Sequence Modeling

Boltzmann Machines trained on evolutionary sequence data have emerged as a powerful paradigm for the data-driven design of artificial proteins. However, the relationship between model architecture, specifically parameter density, and experimental performance remains poorly understood. Here, we investigate this relationship using the Chorismate Mutase enzyme family as a model system. We compare standard fully connected Boltzmann Machines for Direct Coupling Analysis (bmDCA) with sparse models generated via progressive edge activation (eaDCA) and edge decimation (edDCA). We identify a maximum-entropy model (meDCA) along the decimation trajectory that represents an optimal balance between constraint satisfaction and the flexibility of the probability distribution. We synthesized and tested artificial sequences from all models using an in vivo complementation assay, finding that all architectures, regardless of sparsity, generate functional enzymes with high success rates, even at significant divergence from natural sequences. Despite this functional equivalence, we demonstrate that the meDCA model samples a viable sequence space that is more than fifteen orders of magnitude larger than its low-entropy counterparts. Furthermore, comparative analyses reveal that high-entropy models systematically minimize overfitting and better capture the local neutral spaces surrounding natural proteins. These findings suggest that while various models satisfying coevolutionary statistics can generate functional sequences, high-entropy Boltzmann Machines provide a superior representation of the underlying evolutionary fitness landscape.

Capturing user interests across extensive watch histories is critical for short-form video recommendation, yet scaling sequence length is limited by two bottlenecks: the semantic sparsity of atomic Video IDs and the quadratic computational complexity of Transformers. Traditional orthogonal Video IDs fail to capture content relationships and demand large embedding tables, while the quadratic complexity of self-attention restricts the maximum sequence length under strict industrial latency and resource constraints. In this work, we present a production-deployed framework for modeling ultra-long user behavior sequences at a billion-user scale. We first address the representation bottleneck by adopting content-native Semantic IDs. By utilizing depth-truncated, coarse-grained Semantic IDs, we shrink the embedding table size from corpus cardinality. This compact representation naturally generalizes to cold-start content through shared semantic prefixes. Second, to overcome the sequence scaling barrier, we introduce a Global-Aware Compression Transformer that leverages non-parametric temporal folding and unified global query integration to effectively condense the sequence, alleviating both the memory and computational bottlenecks of standard self-attention. Offline profiling on our computing infrastructure demonstrates an order-of-magnitude reduction in peak memory footprint and a drastic decrease in computational overhead. This efficiency gain enables supporting longer sequence lengths at an affordable cost in production, yielding substantial online gains in satisfied user engagement and satisfied content consumption in large-scale online A/B tests.

Offline goal-conditioned RL (GCRL) learns goal-reaching policies from static datasets, but real-world datasets are often partially observable and history-dependent, exhibiting a mix of Markovian and non-Markovian that violate standard RL assumptions. History-aware sequence models such as Decision Transformer (DT) are a natural fit for long-term dependency modeling, yet pure attention is inefficient and brittle when handling local Markovian structure and long-range context simultaneously. Although recent hybrid architectures (e.g., LSDT) introduce local extractors to improve local dependencies modeling, the fixed-window extraction cannot adapt its effective memory to varying dependency lengths in temporally heterogeneous settings, often truncating long-range context rather than compressing its content adaptively. Moreover, sequential offline GCRL faces a key bottleneck: under sparse rewards, return-to-go (RTG) becomes non-discriminative across sub-trajectories, providing little guidance signal for stitching goal-reaching behaviors from diverse demonstrations. To address these, we propose \textbf{QHyer}, which replaces RTG with a flow-parameterized, state-conditioned goal-reaching Q-estimator to support stitching across demonstrations, and introduces a gated Hybrid Attention-Mamba backbone that performs content-adaptive history compression while preserving local dynamics. Extensive experiments demonstrate that \textbf{QHyer} achieves state-of-the-art performance on both non-Markovian and Markovian datasets, validating its effectiveness for diverse scenarios.

Sequential recommendation models often struggle to capture latent periodic patterns in user interests, primarily due to the noise inherent in time-domain behavioral data. While frequency-domain analysis offers a global perspective to address this, existing approaches typically treat user sequences in isolation, overlooking the crucial context of the target item. In this work, we present a novel empirical observation: user attention scores exhibit distinct spectral entropy distributions when conditioned on positive versus negative target items. Specifically, true user interests manifest as highly concentrated spectral patterns with lower entropy in the frequency domain, whereas irrelevant behaviors appear as high-entropy noise. Leveraging this insight, we propose the Frequency-Enhanced Deep Interest Network (FEDIN). FEDIN introduces a frequency-domain branch that utilizes a target-aware spectrum filtering mechanism to isolate these periodic interest signals. Extensive experiments on three public datasets demonstrate that FEDIN consistently outperforms state-of-the-art sequential recommendation baselines, demonstrating superior robustness against noise. We have released our code at: https://github.com/otokoneko/FEDIN.

Existing research largely attributes the global sequence modeling capability of Transformers to the explicit computation of attention weights, a process that inherently incurs quadratic computational complexity. In this work, we offer a novel perspective: we demonstrate that attention can be mathematically reframed as a Multi-Layer Perceptron (MLP) equipped with dynamically predicted parameters. Through this lens, we explain attention's global modeling power not as explicit token-wise aggregation, but as an implicit process where dynamically generated parameters act as a compressed representation of the global context. Inspired by this insight, we investigate a fundamental question: can we achieve Transformer-level sequence global modeling entirely through dynamic parameterization while maintaining linear complexity, effectively replacing explicit attention? To explore this, we design various dynamic parameter prediction strategies and integrate them into standard network layers. Extensive empirical studies on vision models demonstrate that dynamic parameterization can indeed serve as a highly effective, linear-complexity alternative to explicit attention, opening new pathways for efficient sequence modeling. Code is available at https://github.com/LeapLabTHU/WeightFormer.

Sequence learning reduces to similarity-based retrieval over a temporally indexed representation space, a constraint on any sequence model, not a property of a specific architecture. We show that a spiking Sparse Distributed Memory sequence machine (2007) and the transformer (2017) independently instantiate the same five functional operations (encoding, context maintenance, associative retrieval, storage, and decoding), with cosine similarity as the shared retrieval primitive in both. We formalise a Phase-Latency Isomorphism showing that sinusoidal positional phase and spike timing are linearly related, and prove that dot product attention is invariant to this mapping up to a global scale factor on the positional component (Lemma 1). Empirically, frequency-compressed positional encoding fails to converge on a positionally demanding copy task, while a learned rank-based embedding matches or exceeds sinusoidal encoding, indicating that the critical property for positional representation is distance discriminability under dot-product similarity, not sinusoidal form. Time, phase, and rank are three instantiations of the same computational primitive, an ordered index whose structure survives similarity-based retrieval.

De novo functional protein design aims to generate protein sequences that realize specified biochemical functions without relying on evolutionary templates, enabling broad applications in biotechnology and medicine. Existing approaches adopt either direct function-to-sequence mapping or decoupled structure-sequence generation strategies but often fail to achieve functionality and foldability simultaneously. To address this, we propose CodeFP, a Co-generative protein language model for de novo Functional Protein design that simultaneously decodes sequence and structure tokens, thereby enabling superior simultaneous realization of functionality and foldability. CodeFP utilizes functional local structures to enrich functional semantic encodings, overcoming the suboptimal translation of flat encodings into structure tokens, while introducing auxiliary functional supervision to alleviate training ambiguity stemming from the one-to-many structure-to-token mapping. Extensive experiments show that CodeFP consistently achieves average improvements of 6.1% in functional consistency and 3.2% in foldability over the strongest baseline.

