pretrained language model can be retrofitted with recurrent depth and learn an iterative latent transition that persists after outcome-only annealing. Qwen2.5-0.5B-Instruct is split into a Prelude, a weight-tied Recurrent Block, and a Coda, with an identity-preserving one-loop path and a re-entry bridge on later loops. At loop 1 the retrofit remains non-inferior to its base on a preregistered ARC battery. Three findings. First, the mechanism is a reusable procedure rather than terminal-answer lookup, and installs at two budgets: 6M trained parameters over frozen base weights and 180M full-block. With intermediate-step supervision, the model computes one task step per loop and persists when only final answers are graded. The adapter matched the full block overall (83.8% versus 84.0%), led through depth 11, and trailed beyond. Verbal fine-tuning reached 79-86% on controlled verbal renderings (zero-shot transfer was minimal), and adapter verbal training begun from the installed mechanism outpaced matched fresh training by 18.6 points, including on a held-out test set. Second, the operation extrapolates to roughly 1.5 times its supervised depth, holding 70% accuracy through depth 18. Third, a same-size scratchpad-trained model matched the recurrent model within its learned horizon but collapsed beyond it. The recurrent model won overall, 84% versus 72%, retained 53% versus 2.5% beyond depth 10, and answered 7.6 times faster. An iterative transformer can therefore perform deeper reasoning in latent space faster than comparable or larger models fine-tuned on the same task, in a system-level comparison. A second task, running the rule in reverse, exposed the limits: the inverse was learnable in isolation, but no continuation acquired it while preserving the installed mechanism and general capability, a catastrophic-interference boundary. Learned depth selection remains open.

Visual generation increasingly requires high-resolution images, long videos, and multimodal context, making the quadratic cost of full attention prohibitive. We introduce Chimera, a hybrid visual diffusion backbone with a principled scaling recipe. Chimera processes text, image, and video tokens in one raster-ordered stream without positional embeddings. It combines Kimi Delta Attention (KDA) for long-context state tracking with O(N) complexity, interleaved Multi-head Latent Attention (MLA) for direct global interaction, and modality-aware short convolutions for local spatiotemporal context. Sparse Mixture-of-Experts (MoE) layers expand capacity while controlling activated compute. To scale this heterogeneous architecture, we introduce HeteroP, a module-wise scheme that transfers hyperparameters across width and depth according to each tensor's functional fan-in and model depth. HeteroP yields a consistently tuned family used to fit Chinchilla-style compute-optimal laws for activated model size, training-token count, and image-video data ratio. Guided by these laws, we train an 11B-parameter Chimera with 2B activated parameters. Experiments show three results. First, measured by pretraining diffusion loss, the dense backbone is 1.7x as compute-efficient as a matched full-attention Wan-2.1 2B baseline, while the complete system reaches 7.3x. Second, without length-specific fine-tuning, Chimera extrapolates zero-shot from 5-second training clips to 30-second videos, with only 6.5% FID degradation in the last five seconds. Third, the fitted laws show that compute-optimal image pretraining divides compute nearly evenly between activated model size and training-token count, whereas video pretraining modestly favors model size at higher budgets. These results establish a foundation for designing and scaling efficient long-context diffusion architectures.

We derive finite-sample generalization bounds for Transformers trained with dynamic programming recursions. Building on the doubly lifted, measure-valued formulation of Transformer dynamics, we view data sets as probability laws on pairs of empirical input-output measures, allowing us to interpret the training problem as a finite-horizon Markovian control problem. We then analyze a quantized model, derived by quantizing the state, action, and measure-state spaces, and derive explicit finite-sample generalization bounds using concentration inequalities for empirical laws on finite metric spaces together with a Lipschitz stability estimate for the value function. These bounds are transferred to the base model at the cost of an explicit approximation error. Finally, we show that the same machinery yields a distributionally robust control formulation of the training problem, connecting Transformer generalization to Wasserstein distributionally robust optimization.

