Sequence Modeling

Functional annotation of newly sequenced proteins remains a bottleneck in molecular biology: the number of sequences in public repositories grows far faster than the capacity for manual curation. Most computational approaches consider annotation as multi-label classification over a fixed ontology, which constrains predictions to a predefined label set. In this work we study the the protein annotation as a sequence-to-text generation problem. We fine-tune the 3B-parameter Ministral 3 base model with QLoRA (4-bit NF4 quantization with low-rank adapters) on sequence annotation pairs. We assess predictions with an LLM-as-expert protocol: a GPT model prompted as a senior molecular-biology curator scores organism identification as binary and function annotation quality. We conclude that QLoRA-fine-tuned compact LLMs can generate curator-style annotations with genuine biological value for a substantial subset of proteins. We also discuss future directions in data quality, model scaling, and evidence grounding that are needed to make the approach sufficiently reliable for practical use.

In extractive document question answering whose questions were generated from the passages that contain their answers -- so that retrieval recovers 92-99.8% of what any mode combination could reach, whatever its absolute accuracy -- confidence-driven mechanisms have little to gain. Fine-tuning an open language model on a specialized domain corpus yields a model whose own confidence is a tempting control signal: it could decide which queries warrant further adaptation, and which answers to trust. We evaluate both uses under criteria fixed before the runs were executed, across four 7-9B model families whose adaptation moved closed-book F1 by at most +0.03, and both fail: a distillation trigger on all four families, under its pre-specified three-step transfer budget, and a routing-and-abstention policy in its single-model pilot. Retrieval alone recovers 92-99.8% of best-case combined accuracy under every correctness criterion we test, leaving routers no meaningful gain. The sequence-likelihood signal is insufficient relative to that mode -- area under the receiver operating characteristic curve 0.65-0.81 under the registered criterion -- before adaptation as well as after, unchanged by scalar recalibration and not consistently improved by token-level temperature rescaling. And the finer diagnostics depend on the correctness criterion and on answer length; on the three adapted combinations where we could test it, selector ablations show no statistically detectable downstream benefit from the confidence term on any seed; on Gemma, removing it changes the selector from failing to passing both registered criteria. The usable product is a set of pre-specified negatives with their dependencies made explicit.

In previous papers, we began the study of sequence prediction algorithms adapted to stringological word complexity measures. In particular, we defined a complexity measure called Arithmetic Repetition Complexity (ARC) which admits a polynomial-time prediction algorithm with a mistake bound quasilinear in the complexity. Here, we show a weaker complexity measure related to ARC that admits an especially efficient prediction algorithm: an algorithm that runs in quasilinear time and polylog space for appropriate highly-structured sequences. The complexity measure is defined via a restricted class of "zipline programs" (a variant of straight-line programs), which we call layered. We thus get a less expressive measure with a more efficient algorithm (compared to our results for ARC), demonstrating a possible tradeoff.

Static malware detection for Windows Portable Executable files demands a careful balance between detection effectiveness, computational efficiency, and analytical interpretability. This paper introduces Delphi Scanner, a static malware detection system for Windows PE files that balances efficiency with behavioral interpretation. It uses a convolutional neural network (CNN) to model Windows API sequences to classify PE and a decoupled interpretation layer based on a rule-based layer to categorize APIs into high-level malicious capabilities. Evaluated on over 190,000 Windows PE files, the system achieves 95.35% accuracy with a 1.53~MB model footprint. Robustness experiments on 5,647 out-of-distribution MalwareBazaar samples, paired packed and unpacked executables, and three adversarial manipulation strategies confirm generalization beyond the training distribution and resistance to functionality-preserving evasion techniques. Overall, these results demonstrate that API sequence-based static analysis offers a practical, interpretable, and efficient foundation for malware triage in local deployment scenarios.

We propose a compact NISQ-compatible quantum transformer architecture for synthetic QNLP sequence modelling. The model preserves the autoregressive next-token interface of a classical transformer, but replaces attention and feed-forward sublayers with variational quantum encoder blocks, connector circuits, decoder blocks and a direct two-qubit measurement readout. Token contexts are angle-encoded into small quantum registers, processed by parallel variational heads and encoder integration circuits and conditioned through decoder ancillae to produce a distribution over a four-token vocabulary. We evaluate several architecture variants on deterministic and lexicographic grammar-generation tasks against a compact classical transformer baseline. The quantum models are trainable end-to-end and learn nontrivial grammar structure, including perfect deterministic generation in individual runs and high lexicographic validity in the strongest variant. The classical baseline remains more accurate and stable and the quantum models are sensitive to initialization. The contribution is therefore not a claim of quantum advantage, but a concrete architecture and evaluation of transformer-inspired QNLP sequence modelling under near-term quantum constraints.