The scalability of Large Language Models to long sequences is hindered by the quadratic cost of attention and the limitations of positional encodings. To address these, we introduce Caracal, a novel architecture that replaces attention with a parameter-efficient, O(L log(L)) Multi-Head Fourier (MHF) module. Our contributions are threefold: (1) We leverage the Fast Fourier Transform (FFT) for sequence mixing, inherently addressing both bottlenecks mentioned above. (2) We apply a frequency-domain causal masking technique that enforces autoregressive capabilities via asymmetric padding and truncation, overcoming a critical barrier for Fourier-based generative models. (3) Unlike efficient models relying on hardware-specific implementations (e.g., Mamba), we uses standard library operators. This ensures robust portability, eliminating common deployment barriers. Evaluations demonstrate that Caracal performs competitively with Transformer and SSM baselines, offering a scalable and simple pathway for efficient long-sequence modeling. Code is available in Appendix.

Proteins are shaped by gradual evolution under biophysical and functional constraints. Protein language models learn rich evolutionary constraints from large-scale sequences, and discrete diffusion-based protein language models~(\eg, DPLMs) are promising for both understanding and generation. However, existing DPLMs typically rely on masked diffusion that contradicts a simple biological intuition: proteins evolve through accumulated edits, not by emerging from masks. Consequently, these frameworks lack explicit pretraining objectives for substitution and insertion/deletion (indel) operations, limiting both optimization-style post-editing and flexible guided generation. To address these limitations, we present DPLM-Evo, an evolutionary discrete diffusion framework that explicitly predicts substitution, insertion, and deletion operations during denoising. DPLM-Evo decouples an upsampled-length latent alignment space from the variable-length observed sequence space, which makes indel-aware generation tractable. To better align substitutions with real evolution, we further introduce a contextualized evolutionary noising kernel that produces biologically informed, context-dependent mutation patterns. Across tasks, DPLM-Evo improves sequence understanding and achieves state-of-the-art mutation effect prediction performance on ProteinGym in the single-sequence setting. It also enables variable-length simulated evolution, and post-editing/optimization of existing proteins via explicit edit trajectories.

The proliferation of capable and efficient machine learning (ML) models marks one of the strongest methodological shifts in signal processing (SP) in its nearly 100-year history. ML models support the development of SP systems that represent complex, nonlinear relationships with high predictive accuracy. Adapting these models often requires sequential inference, which differs both theoretically and methodologically from the usual paradigm of ML, where data are often assumed independent and identically distributed. Gaussian processes (GPs) are a flexible yet principled framework for modeling random functions, and they have become increasingly relevant to SP as statistical and ML methods assume a more prominent role. We provide a self-contained, tutorial-style overview of GPs, with a particular focus on recent methodological advances in sequential, incremental, or streaming inference. We introduce these techniques from a signal-processing perspective while bridging them to recent advances in ML. Many of the developments we survey have direct applications to state-space modeling, sequential regression and forecasting, anomaly detection in time series, sequential Bayesian optimization, adaptive and active sensing, and sequential detection and decision-making. By organizing these advances from a signal-processing perspective, we intend to equip practitioners with practical tools and a coherent roadmap for deploying sequential GP models in real-world systems.

With the rapid development of the Internet, users have increasingly higher expectations for the recommendation accuracy of online content consumption platforms. However, short videos often contain diverse segments, and users may not hold the same attitude toward all of them. Traditional binary-classification recommendation models, which treat a video as a single holistic entity, face limitations in accurately capturing such nuanced preferences. Considering that user consumption is a temporal process, this paper demonstrates that the timing of user actions can represent diverse intentions through statistical analysis and examination of action patterns. Based on this insight, we propose a novel modeling paradigm: Action-Aware Generative Sequence Network (A2Gen), which refines user actions along the temporal dimension and chains them into sequences for unified processing and prediction. First, we introduce the Context-aware Attention Module (CAM) to model action sequences enriched with item-specific contextual features. Building upon this, we develop the Hierarchical Sequence Encoder (HSE) to learn temporal action patterns from users' historical actions. Finally, through leveraging CAM, we design a module for action sequence generation: the Action-seq Autoregressive Generator (AAG). Extensive offline experiments on the Kuaishou's dataset and the Tmall public dataset demonstrate the superiority of our proposed model. Furthermore, through large-scale online A/B testing deployed on Kuaishou's platform, our model achieves significant improvements over baseline methods in multi-task prediction by leveraging sequential information. Specifically, it yields increases of 0.34% in user watch time, 8.1% in interaction rate, and 0.162% in overall user retention (LifeTime-7), leading to successful deployment across all traffic, serving over 400 million users every day.

Every Transformer architecture dedicates enormous capacity to learning rich representations in semantic embedding space -- yet the rotation manifold acted upon by Rotary Positional Embeddings (RoPE) has been treated as a fixed, hand-crafted structure, populated only by discrete ordinal indices. We argue that this rotation space is a largely overlooked second dimension of expressivity in the attention mechanism, one whose systematic exploration may open a new door for attention-based architectures. The analogy to complex numbers is instructive: just as introducing the imaginary axis -- orthogonal to and independent of the real line -- unlocked new algebraic structure once believed impossible, treating the rotation manifold as a learnable, signal-conditioned space opens an orthogonal degree of freedom in attention. In this framing, the token embedding encodes the semantic (real) component of a representation -- what a token means -- while the rotation encodes its dynamic (imaginary) component -- how it relates to every other token across time, position, and context. We introduce SIREN-RoPE, a concrete instantiation of this idea, which populates the rotation dimension with heterogeneous signals -- continuous timestamps, cyclical temporal patterns, and categorical metadata -- via a dual-branch Sinusoidal Representation Network (SIREN). As a proof of concept, we evaluate on a production-scale news feed dataset from a major social network using a generative recommender as the ranking model, demonstrating that activating this hidden dimension yields consistent improvements across calibration and ranking objectives with negligible computational overhead. We invite the community to view the rotation space not as a solved positional-encoding detail, but as an untapped axis whose rich structure may prove as consequential for attention as the imaginary unit proved for algebra.

Multi-behavior recommendation aims to predict user conversions by modeling various interaction types that carry distinct intent signals. Recently, generative sequence modeling methods have emerged as an important paradigm for multi-behavior recommendation by achieving flexible sequence generation. However, existing generative methods typically treat behaviors as auxiliary token features and feed them into unified attention mechanisms. These models implicitly assume uniform activation of dependencies among historical behaviors, thereby failing to discern differences in intensity or capture transition patterns. To address these limitations, we propose BITRec, a novel generative multi-behavior recommendation framework that introduces structured behavioral modeling through selective dependency activation. BITRec incorporates (i) Hierarchical Behavior Aggregation (HBA), which explicitly models behavioral intensity differences through separated exploration and commitment pathways, and (ii) Transition Relation Encoding (TRE), which encodes transition structures through explicit learnable relation matrices. Experiments on four large-scale datasets (RetailRocket, Taobao, Tmall, Insurance Dataset) with millions of interactions achieve consistent improvements of 15-23% across multiple metrics, with peak gains of 22.79% MRR on Tmall and 17.83% HR@10, 17.55% NDCG@10 on Taobao.