Standard masked-language-model fine-tuning applies a uniform masking probability across every token position, assuming reconstruction difficulty is position-agnostic. When the degradation process is characterised and concentrated at predictable positions, this assumption fails: at peak damage sites the model can underperform a frequency-matched random predictor. We introduce VESTIGE, a parameter-free, drop-in replacement for the standard MLM collator that aligns the masking distribution with an empirically measured per-position corruption profile. We apply it to ancient DNA (aDNA) reconstruction, where cytosine deamination produces a position-dependent C-to-T / G-to-A gradient quantified per-position by mapDamage2. Rescaling so the mean C/G masking rate equals 15% - identical to standard MLM - isolates spatial redistribution as the sole variable, with model, data, seed, and hyperparameters held fixed across both DNABERT-2 runs on a mammoth CDS corpus (two specimens, seven genes). Across six terminal-zone widths and 626 paired windows, VESTIGE leads standard MLM at every width (Delta = +4.18 to +10.35 pp, all p < 10^-8), cuts validation cross-entropy by 13% (3.274 vs. 3.757), and yields ESMFold reconstructions with TM-score > 0.95 across all six reconstructions (three genes) even under damage amplified 10-30x beyond authentic PMD rates. A 1D CNN biosecurity classifier returns AUC = 0.935 and clears 98.2% of reconstructed windows, the 1.76% remainder attributable to reference-genome features, not reconstruction artefacts. The principle is domain-agnostic: any measurable position- or context-specific corruption profile - FFPE, bisulfite, metagenomic, or nanopore - substitutes directly for the PMD array, making VESTIGE a knowledge-guided training routine for intelligent systems operating on degraded or noisy sequence inputs.

Looped Transformers create a useful train- and test-time compute axis by reusing the same Transformer block over recurrent depth, increasing effective depth at a fixed parameter count. However, that shared block must then govern an entire trajectory of varying hidden states over trained and extrapolated depths. Furthermore, in additive-injection looped Transformers, an input-conditioned signal is reintroduced at every recurrent step, so applying the shared transition at an input-conditioned reference can still move the hidden state. In this paper, we propose Source-Centered State Evolution (SCSE), which is designed to reconcile input conditioning with reference-preserving shared recurrence. Specifically, SCSE retains input dependence through its learned anchor and initial deviation, allows nonzero deviations to drive recurrent computation while mapping zero deviation to zero, and guarantees exact anchor invariance through its zero-deviation mask. The designated anchor is thereby a one-step fixed point by construction. The zero-deviation forcing bias is the next deviation produced from the anchor itself and vanishes in SCSE, while nonzero deviations remain active and support state-dependent recurrent computation. Our theory shows that the zero-deviation forcing bias is a design degree of freedom whose task effect can be harmful, neutral, or beneficial; SCSE resolves this choice in favor of exact anchor invariance by setting the bias to zero. Across WikiText-2, WikiText-103, direct web-corpus pretraining, held-out web-text transfer, and LAMBADA completion, SCSE improves the controlled recurrent quality frontier. Ablation studies identify the learned anchor and the anchor-coordinate deviation recurrence as the primary contributors to the gain, and a trained-model case study grounds the anchor-response diagnostic in observed recurrent motion.

Emergency Departments (EDs) are critical access points in healthcare systems, yet they face persistent pressure from unpredictable patient demand, seasonal surges, and non-urgent visits. Effective ED planning requires forecasts at multiple decision-making levels: hospitals need local demand estimates for staffing and bed management, regions require forecasts to coordinate healthcare units, and national authorities need system-wide projections for capacity planning. However, most existing approaches forecast ED demand independently at a single level, ignoring the hierarchy linking hospitals, regions, and national systems. This can produce incoherent predictions, where hospital-level forecasts do not aggregate consistently to regional or national demand. We propose HierSTT, a hierarchical Transformer-based framework for coherent multi-level ED forecasting. HierSTT jointly predicts hospital, regional, and national level demand in a single end-to-end model. A Temporal Fusion Transformer captures national dynamics, while spatio-temporal Transformer encoder-decoder modules model regional and hospital demand conditioned on higher-level forecasts. A coherence-aware loss penalizes cross-level inconsistencies during training. We further introduce a nationwide Portuguese ED dataset covering 81 hospitals across 5 regional health administrations, with heterogeneous covariates at each level. Experiments show that HierSTT reduces average WAPE by 32% relative to the best non-hierarchical deep learning baseline and outperforms all classical hierarchical reconciliation methods, while producing near-coherent predictions across levels. Additional resources associated with this work are available at https://github.com/FilipaLino/HierSTT.

What types of decision problems can a causally masked, finite-precision transformer solve for inputs of arbitrary length? Existing answers often rely on idealized arithmetic, but under finite precision, rounding and evaluation order can change what information attention retains and therefore what the model can compute. We develop an algebraic formalization that derives expressivity directly from the model's implemented dynamics. Its central object is its memory; the finite internal state computed by attention that summarizes the information from the prefix available to all future queries. Each attention head updates its own state independently within a layer, while layers compose hierarchically, providing a uniform route from model assumptions to expressivity bounds. Applying this method to transformers without positional embeddings, we obtain an expressivity hierarchy governed by the attention type under specific numerical semantics. Width-one sliding-window attention supports bounded-suffix memory, while a modified form of soft attention supports irreversible, checklist-like state, and combining the two mechanisms provides an interplay of both. Ordinary left-to-right floating-point soft attention can realize more expressive memory operations than any of the above. Algebraically, the four cases correspond to definite, R-trivial, locally R-trivial, and aperiodic semigroups. Under an explicit free-wiring assumption, all four bounds are tight.