Hyperbolic geometry provides a natural inductive bias for genomic representation learning, but existing hyperbolic genomic models primarily use Lorentz convolutions to learn local sequence representations, while their residual pathways do not directly aggregate full Lorentz representations. We propose HyCoSeq, a contextual hyperbolic representation learning framework for genomic sequences. HyCoSeq incorporates weighted Lorentzian residual aggregation into multi-curvature Lorentz encoding, allowing full Lorentz representations to participate directly in geometry-consistent local aggregation. It further introduces a bidirectional long short-term memory network that integrates information from both sequence directions to learn contextual relationships among local representations at different positions within a genomic sequence, thereby extending local hyperbolic convolutional encoding to sequence-level contextualized representations. Extensive experiments across diverse genomic tasks show that HyCoSeq outperforms existing hyperbolic baselines and, without large-scale genomic pretraining, achieves competitive performance against substantially larger pretrained DNA language models.

State Space Models (SSMs) have emerged as a compelling alternative to Transformers, enabling sequence modeling with constant memory and linear compute. Although SSMs exhibit reasonable performance and favorable computational characteristics, they continue to lag behind Transformers on tasks that require in-context learning and precise retrieval, slowing their adoption for large-scale language modeling. In this work, we demonstrate that both the success and failure of SSMs in these domains can be explained by studying the role of the gating mechanism, a prevalent component in modern recurrent networks. Specifically, we show through theory and experiments that this gating mechanism causes SSMs to first learn an in-weights "memorization" solution, while delaying, or even preventing, convergence to a correct in-context learning solution. Importantly, this happens even in cases where there are no fundamental limitations due to the architecture or its memory capacity. On the other hand, we find that gating is often beneficial for improving generalization to long sequence lengths. Our results illuminate the crucial role of the gating mechanism in shaping both the training dynamics and generalization of SSMs, and provide a basis for understanding and improving linear-time models.

Transformers and state-space models (SSMs) are the two dominant families of sequence models, and a central open question is how far the analytical knowledge built for transformers transfers to SSMs. We address this through the lens of layer importance which underpins compression, selective fine-tuning, and interpretability across both families. We decompose layer importance into two distinct notions. \emph{Necessity} captures how much the pretrained model depends on a layer's existing contribution, measured by the loss increase from bypassing it. \emph{Plasticity} captures where the model absorbs new information during fine-tuning, measured by the magnitude of task-specific weight updates. Our analysis reveals that the two families behave fundamentally differently: in every evaluated residual transformer up to $14$B parameters, Necessity and Plasticity anti-align across depth, whereas in the evaluated Mamba-style SSMs they point to overlapping regions. The sign of this alignment also predicts downstream adaptation behavior. In the evaluated transformers, concentrating updates in the most plastic layers increases catastrophic forgetting, while this tier-dependent effect disappears in the evaluated Mamba-style SSMs.

Complete suffix prediction is challenging in sequential decision settings, where the same prefix can remain compatible with several plausible suffixes. We propose a graphbased metric-learning framework that reformulates complete suffix prediction as latent retrieval over process graphs. Prefixes and suffixes are represented as directed attributed graphs and encoded by edge-conditioned graph neural networks, allowing event-level activities and transition-level durations to be modelled jointly. Prefix representations are projected into the latent suffix space through a predictor trained with a joint reconstruction and contrastive objective strengthened using process-aware hard negatives. To stabilise the learned retrieval geometry, spectral normalisation, and retrieval robustness, spectral normalisation is applied to enforce a Lipschitz constraint on both encoders and predictor. Experiments on two real-life process datasets demonstrate that the proposed framework achieves the best overall results across nearly all evaluated criteria. It improves semantic suffix accuracy measured by normalized Damerau-Levenshtein distance, yields strong retrieval quality through Recall@1, Recall@5, and MRR@5, and maintains temporal plausibility according to Mean Absolute Error. These results show that graph-based latent retrieval is an effective alternative to sequential suffix prediction for recommendation-oriented process monitoring under structural and KPI-related constraints.

Linear attention and state-space models provide linear-time sequence modeling, but their recurrent memory remains a second-order tensor (a matrix), limiting the order of interactions that can be represented in the state. We introduce the RunningTensor, which generalizes this memory to an order-$o$ tensor, updated by a rank-1 outer product and read by contracting against $o-1$ vector queries. Order $2$ recovers linear attention; we study order $3$ as a proof of concept, retaining both recurrent and parallel forms while remaining linear in sequence length $T$ and improving working memory capacity from $\mathcal{O}(W^2)$ to $\mathcal{O}(W^o)$. On synthetic multi-query associative recall, RunningTensor outperforms linear-attention and SSM baselines. After pretraining, it also improves performance on language-understanding and non-synthetic retrieval tasks, suggesting that higher-order recurrent state can provide useful additional memory capacity beyond matrix-valued state.