Automatic chord recognition (ACR) extracts time-aligned chord labels from music audio recordings. Despite recent advances, ACR still struggles with oversegmentation, data scarcity, and imbalance, especially in recognizing complex chords such as non-triads, which are unpopular in existing datasets. To address these challenges, we reformulate ACR as a segment-level sequence-to-sequence prediction task, where chord sequences are predicted auto-regressively rather than frame by frame. This design mitigates excessive segmentation by detecting chord changes only at segment boundaries. We further introduce two types of token representations and an encoder pre-training method, both specifically designed for time-aligned chord modeling. Experimental results show that our model improves performance in both chord recognition and segmentation, with notable gains for complex and infrequent chord types. These findings demonstrate the effectiveness of segment-level sequence modeling, structured tokenization, and representation learning for advancing chord recognition systems.

Fine-tuned autoregressive models for graph-to-sequence generation (G2S) often struggle with factual grounding and edit sensitivity. To tackle these issues, we propose a non-autoregressive diffusion framework that generates text by iterative refinement conditioned on an input graph, named as Diffusion Language Model for Graphs (DLM4G). By aligning graph components (entities/relations) with their corresponding sequence tokens, DLM4G employs an adaptive noising strategy. The proposed strategy uses per-token denoising error as a signal to adaptively modulate noise on entity and relation tokens, improving preservation of graph structure and enabling localized updates under graph edits. Evaluated on three datasets, DLM4G consistently outperforms competitive G2S diffusion baselines trained on identical splits across both surface-form and embedding-based metrics. DLM4G further exceeds fine-tuned autoregressive baselines up to 12x larger (e.g., T5-Large) and is competitive with zero-shot LLM transfer baselines up to 127x larger. Relative to the strongest fine-tuned PLM baseline, DLM4G improves factual grounding (FGT@0.5) by +5.16% and edit sensitivity (ESR) by +7.9%; compared to the best diffusion baseline, it yields gains of +3.75% in FGT@0.5 and +23.6% in ESR. We additionally demonstrate applicability beyond textual graphs through experiments on molecule captioning, indicating the method's generality for scientific G2S generation.

Modern Deep Learning Recommendation Models (DLRMs) follow scaling laws with sequence length, driving the frontier toward ultra-long User Interaction History (UIH). However, the industry-standard "Fat Row" paradigm, which pre-materializes these sequences into every training example, creates a storage and I/O wall where data infrastructure usage exceeds GPU training capacity due to data redundancy that is amplified in multi-tenant environments where models with vastly different sequence length requirements share a union dataset. We present a \emph{versioned late materialization} paradigm that eliminates this redundancy by storing UIH once in a normalized, immutable tier and reconstructing sequences just-in-time during training via lightweight versioned pointers. The system ensures Online-to-Offline (O2O) consistency through a bifurcated protocol that prevents future leakage across both streaming and batch training, while a read-optimized immutable storage layer provides multi-dimensional projection pushdown for heterogeneous model tenants. Disaggregated data preprocessing with pipelined I/O prefetching and data-affinity optimizations masks the latency of training-time sequence reconstruction, keeping training throughput compute-bound by GPUs. Deployed on production DLRMs, the system reduces training data infrastructure resource usage while enabling aggressive sequence length scaling that delivers significant model quality gains, serving as the foundational data infrastructure for modern recommendation model architectures, including HSTU and ULTRA-HSTU.

High-performance semantic segmentation has achieved significant progress in recent years, often driven by increasingly large backbones and higher computational budgets. While effective, such approaches introduce substantial computational overhead and limit accessibility under constrained hardware settings. In this paper, we propose DGM-Net (Directional Geometric Mamba Network), an efficient architecture that improves modeling capability through structural design rather than increasing model capacity. We introduce Directional Geometric Mamba (G-Mamba), a linear-complexity O(N) operator as an alternative to conventional context modeling modules such as ASPP and PPM. To further enhance structural awareness in state space model (SSM)-based modeling, we design the DGM-Module, which extracts centripetal flow fields and topological skeletons to guide the scanning process and improve boundary preservation. Without relying on large-scale pretraining or heavy backbone scaling, DGM-Net achieves 80.8% mIoU within 28k iterations, 82.3% mIoU on Cityscapes test set, and 45.24% mIoU on ADE20K. In addition, the model maintains stable performance under constrained hardware settings (e.g., batch size of 2 on 8GB VRAM), highlighting its efficiency and practicality. These results demonstrate that incorporating geometric guidance into SSM-based architectures provides an effective and resource-efficient direction for semantic segmentation.

Transformer-based large language models are in some respects limited by the quadratic time and space computational complexity of attention. We introduce the Toeplitz MLP Mixer (TMM), a transformer-like architecture that swaps attention for triangular-masked Toeplitz matrix multiplication over the sequence dimension resulting in $\mathcal{O} (dn \log n)$ time and $\mathcal O(dn)$ space complexity during training and $\mathcal O(dn)$ time and space at inference prefill. Despite the lack of sophisticated input modulation or state maintenance present in other sub-quadratic architectures, TMMs yield greater training efficiency in terms of loss achieved per compute and device memory. We demonstrate that TMMs are capable of retaining more input information resulting in improved copying ability, which we argue results from a lack of architectural biases. Consistent with higher input information retention, TMMs exhibit superior information retrieval and in-context learning benchmark accuracy compared to comparable architectures. We conclude with an analysis from the perspective of operator index theory and show that, counterintuitively, trained Toeplitz layers of causal non-invertible models are more likely to be invertible or nearly so than models that are actually invertible over their inputs.

Selecting a small, high-quality subset from a large corpus for fine-tuning is increasingly important as corpora grow to tens of millions of datapoints, making full fine-tuning expensive and often unnecessary. We propose CRAFT (Clustered Regression for Adaptive Filtering of Training data), a vectorization-agnostic selection method for training sequence-to-sequence models. CRAFT decomposes the joint source-target distribution and performs a two-stage selection: (i) match the validation source distribution through proportional budget allocation across k-means clusters, and (ii) within each source cluster, select training pairs whose target embeddings minimize a conditional expected distance derived from the validation target distribution. We prove that proportional cluster allocation bounds the continuous KL divergence between selected and validation distributions, with the residual controlled by cluster diameters. We evaluate CRAFT on English-Hindi translation by selecting training data from 33 million NLLB sentence pairs and fine-tuning mBART via LoRA. CRAFT achieves 43.34 BLEU, outperforming TSDS (41.21) by 2.13 points on the same candidate pool and encoder while completing selection over 40 times faster. With TF-IDF vectorization, the entire pipeline completes in under one minute on CPU. TAROT achieves 45.61 BLEU, but CRAFT completes selection in 26.86 seconds versus TAROT's 75.6 seconds, a 2.8 time speedup.

We introduce HubRouter, a pluggable module that replaces O(n^2) attention layers with O(nM) hub-mediated routing, where M << n is a small number of learned hub tokens. We demonstrate it in two from-scratch architectures: a Jamba-style hybrid and a 12-layer Transformer; retrofit into pretrained models is a tested negative case. HubRouter implements an encode-decode-score-council pipeline: M learned hubs cross-attend to all tokens, tokens project against hubs for routing fingerprints, a score head selects top-k tokens, and a sparse council attends only to the selected subset. We validate HubRouter in three settings. (1) Hub-Jamba yields a nominal 4.2% PPL improvement (200.2 vs 209.0, single seed; possibly within seed noise) and up to ~90x training throughput at sequence length 1024 in matched PyTorch-native baselines; an optimised baseline would narrow this to ~10-15x. (2) Graduated replacement of 25% of Transformer attention layers gives the best perplexity in our matched-budget sweep (268.0 vs 282.4 pure Transformer). (3) Hub-GPT provides strictly causal routing, achieving PPL 211.5 +/- 0.4 over 3 seeds (post council-causal fix); approximately 3 PPL worse than Jamba's 208.5 +/- 0.7, a measurable quality cost for avoiding O(n^2) computation. Post-fix, chunk size C has little effect; the pre-fix chunk-size benefit was an artifact of a bidirectional-council leak we found in adversarial review. A multi-seed hub-count sweep (~105 runs across M=1-32) reveals M=8-14 as the reliably-converging sub-band (4-5/5 seeds); M=6 is rescued to 5/5 by orthogonal regularization, while M>=20 shows increasing seed sensitivity. Companion paper arXiv:2603.20997 (Basu, 2026) defines the routing diagnostic task. Code and scripts will be released.