Plant biosynthetic gene clusters (BGCs) encode specialized-metabolite pathways, yet curated plant BGC labels remain scarce, hindering supervised discovery at genome scale. Existing plant BGC mining tools are largely signature- and rule-driven and do not fully leverage recent advances in contextual representation learning for modeling long-range domain context and controlling false positives under strong domain shift. We seek an AI-assisted workflow that narrows experimental search space by transferring supervision from well-annotated microbial BGCs to plant genomes. We present PlantBGC, representing genomes as ordered Pfam-domain sequences and learning BGC-likeness with an encoder-only Transformer trained on MIBiG microbial BGCs and adapted to plants via label-free masked language modeling. On microbial benchmarks, PlantBGC achieves token-level AUC = 0.988 (10-fold CV) and 0.979 (leave-class-out). On plants, adaptation improves known-BGC recovery on n = 34 curated loci under strict 100% coverage, increasing recovery from 29.4% to 67.6% and indicating more complete boundaries. GO/KEGG-derived weak supervision reduces proxy primary-like ratio by 48.40% (GO) and 45.20% (KEGG), with consistent per-species reductions (paired Wilcoxon p = 1.53e-5). Compared to plantiSMASH, PlantBGC yields more compact loci on matched regions (median length ratio = 0.278; 93.8% of pairs are shorter).

Recently, photonic transformer accelerators (PTAs) have successfully achieved significant speedup and energy efficiency improvements over electronic accelerators for expediting Transformer inference. However, state-of-the-art rely on expensive multi-wavelength light generation and large dot-product units due to active phase-shifter components, thus making their approach inefficient and impractical. To address this, we propose MDTransformer, a novel hardware-software co-design of PTA based on mode-division optical dataflow and operations. Specifically, MDTransformer performs complex matrix operations using spatial-mode interference, that leverages the inverse-designed multi-mode couplers, crossings, and Mach-Zehnder IQ modulators into a compact mode-division photonic tensor core (MPTC), capable of executing matrix multiplications in the optical domain. Its each guided mode (i.e., TE0-TE3) acts as an independent computational lane, enabling four-fold parallelism-per-waveguide without spectral filtering or free-spectral-range limitations. Moreover, its coherent detection and IQ modulation jointly encode amplitude and phase, realizing complex-valued arithmetic for full-range operations in transformers. MDTransformer offers analog multiplication with sub-4-bit effective precision and inter-modal crosstalk below -30 dB. Its inverse-designed approach also offers scalable and full compatibility with single-laser continuous-wave operation at 1550 nm. Experimental results show that MDTransformer achieves 40.4% area reduction, 63.6% power saving, 40.6% energy saving, and comparable latency over the state-of-the-art PTA across different workloads (i.e., DeiT-Tiny/Small/Base and BERT-Base/Large). These results show that MDTransformer offers a practical solution for high-performance and energy-efficient transformer-based systems.

An often overlooked factor of robot manipulation performance is the embodiment of the robot itself. Motivated by this problem, we study motion-conditioned robot co-design, where the goal is to generate complete robot designs that track target end-effector trajectories (from human demonstrations) while optimizing user-defined rewards. We introduce Transformer Transformer, a diffusion transformer trained on RoboTokens, a unified tokenization of robot embodiments, states, and actions. The same architecture can be used across embodiment spaces (e.g., wheeled bimanual, quadrupeds, humanoids) and use cases (embodiment generation, cross embodiment controller). Rather than overfitting to one reward function, Transformer Transformer is a dynamics model, whose reward-agnostic state and action predictions can be converted into reward-specific value predictions. These value predictions are used to steer embodiment diffusion towards high value robot designs, through a procedure we call Dynamics Self-Guidance. Experiments across multiple design spaces show zero-shot optimization of unseen rewards and trajectories, improving performance and runtime over the evolutionary baseline. Finally, we fabricated an optimized ALOHA design, which reduced tracking error by over 70% compared to the original design.