Sequential recommender systems have achieved significant success in modeling temporal user behavior but remain limited in capturing rich user semantics beyond interaction patterns. Large Language Models (LLMs) present opportunities to enhance user understanding with their reasoning capabilities, yet existing integration approaches create prohibitive inference costs in real time. To address these limitations, we present a novel knowledge distillation method that utilizes textual user profile generated by pre-trained LLMs into sequential recommenders without requiring LLM inference at serving time. The resulting approach maintains the inference efficiency of traditional sequential models while requiring neither architectural modifications nor LLM fine-tuning.

To address the increasing long-context compute limitations of softmax attention, several subquadratic recurrent operators have been developed. This work includes models such as Mamba-2, DeltaNet, Gated DeltaNet (GDN), and Kimi Delta Attention (KDA). As the space of recurrences grows, a parallel line of work has arisen to taxonomize them. One compelling view is the test-time regression (TTR) framework, which interprets recurrences as performing online least squares updates that learn a linear map from the keys to values. Existing delta-rule recurrences can be seen as first-order approximations to this objective, but notably ignore the curvature of the least-squares loss during optimization. In this work, we address this by introducing preconditioning to these recurrences. Starting from the theory of online least squares, we derive equivalences between linear attention and the delta rule in the exactly preconditioned case. Next, we realize this theory in practice by proposing a diagonal approximation: this enables us to introduce preconditioned variants of DeltaNet, GDN, and KDA alongside efficient chunkwise parallel algorithms for computing them. Empirically, we find that our preconditioned delta-rule recurrences yield consistent performance improvements across synthetic recall benchmarks and language modeling at the 340M and 1B scale.

We define a multi-scale metric $d_ρ$ on strings by aggregating angle distances between all $n$-gram count vectors with exponential weights $ρ^n$. We benchmark $d_ρ$ in DBSCAN clustering against edit and $n$-gram baselines, give a linear-time suffix-tree algorithm for evaluation, prove metric and stability properties (including robustness under tandem-repeat stutters), and characterize isometries.

We establish a mathematical correspondence between state space models, a state-of-the-art architecture for capturing long-range dependencies in data, and an exactly solvable nonlinear oscillator network. As a specific example of this general correspondence, we analyze the diagonal linear time-invariant implementation of the Structured State Space Sequence model (S4). The correspondence embeds S4D, a specific implementation of S4, into a ring network topology, in which recent inputs are encoded, as waves of activity traveling over the one-dimensional spatial layout of the network. We then derive an exact operator expression for the full forward pass of S4D, yielding an analytical characterization of its complete input-output map. This expression reveals that the nonlinear decoder in the system induces interactions between these information-carrying waves that enable classifying real-world sequences. These results generalize across modern SSM architectures, and show that they admit an exact mathematical description with a clear physical interpretation. These insights enable a new level of interpretability for these systems in terms of nonlinear oscillator networks.

Structured sequence generation often requires a model to satisfy several input-derived constraints in a single output. Standard decoding methods may assign high probability to fluent continuations while placing low mass on continuations that realize all required anchors jointly. We study this regime as a rare-event sequential inference problem. LatticeBridge combines a compact prefix language model, instance-compiled surface automata, and a twisted sequential Monte Carlo (SMC) decoder with resampling, multilevel splitting, and a source-support proposal term derived from instance-provided phrases. The constraint representation is compiled from each input instance and does not rely on manually curated lexical classes. On 2,610 attainable validation tasks spanning CommonGen, E2E NLG, and WikiBio, the particle decoder improves exact anchor satisfaction and mean anchor coverage over greedy, beam-filtered, and best-of-k ancestral baselines under a shared proposal model. Since exact anchor satisfaction alone does not rule out unsupported attribute substitutions, the evaluation reports required-anchor coverage, source coverage, source-intrusion diagnostics, overlap, runtime, and particle statistics jointly. The benchmark characterizes the faithfulness-overlap-latency frontier under a fixed proposal model.

This paper introduces \textit{Bangla Key2Text}, a large-scale dataset of $2.6$ million Bangla keyword--text pairs designed for keyword-driven text generation in a low-resource language. The dataset is constructed using a BERT-based keyword extraction pipeline applied to millions of Bangla news texts, transforming raw articles into structured keyword--text pairs suitable for supervised learning. To establish baseline performance on this new benchmark, we fine-tune two sequence-to-sequence models, \texttt{mT5} and \texttt{BanglaT5}, and evaluate them using multiple automatic metrics and human judgments. Experimental results show that task-specific fine-tuning substantially improves keyword-conditioned text generation in Bangla compared to zero-shot large language models. The dataset, trained models, and code are publicly released to support future research in Bangla natural language generation and keyword-to-text generation tasks.

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

An active challenge in developing multimodal machine learning (ML) models for healthcare is handling missing modalities during training and deployment. As clinical datasets are inherently temporal and sparse in terms of modality presence, capturing the underlying predictive signal via diagnostic multimodal ML models while retaining model explainability remains an ongoing challenge. In this work, we address this by re-framing clinical diagnosis as an autoregressive sequence modeling task, utilizing causal decoders from large language models (LLMs) to model a patient's multimodal trajectory. We first introduce a missingness-aware contrastive pre-training objective that integrates multiple modalities in datasets with missingness in a shared latent space. We then show that autoregressive sequence modeling with transformer-based architectures outperforms baselines on the MIMIC-IV and eICU fine-tuning benchmarks. Finally, we use interpretability techniques to move beyond performance boosts and find that across various patient stays, removing modalities leads to divergent behavior that our contrastive pre-training mitigates. By abstracting clinical diagnosis as sequence modeling and interpreting patient stay trajectories, we develop a framework to profile and handle missing modalities while addressing the canonical desideratum of safe, transparent clinical AI.

Modern sequence modeling is dominated by two families: Transformers, whose self-attention can access arbitrary elements of the visible sequence, and structured state-space models, which propagate information through an explicit recurrent state. These mechanisms face different limitations on long contexts: when attention is diffuse, the influence of individual tokens is diluted across the effective support, while recurrent state propagation can lose long-range sensitivity unless information is actively preserved. As a result, both mechanisms face challenges in preserving and selectively retrieving information over long contexts. We propose Sessa, a decoder that places attention inside a recurrent feedback path. This creates many attention-based paths through which past tokens can influence future states, rather than relying on a single attention read or a single recurrent chain. We prove that, under explicit assumptions and matched regimes, Sessa admits power-law memory tails $O(\ell^{-β})$ for $0 < β< 1$, with slower decay than in the corresponding Transformer and Mamba-style baselines. We further give an explicit construction that achieves this power-law rate. Under the same assumptions, Sessa is the only model class among those considered that realizes flexible selective retrieval, including profiles whose influence does not decay with distance. Consistent with this theoretical advantage, across matched experiments, Sessa achieves the strongest performance on long-context benchmarks while remaining competitive with Transformer and Mamba-style baselines on short-context language modeling.

Biological classification with interpretability remains a challenging task. For this, we introduce a novel encoding framework, Multi-Scale Reversible Chaos Game Representation (MS-RCGR), that transforms biological sequences into multi-resolution geometric representations with guaranteed reversibility. Unlike traditional sequence encoding methods, MS-RCGR employs rational arithmetic and hierarchical k-mer decomposition to generate scale-invariant features that preserve complete sequence information while enabling diverse analytical approaches. Our framework bridges three distinct paradigms for sequence analysis: (1) traditional machine learning using extracted geometric features, (2) computer vision models operating on CGR-generated images, and (3) hybrid approaches combining protein language model embeddings with CGR features. Through comprehensive experiments on synthetic DNA and protein datasets encompassing seven distinct sequence classes, we demonstrate that MS-RCGR features consistently enhance classification performance across all paradigms. Notably, our hybrid approach combining pre-trained language model embeddings (ESM2, ProtT5) with MS-RCGR features achieves superior performance compared to either method alone. The reversibility property of our encoding ensures no information loss during transformation, while multi-scale analysis captures patterns ranging from individual nucleotides to complex motif structures. Our results indicate that MS-RCGR provides a flexible, interpretable, and high-performing foundation for biological sequence analysis.

Large language models often appear strong on symbolic and algorithmic tasks, yet this apparent strength can hide brittle behaviour when problems become longer, harder, or slightly out of distribution. A major limitation of current reasoning benchmarks is that many primarily test whether a model can produce a valid answer, while paying less attention to whether the solution is minimal, robust, and stable under controlled difficulty scaling. We introduce RecurrReason, a difficulty-controlled benchmark of four recurrent logic puzzles (Tower of Hanoi, River Crossing, Block World, and Checkers Jumping) with BFS-optimal trajectories and a single interpretable difficulty parameter $N \in \{1,\dots,10\}$, totalling 10{,}817 unique puzzles and 285{,}933 moves. We benchmark two Transformer families, an encoder-decoder model (T5-style) and a decoder-only model (GPT-2-style), under consistent data splits and evaluation criteria, training on $N{=}1$ to $7$ and evaluating on both held-out in-distribution instances and harder out-of-distribution instances at $N{=}8$ to $10$. Fine-tuned pre-trained T5 achieves 97.27% validation and 81.00% OOD accuracy on Block World; all models score 0.00% on River Crossing under all conditions. Failure mode analysis reveals that architecture is a stronger determinant of success than scale. Pre-training transfers only to puzzles with locally structured transition functions. Our code and dataset will be open-sourced upon acceptance.

Time series forecasting is traditionally dominated by sequence-based architectures such as recurrent neural networks and attention mechanisms, which process all time steps uniformly and often incur substantial computational cost. However, real-world temporal signals typically exhibit heterogeneous structure, where informative patterns are sparsely distributed and interspersed with redundant observations. This work introduces \textbf{SPaRSe-TIME}, a structured and computationally efficient framework that models time series through a decomposition into three complementary components: saliency, memory, and trend. The proposed approach reformulates temporal modeling as a projection onto informative subspaces, where saliency acts as a data-dependent sparsification operator, memory captures dominant low-rank temporal patterns, and trend encodes low-frequency dynamics. These components are integrated through a lightweight, adaptive mapping that enables simplified, selective, and interpretable temporal reasoning. Extensive experiments on diverse real-world datasets demonstrate that SPaRSe-TIME achieves competitive predictive performance compared to recurrent and attention-based architectures, while significantly reducing computational complexity. The model is particularly effective in structured time series with clear temporal components and provides explicit interpretability through component-wise contributions. Furthermore, analysis reveals both the strengths and limitations of decomposition-based modeling, highlighting challenges in highly stochastic and complex multivariate settings. Overall, SPaRSe-TIME offers a principled alternative to monolithic sequence models, bridging efficiency, interpretability, and performance, and providing a scalable framework for time series learning.

This paper investigates the length problem in sequence-level relative reinforcement learning. We observe that, although existing methods partially alleviate length-related phenomena, a more fundamental issue remains insufficiently characterized: the comparison units used during training lack inherent comparability. Building on this observation, we propose a new perspective: the length problem should not be viewed merely as a loss-scaling or normalization bias, but rather as a \emph{comparison unit construction} problem. We further establish a sample-construction-based training framework that, instead of applying post-hoc corrections to unequal-length responses, proactively constructs equal-length, alignable, and comparable training segments during generation. Within this framework, we propose EqLen, a concrete method applicable to group-relative comparison algorithms such as GRPO, GSPO, and RLOO. Through dual-track synchronous generation, prefix inheritance, and segment masking, EqLen efficiently collects effective equal-length training segments and enables stable

We introduce RosettaSearch, an inference-time multi-objective optimization approach for backbone conditioned protein sequence design. We use large language models (LLMs) as a generative optimizer within a search algorithm capable of controlled exploration and exploitation, using rewards computed from RosettaFold3, a structure prediction model, under a strict computational budget. In a large-scale evaluation, we apply RosettaSearch to 400 suboptimal sequences generated by LigandMPNN (a state-of-the-art model trained for protein sequence design), recovering high-fidelity designs that LigandMPNN's single-pass decoding fails to produce. RosettaSearch's designs show improvements in structural fidelity metrics ranging between 18% to 68%, translating to a 2.5x improvement in design success rate. We observe that these gains in success rate are robust when RosettaSearch-designed sequences are evaluated with an independent structure prediction oracle (Chai-1) and generalize across two distinct LLM families (o4-mini and Gemini-3), with performance scaling consistently with reasoning capability. We further demonstrate that RosettaSearch improves the sequence fidelity of ProteinMPNN designs for de novo backbones from the Dayhoff atlas, showing that the approach generalizes beyond native protein structures to computationally generated backbones. We also demonstrate a multi-modal extension of RosettaSearch with vision-language models, where images of predicted protein structures are used as feedback to incorporate structural context to guide protein sequence generation. To our knowledge, this is the first large-scale demonstration that LLMs can serve as effective generative optimizers for backbone-conditioned protein sequence design, yielding systematic gains without any model retraining.

Designing proteins that satisfy natural language functional requirements is a central goal in protein engineering. A straightforward baseline is to fine-tune generic instruction-tuned LLMs as direct text-to-sequence generators, but this is data- and compute-hungry. With limited supervision, LLMs can produce coherent plans in text yet fail to reliably realize them as sequences. This plan-execute gap motivates ProtoCycle, an agentic framework for protein design that uses LLMs primarily to drive a multi-round, feedback-driven decision cycle. ProtoCycle couples an LLM planner with a lightweight tool environment designed to emulate the iterative workflow of human protein engineering and uses LLM-driven reflection on tool feedback to revise plans. Trained with supervised trajectories and online reinforcement learning, ProtoCycle achieves strong language alignment while maintaining competitive foldability, and ablations show that reflection substantially improves sequence quality.

Augmentation has become a central technique for improving deep forecasting models, but classification-style transformations tend to break the coherence between the look-back window and its continuous future target. We describe a simple procedure that unfolds the joint input-target sequence into overlapping sliding windows, randomly reorders a controlled fraction of them-prioritized by a lightweight variance criterion-and reconstructs the sequence by averaging across the overlaps, producing synthetic samples with controlled variation while limiting temporal distortion. The procedure is model-agnostic, introduces only three interpretable hyperparameters, and achieves strong improvements over a comprehensive set of competing augmentations across nine long-term forecasting benchmarks with five backbone families (TSMixer, DLinear, PatchTST, TiDE, LightTS) and four short-term traffic benchmarks with PatchTST. Component-wise ablations, hyperparameter sensitivity studies, distributional-alignment diagnostics, probabilistic forecasting evaluation, and a transfer experiment to univariate and multivariate time series classification clarify the contribution of each design choice.