Transformer adaptation is typically distributed across model depth, even when the intended change is narrow. We investigate how adaptation site shapes what a model learns, how well that learning generalizes, and how selectively it is applied. We introduce a controlled benchmark spanning five objectives (lexical binding, factual association, behavioral policy learning, causal mapping, and procedural reasoning) and define each objective's "adaptation geometry" as its profile of acquisition, transfer, and boundedness under full-stack and early-, middle-, or late-layer LoRA. The objectives exhibit distinct geometries. Lexical binding favors early-layer adaptation for acquisition and boundedness but requires broader updates for transfer; factual association favors later layers among localized adapters; behavioral learning separates late-layer action acquisition from middle-layer policy gating; and causal and procedural transfer benefit most from middle- or full-stack adaptation. These patterns largely persist under parameter-matched controls, and most corresponding directional contrasts replicate across five model families. These findings establish adaptation site as a key design variable for controlling what models learn, generalize, and leave unchanged.

Fine-grained weight pruning and activation sparsification have emerged as effective approaches for reducing the compute and memory cost of inference for Transformer models. In the moderate-sparsity regime, Gustavson's dataflow provides a natural execution model for exploiting both activation and weight sparsity on vector processors through metadata-driven indexed accumulation. However, existing RVV architectures lack native support for this pattern, forcing kernels to rely on software index decoding and L1-backed indexed memory operations that keep sparse tensor contractions far below their roofline performance bound. We present Ventaglio, a runtime-configurable sparse execution unit coupled with RVV ISA extensions that drives sparse tensor contractions toward their roofline through indexed gather-accumulate-scatter support. Integrated into an open-source vector processing cluster and implemented in 12nm FinFET, Ventaglio accelerates sparse tensor contraction kernels by $6.9\text{--}7.4\times$ over optimized RVV baselines, with only $3.1\%$ area overhead for a cluster of tightly-L1 coupled vector processing elements. We build a performance-accurate instruction-level model of the Ventaglio extension, calibrate it against RTL implementation, and leverage it for scale-out performance analysis on a large $4\times4$ multi-cluster system. Using a DuoGPT-pruned LLaMA-3-8B model with practical $40\text{--}60\%$ dual sparsity, Ventaglio achieves $2.40\text{--}5.25\times$ and $2.06\text{--}3.16\times$ speedup over dense baselines during prefill and autoregressive decoding, respectively.

Transformer architectures have attracted increasing attention for solving partial differential equations (PDEs), owing to their flexibility in handling irregular discretizations and their ability to capture long-range physical dependencies. However, unlike discrete language tokens or fixed-resolution image patches, observed physical fields are finite samples of underlying infinite-dimensional functions. Consequently, effectively applying Transformers to PDEs requires a tokenizer that respects the functional nature of physical fields and constructs physically expressive tokens from arbitrary discretizations.To this end, we propose \methodname{Physics Transformer}, a function-projection-based Transformer architecture for physical field prediction. Physics Transformer treats a physical field as a continuous function and partitions its discretization into locality-preserving spatial patches. Within each patch, it dynamically learns a set of adaptive local basis functions and projects the sampled field onto these bases to obtain compact physics tokens. The resulting tokens capture diverse latent physical states while preserving fine-scale spatial structures, enabling efficient global interaction through factorized attention across space and physical states. The projected representation further supports efficient decoding at arbitrary query locations. Extensive experiments on diverse benchmarks, ranging from two-dimensional PDE dynamics to industrial-scale three-dimensional CFD simulations, demonstrate that Physics Transformer accurately captures fine-grained physical structures and achieves state-of-the-art predictive performance. These results establish function projection as a practical and effective foundation for designing Transformer architectures for PDE solving.

A central question in the in-context learning literature is whether transformers can organize episode-level adaptation around different inductive-bias families. We study this question in a controlled setting through latent algorithm routing: route-like behavior in which the solver-family preference changes with the latent data-generating regime while prompt form is held fixed, remains stable under nuisance perturbations, and is selectively influenced by targeted activation interventions without large losses in answer quality. We introduce ROUTEBENCH, a diagnostic benchmark whose regimes differentially favor global shrinkage, sparsity, robustness, and locality, operationalized by ridge-like, lasso-like, Huber-like, and kNN-like family representatives. Across dense decoder-only transformers trained from scratch at 44M-612M parameters, a 306M model closes 80.9 percent of the oracle-routing gap and achieves route F1 of 84.1. The effect remains substantial under natural-language renderings, shuffled supports, lexical paraphrases, and a unified four-way routing setting. Stronger adaptive alternatives, including an input-conditioned soft mixture and an unsupervised Gumbel router, narrow the gap but remain below the 306M and 612M models on route F1 and OOD performance. Probe controls and matched activation-patching controls further show that route-relevant internal directions are decodable and functionally involved in solver-family-consistent output behavior. These results provide controlled evidence that dense transformers trained on ROUTEBENCH can develop route-like internal variables, but they do not establish universal routing in pretrained language models or unrestricted natural-language reasoning.