We study out of distribution generalization in streaming tasks where models are trained on short sequences but must operate over much longer, unknown horizons under bounded memory. Our focus is on a persistent fast slow recurrent formulation in which a latent state is maintained across observations rather than reset at each stream step. For each incoming observation, the model performs multiple weight-shared latent updates with a recurrent core and then carries the resulting state forward to the next observation. This allows the model to maintain and refine a compact stream-level state without reprocessing a growing context. We evaluate this formulation across symbolic sequence prediction, supervised navigation, and partially observable reinforcement learning tasks. Across these settings, persistent latent recurrence improves OOD generalization over recurrent, state-space, and Transformer baselines. Through recurrent-core ablations, we identify architectural ingredients that are consistently associated with strong OOD performance, including state-dependent transitions and feature-wise nonlinear mixing. Together, these results highlight the value of revisiting persistent recurrence as an architectural bias for more generalizable sequence prediction.

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.

Generating novel protein sequences that respect a family's statistical constraints typically requires training deep generative models on thousands to millions of examples. Yet most protein families are small: the median Pfam seed alignment contains only 22 sequences, a regime where learned models overfit or collapse. We propose \emph{stochastic attention} (SA), a training-free sampler that treats the modern Hopfield energy over stored sequences as a Boltzmann distribution and draws samples via Langevin dynamics. The score function is the residual of a single softmax attention operation, eliminating the need for a trained score network, pretraining data, or graphics processing units (GPUs). Across eight Pfam families spanning 37 to 420 sequences and 23 to 262 residues, SA generates sequences with low composition divergence, novelty, and structural plausibility supported by ESMFold and AlphaFold2. Compared with profile hidden Markov models (HMMs), EvoDiff, and the multiple sequence alignment (MSA) Transformer, SA is the only tested method to simultaneously achieve low composition divergence, genuine novelty, and sequence identity within each family's nearest-neighbor identity range; the others drift outside this range or produce near-copies. The critical inverse temperature is predicted from principal component analysis (PCA) dimensionality alone, enabling fully automatic operation from a seed alignment. In two domains with deep mutational scanning data, SA-generated substitutions are enriched for experimentally tolerated mutations beyond a position-matched null, and an independent language model (ESM2-650M) scores them within the natural range. Stochastic attention thus opens training-free sequence generation to the long tail of protein families too small for deep learning.

Modern recommender systems leverage ultra-long user behavior sequences to capture dynamic preferences, but end-to-end modeling is infeasible in production due to latency and memory constraints. While summarizing history via interest centers offers a practical alternative, existing methods struggle to (1) identify user-specific centers at appropriate granularity and (2) accurately assign behaviors, leading to quantization errors and loss of long-tail preferences. To alleviate these issues, we propose Hierarchical Sparse Activation Compression (HiSAC), an efficient framework for personalized sequence modeling. HiSAC encodes interactions into multi-level semantic IDs and constructs a global hierarchical codebook. A hierarchical voting mechanism sparsely activates personalized interest-agents as fine-grained preference centers. Guided by these agents, Soft-Routing Attention aggregates historical signals in semantic space, weighting by similarity to minimize quantization error and retain long-tail behaviors. Deployed on Taobao's "Guess What You Like" homepage, HiSAC achieves significant compression and cost reduction, with online A/B tests showing a consistent 1.65% CTR uplift -- demonstrating its scalability and real-world effectiveness.

Time series reasoning tasks often start with a natural language question and require targeted analysis of a time series. Evidence may span the full series or appear in a few short intervals, so the model must decide what to inspect. Most existing approaches encode the entire time series into a fixed representation before inference, regardless of whether or not the entire sequence is relevant. We introduce ARTIST, which formulates time-series reasoning as a sequential decision problem. ARTIST interleaves reasoning with adaptive temporal segment selection. It adopts a controller-reasoner architecture and uses reinforcement learning to train the controller role to select informative segments and the reasoner role to generate segment-conditioned reasoning traces and final answers. During inference, the model actively acquires task-relevant information instead of relying on a static summary of the full sequence. We use a novel hierarchical policy optimization approach for post-training that allows the model to excel in both segment selection and question-answering behavior. We evaluate ARTIST on six time-series reasoning benchmarks and compare it with large language models, vision-language models, and prior time-series reasoning systems. ARTIST improves average accuracy by 6.46 absolute percentage points over the strongest baseline. The largest gains appear on rare event localization and multi-segment reasoning tasks. Supervised fine-tuning improves performance, and reinforcement learning provides additional gains by optimizing question-adaptive segment selection. These results show that selective data use drives effective time-series reasoning.

Over the last years, state-tracking tasks, particularly permutation composition, have become a testbed to understand the limits of sequence models architectures like Transformers and RNNs (linear and non-linear). However, these are often sequence-to-sequence tasks: learning to map actions (permutations) to states, which is incompatible with the next-token prediction setting commonly used to train language models. We address this gap by converting permutation composition into code via REPL traces that interleave state-reveals through prints and variable transformations. We show that linear RNNs capable of state-tracking excel also in this setting, while Transformers still fail. Motivated by this representation, we investigate why tracking states in code is generally difficult: actions are not always fully observable. We frame this as tracking the state of a probabilistic finite-state automaton with deterministic state reveals and show that linear RNNs can be worse than non-linear RNNs at tracking states in this setup.

Time Series Language Models (TSLMs) promise reasoning over real-world temporal data, but their ability to retrieve and reason over long time-series remains largely untested. We introduce TS-Haystack, a multi-domain retrieval benchmark with ten event-grounded question-answering tasks over contexts from 100 seconds to 24 hours, spanning direct retrieval, temporal reasoning, multi-step reasoning, and contextual anomaly detection. Existing TSLMs exhibit severe long-context degradation: accuracy declines with context length, direct-tokenization models run out of memory beyond 100 seconds on high-rate signals, and time-interval-grounded tasks collapse toward near-zero accuracy when increasing the time-series lengths, aligning with existing literature on text and multi-modal long context retrieval. An agentic retrieval framework using specialized time-series classifier tools matches or outperforms SoTA TSLMs on 9 of 10 tasks, highlighting agentic retrieval as a promising approach for long-context TSLMs.

Generative sequence modeling faces a fundamental tension between the expressivity of Transformers and the efficiency of linear sequence models. Existing efficient architectures are theoretically bounded by shallow, single-step linear updates, while powerful iterative methods like Test-Time Training (TTT) break hardware parallelism due to two dimensions of serial dependency: token-level state reliance and step-level iteration loops. We propose PRISM (Parallel Residual Iterative Sequence Model) to resolve this tension. PRISM explicitly approximates the expressive gate-residual-direction iteration pattern of TTT in a parallelizable form. We employ a Write-Forget Decoupling strategy that isolates non-linearity within the injection operator. To bypass the serial dependency of explicit solvers, PRISM utilizes a two-stage proxy architecture: a short-convolution anchors the initial residual using local history energy, while a learned predictor estimates the refinement updates directly from the input. This design distills structural patterns associated with iterative correction into a parallelizable feedforward operator. Theoretically, we prove that this formulation achieves Rank-$L$ accumulation, structurally expanding the update scheme beyond the single-step Rank-$1$ bottleneck. Empirically, it achieves comparable performance to explicit optimization methods while achieving \textbf{174x higher throughput}. Codes are available in https://github.com/gpr-prism/prism/.

How do protein structure prediction models fold proteins? We investigate this question through causal interventions on the folding trunks of ESMFold, OpenFold, and Boltz-1. Across all three models, we find a shared two-stage computational structure. In the first stage, early blocks initialize pairwise biochemical signals: features like charge propagate from sequence into pairwise representations through architecture-specific pathways. In the second stage, late blocks develop pairwise spatial features: distance and contact information accumulate in the pairwise representation. We verify these mechanisms causally by showing that steering charge and distance features induces predictable structural changes. Furthermore, these representations are functionally interchangeable: pairwise states can be linearly aligned and substituted across models. Together, these results suggest that folding trunks with different architectures, inputs, and training procedures converge on a shared representational organization for mapping sequence chemistry into spatial geometry.

Neural Controlled Differential Equations (Neural CDEs) provide a powerful continuous-time framework for sequence modeling, yet the roughness of the driving control path often restricts their efficiency. Standard splines introduce high-frequency variations that force adaptive solvers to take excessively small steps, driving up the Number of Function Evaluations (NFE). We propose a novel approach to Neural CDE path construction that replaces exact interpolation with Kernel and Gaussian Process (GP) smoothing, enabling explicit control over trajectory regularity. To recover details lost during smoothing, we propose an attention-based Multi-View CDE (MV-CDE) and its convolutional extension (MVC-CDE), which employ learnable queries to inform path reconstruction. This framework allows the model to distribute representational capacity across multiple trajectories, each capturing distinct temporal patterns. Empirical results demonstrate that our method, MVC-CDE with GP, achieves state-of-the-art accuracy while significantly reducing NFEs and total inference time compared to spline-based baselines.

The core of video-based visible-infrared person re-identification (VVI-ReID) lies in learning sequence-level modal-invariant representations across different modalities. Recent research tends to use modality-shared language prompts generated by CLIP to guide the learning of modal-invariant representations. Despite achieving optimal performance, such methods still face limitations in efficient spatial-temporal modeling, sufficient cross-modal interaction, and explicit modality-level loss guidance. To address these issues, we propose the language-driven sequence-level modal-invariant representation learning (LSMRL) method, which includes spatial-temporal feature learning (STFL) module, semantic diffusion (SD) module and cross-modal interaction (CMI) module. To enable parameter- and computation-efficient spatial-temporal modeling, the STFL module is built upon CLIP with minimal modifications. To achieve sufficient cross-modal interaction and enhance the learning of modal-invariant features, the SD module is proposed to diffuse modality-shared language prompts into visible and infrared features to establish preliminary modal consistency. The CMI module is further developed to leverage bidirectional cross-modal self-attention to eliminate residual modality gaps and refine modal-invariant representations. To explicitly enhance the learning of modal-invariant representations, two modality-level losses are introduced to improve the features' discriminative ability and their generalization to unseen categories. Extensive experiments on large-scale VVI-ReID datasets demonstrate the superiority of LSMRL over AOTA methods.

While NLP typically treats documents as independent and unordered samples, in longitudinal studies, this assumption rarely holds: documents are nested within authors and ordered in time, forming person-indexed, time-ordered $\textit{behavioral sequences}$. Here, we demonstrate the need for and propose a longitudinal modeling and evaluation paradigm that consequently updates four parts of the NLP pipeline: (1) evaluation splits aligned to generalization over people ($\textit{cross-sectional}$) and/or time ($\textit{prospective}$); (2) accuracy metrics separating between-person differences from within-person dynamics; (3) sequence inputs to incorporate history by default; and (4) model internals that support different $\textit{coarseness}$ of latent state over histories (pooled summaries, explicit dynamics, or interaction-based models). We demonstrate the issues ensued by traditional pipeline and our proposed improvements on a dataset of 17k daily diary transcripts paired with PTSD symptom severity from 238 participants, finding that traditional document-level evaluation can yield substantially different and sometimes reversed conclusions compared to our ecologically valid modeling and evaluation. We tie our results to a broader discussion motivating a shift from word-sequence evaluation toward $\textit{behavior-sequence}$ paradigms for NLP.

DuaDeep-SeqAffinity is a sequence-only deep learning framework that predicts antibody--antigen binding affinity directly from primary amino acid sequences, avoiding the cost and scarcity of resolved three-dimensional structures. The antigen and the antibody heavy and light chains are processed as three independent streams, each embedded with a frozen ESM-2 protein language model and passed through parallel Transformer and convolutional neural network (CNN) branches before late fusion, a decoupled design intended to preserve local complementarity-determining region (CDR) signal that monolithic encoders can dilute. On a sequence-disjoint split of the AbRank benchmark, the model achieves a Pearson correlation of 0.683, an R^2 of 0.460, and a pairwise ranking AUC of 0.895, significantly outperforming single-branch ablations (paired t-test, p < 0.05). Attention-map and gradient-based saliency analyses further show that the model preferentially attends to CDR loops and candidate epitope residues, supporting its use as a scalable, structure-free tool for high-throughput antibody screening.

Structured State Space Models (SSMs), which are at the heart of the recently popular Mamba architecture, are powerful tools for sequence modeling. However, their theoretical foundation relies on a complex, multistage process of continuous-time modeling and subsequent discretization, which can obscure intuition. We introduce a direct, first-principles framework for constructing discrete-time SSMs that is both flexible and modular. Our approach is based on a novel lag operator, which geometrically derives the discrete-time recurrence by measuring how the system's basis functions undergo what we call a domain expansion from one timestep to the next. The resulting state matrices are computed via a single inner product involving this operator, enabling a modular design space for creating novel SSMs by flexibly combining different basis functions and time-warping schemes. To validate our framework, we demonstrate that a specific instance exactly recovers the recurrence of the influential HiPPO model. Numerical simulations confirm our derivation, providing new theoretical tools for designing flexible and robust sequence models.

Electronic health Records (EHRs) have become a cornerstone in modern-day healthcare. They are a crucial part for analyzing the progression of patient health; however, their complexity, characterized by long, multivariate sequences, sparsity, and missing values poses significant challenges in traditional deep learning modeling. While Transformer-based models have demonstrated success in modeling EHR data and predicting clinical outcomes, their quadratic computational complexity and limited context length hinder their efficiency and practical applications. On the other hand, State Space Models (SSMs) like Mamba present a promising alternative offering linear-time sequence modeling and improved efficiency for handling long sequences, but focus mostly on mixing sequence-level information rather than channel-level data. To overcome these challenges, we propose HyMaTE (A Hybrid Mamba and Transformer Model for EHR Representation Learning), a novel hybrid model tailored for representing longitudinal data, combining the strengths of SSMs with advanced attention mechanisms. By testing the model on predictive tasks on multiple clinical datasets, we demonstrate HyMaTE's ability to capture an effective, richer, and more nuanced unified representation of EHR data. Additionally, the interpretability of the outcomes achieved by self-attention illustrates the effectiveness of our model as a scalable and generalizable solution for real-world healthcare applications. Codes are available at: https://github.com/healthylaife/HyMaTE.

Target-conditioned sequence models provide a simple interface for controllable offline decision making, but the requested target return can be an unreliable control signal, especially when the target return lies in underrepresented regions of the dataset. This paper proposes Doctor, a hybrid sequence modeling and reinforced verification framework for controllable target-conditioned offline decision making. Doctor trains a shared masked trajectory Transformer with two complementary objectives: masked trajectory reconstruction for candidate generation and in-sample value learning for action-value verification. At inference time, the model samples multiple nearby target returns, generates candidate actions in parallel, and selects the action whose verified value is closest to the requested target return. We analyze this verifier-guided selection rule and show that its value-level alignment error is bounded by candidate-value coverage around the target return and verifier accuracy. Experiments on D4RL and EpiCare show that Doctor improves target-return alignment under reduced high-return coverage, remains competitive on standard offline return-maximization benchmarks, and enables a single policy to modulate between conservative and aggressive operating points in a simulated clinical decision-making task. These results suggest that reinforced verification can improve the controllability of target-conditioned policies.

Owing to the unprecedented capability in semantic understanding and logical reasoning, large language models (LLMs) have shown fantastic potential in developing next-generation sequential recommender systems (RSs). However, existing LLM-based sequential RSs mostly separate index generation from sequential recommendation, leading to insufficient integration between semantic information and collaborative information. On the other hand, the neglect of user-related information hinders LLM-based sequential RSs from exploiting high-order user-item interaction patterns. In this paper, we propose the End-to-End Dual Dynamic (ED$^2$) recommender, the first LLM-based sequential RS which adopts dual dynamic index mechanism, targeting resolving the above limitations simultaneously. The dual dynamic index mechanism can not only assembly index generation and sequential recommendation into a unified LLM-backbone pipeline, but also make it practical for LLM-based sequential recommender to take advantage of user-related information. Specifically, to facilitate the LLM comprehension ability to dual dynamic index, we propose a multigrained token regulator which constructs alignment supervision based on LLMs semantic knowledge across multiple representation granularities. Moreover, the associated user collection data and a series of novel instruction tuning tasks are specially customized to capture the high-order user-item interaction patterns. Extensive experiments on three public datasets demonstrate the superiority of ED$^2$, achieving an average improvement of 19.62% in Hit-Rate and 21.11% in NDCG.

Linear recurrent neural networks, such as State Space Models (SSMs) and Linear Recurrent Units (LRUs), have recently shown state-of-the-art performance on long sequence modelling benchmarks. Despite their success, their empirical performance is not well understood and they come with a number of drawbacks, most notably their complex initialisation and normalisation schemes. In this work, we address some of these issues by proposing RotRNN -- a linear recurrent model which utilises the convenient properties of rotation matrices. We show that RotRNN provides a simple and efficient model with a robust normalisation procedure, and a practical implementation that remains faithful to its theoretical derivation. RotRNN also achieves competitive performance to state-of-the-art linear recurrent models on several long sequence modelling datasets.

Is it possible to understand the intricacies of a dynamical system not solely from its input/output pattern, but also by observing the behavior of other systems within the same class? This central question drives the study presented in this paper. In response to this query, we introduce a novel paradigm for system identification, addressing two primary tasks: one-step-ahead prediction and multi-step simulation. Unlike conventional methods, we do not directly estimate a model for the specific system. Instead, we learn a meta model that represents a class of dynamical systems. This meta model is trained on a potentially infinite stream of synthetic data, generated by simulators whose settings are randomly extracted from a probability distribution. When provided with a context from a new system-specifically, an input/output sequence-the meta model implicitly discerns its dynamics, enabling predictions of its behavior. The proposed approach harnesses the power of Transformers, renowned for their \emph{in-context learning} capabilities. For one-step prediction, a GPT-like decoder-only architecture is utilized, whereas the simulation problem employs an encoder-decoder structure. Initial experimental results affirmatively answer our foundational question, opening doors to fresh research avenues in system identification.

Structured data is widely used in domains such as healthcare, finance, and scientific data management. Recent studies on structured data foundation models (SFMs) aim to support data analysis and mining tasks over such data, but still face scalability and generalization challenges when applied to real-world enterprise databases. First, many SFMs rely on full self-attention, which introduces an O(N^2) computational bottleneck and limits the number of tuples that can be processed jointly. Second, directly replacing attention with linear-complexity sequence models may conflict with the permutation-invariant nature of structured data, introducing artificial order bias and degrading representation quality. Moreover, models trained only on synthetic data may struggle to generalize to the heavy-tailed and heterogeneous distributions commonly found in real-world databases. To address these challenges, we propose FEAT, a linear-complexity foundation model for extremely large structured data. FEAT replaces quadratic attention with a multi-layer dual-axis encoding architecture. It integrates an adaptive-fusion bidirectional state-space model (AFBM) with convolutional gated linear attention (Conv-GLA), enabling cross-tuple contextualization in O(N) time while supporting permutation-invariant representation learning. To improve robustness under real-world data skewness, FEAT further adopts a hybrid structural causal pre-training pipeline with a robust reconstruction objective. Experiments on 12 real-world database benchmarks show that FEAT consistently outperforms representative SFMs on zero-shot tasks and scales linearly with structured-data sample length, achieving up to 50x faster inference latency.

Some low-cost Internet of Things (IoT) sensor deployments lack device-level source authentication, leaving them vulnerable to impersonation or injected sensor readings. We present a lightweight approach to sensor impersonation detection in a small proof-of-concept study. We formulate detection as a sequence-prediction problem. A model with three LSTM layers and two fully connected layers is trained only on univariate temperature readings from a genuine sensor, and a window of readings is flagged when its mean absolute prediction error exceeds the mean genuine error by more than six standard deviations. The model is converted to TensorFlow Lite in three variants, non-quantized (554 KB), 16-bit weight quantized (298.5 KB), and 8-bit weight quantized (185 KB), targeting an Arduino Nano 33 BLE aggregator. The variants were evaluated with the TensorFlow Lite interpreter on the local server, since on-device execution of LSTM models was not yet supported by TensorFlow Lite for Microcontrollers at the time of the study. On a controlled testbed with the impostor sensor placed in a hotter outdoor location, the three variants reached detection accuracies of 99.980%, 99.972%, and 98.206%, and each flagged the change point when a test sequence switched from genuine to impostor data. Quantization made the model smaller but slower in our measurements. The genuine and impostor distributions were well separated, so these results show detection of a controlled distribution shift and should not be read as evidence of general device authentication.

\textbf{Motivation:} Pre-trained protein language models (PLMs) such as ESM-2 have become the default representation for biological sequence tasks, but they are computationally heavy and require GPUs both for embedding and for fine-tuning. Whether they are actually necessary for sequence \emph{classification}, as opposed to structure prediction, is rarely tested against strong, principled, lightweight alternatives. This question has direct practical stakes for large-scale genomic surveillance, where embedding millions of sequences on commodity hardware is a recurring bottleneck.\ \textbf{Results:} We introduce Murmur2Vec, an alignment-free, training-free embedding that aggregates $k$-mer counts into a small hash table via the deterministic MurmurHash function, and we cast it as a randomized sketch of the classical $k$-mer spectrum kernel. We provide a complete theoretical treatment: closed-form bias/variance of the inner product, an unbiased signed variant with a Johnson--Lindenstrauss-type concentration bound, an excess-risk bound for downstream linear classifiers that makes the bias--variance trade-off in the hash-table size explicit, and an implicit-regularization mechanism by which collisions damage frequent non-discriminative $k$-mers more than rare lineage-defining ones. Across four classification tasks, SARS-CoV-2 spike lineage (22 classes), HIV-1 Env subtype (8 classes), and two protein-family benchmarks (8 and 6 classes), Murmur2Vec matches a LoRA-fine-tuned 650M-parameter ESM-2 model on the two tasks for which LoRA fine-tuning was run to convergence (SARS-CoV-2 and HIV-1) and ties frozen ESM-2 on the two protein-family tasks, and it \emph{outperforms} the fine-tuned model on the hardest task (SARS-CoV-2 lineage: $0.854$ vs.\ $0.807$ accuracy; macro-F1 $0.684$ vs.\ $0.401$).