Nucleotide sequence analysis is central to problems spanning regulatory genomics, evolutionary biology, and phenotype prediction. Classical bioinformatics methods extract interpretable sequence properties such as motifs and k-mer composition, but their flexibility is limited. In contrast, modern deep learning models can learn powerful predictive representations directly from raw sequences, yet their internal representations and decision mechanisms are difficult to inspect. Interpretable machine learning methods (e.g., sparse linear models and decision trees) provide human-understandable representations of predictive relationships but are not designed to operate directly on nucleotide sequences. Here, we introduce SeqMaestro, a machine learning framework that proposes biological hypotheses from nucleotide sequences using interpretable models. Our solution is centered around a two-layer interface that connects nucleotide sequences with the broader ecosystem of interpretable machine learning. SeqMaestro uses this interface to fit diverse combinations of interpretable models, feature representations, and extraction strategies, leveraging variability across transparent models to identify robust biological signals and richer predictive relationships than feature importance alone can provide. The system also supports data transformation and cleaning, model fitting, hyperparameter tuning, reliability analysis, and synthesis of results into a contextualized written report. By providing these capabilities through a no-code workflow, SeqMaestro is designed to make interpretable sequence analysis accessible to researchers without requiring extensive programming or machine learning expertise. SeqMaestro thereby provides an accessible route from nucleotide sequences to biological hypotheses.

We predict single-sequence model throughput from GGUF metadata using roofline-shaped predictors with quantization-specific scale factors fitted on reference models. The scored cohort comprises 318 phase-depth measurements from 53 host-file configurations on two Apple M4 Max systems and an NVIDIA RTX 5080. On host-specific held-out sets of four, five, and two configurations, an active-parameter decode model obtains 13.1%, 14.4%, and 36.1% mean absolute percentage error (MAPE), versus 49.4%, 55.3%, and 51.9% when charging total parameters. Leave-one-host-out coefficients fitted on the other two systems yield 11.6%, 16.8%, and 36.0% test MAPE. A low-bit model ladder changes ordering across runtime stacks. The P2 prefill baseline gives 18.7%, 22.2%, and 108.2% test MAPE. GGUF structure helps on all three systems, but fitted efficiencies are not universal.

Modeling long-term user behavior is central to sequential recommendation and billion-scale industrial recommender systems, yet production ranking models operate under strict latency, memory, communication, and training-throughput constraints. At the 100K scale, the challenge extends beyond attention complexity: raw sequence features must be stored, transferred, and repeatedly processed during training and online serving. Existing approaches based on history truncation, multi-stage behavior retrieval, compressed lifelong histories, or train-short/infer-long extrapolation either weaken end-to-end optimization or retain substantial length-dependent cost. We present SequenceO1, an end-to-end framework for ultra-long user behavior sequence modeling, deployed at full traffic on Douyin with histories of up to 100K interactions. SequenceO1 follows a compress-then-reason design. Its Sketch Attention (SA) uses learnable prototypes and prototype-wise normalization to compress the raw history into a fixed-size, target-agnostic user representation. Target-conditioned Stacked Target-to-History Cross Attention (STCA) then models complementary time scales: a recent 10K suffix for short-term interests and the compact sketch for long-term preferences. To make training and inference practical, SequenceO1 combines low-rank user representation caching, multi-request user-level batching, pipeline lift, and a fused FlashSA kernel to amortize feature storage, communication, and computation across targets, training instances, and consecutive requests. Production experiments show consistent offline and online gains, while the compact cached sketch retains most of the benefit of directly scaling end-to-end sequence ranking to 100K. These results provide a practical model-system approach to efficient attention, sequence compression, and scalable long-sequence and long-context recommendation systems.

Proteins perform diverse cellular functions, and even single amino-acid substitutions can alter stability, activity, or molecular interactions. Protein language models (PLMs) provide a scalable approach for modeling such sequence--function relationships from unlabeled sequences, but increasing the size of dense Transformer backbones often brings substantial computational cost without consistently improving mutation-sensitive prediction. We introduce ProtLingo, an efficient PLM framework that augments a pretrained single-sequence backbone with conditional local memory and sparse expert routing. ProtLingo maps contextual residue representations into route-specific discrete codes, composes centered local windows into latent $N$-gram addresses, and retrieves reusable residual signals associated with recurring local sequence contexts. In parallel, selected feed-forward blocks are upcycled into sparse Mixture-of-Experts layers with shared and routed experts, enabling residue-dependent computation while activating only a subset of parameters. Experiments on protein fitness prediction, FLIP benchmarks, and supervised contact prediction show that ProtLingo achieves competitive performance with a 150M-scale backbone, including strong parameter efficiency on mutation-effect prediction and preserved long-range structural representations.

Generalising to unseen tasks remains a fundamental challenge in offline multi-agent reinforcement learning (MARL). In this work, we present a principled analysis of zero-shot task generalisation in the offline setting and conduct an extensive empirical investigation into the scaling behaviour governing task diversity, dataset size, and network capacity. To facilitate this study, we extend offline sequence modelling architectures to handle multi-task observation and action spaces alongside variable agent counts across tasks. Our primary finding is that scaling task diversity---rather than sheer dataset size is the dominant factor in achieving robust zero-shot transfer. Through large-scale experiments across four challenging environments (Connector, RWARE, SMAX, and LBF), we demonstrate that our multi-task approach achieves a mean improvement of 3.2x on held-out test tasks compared to single-task models and consistently outperforms strong behaviour cloning baselines. These results suggest that the development of generalisable MARL agents should prioritise the diversity of the training distribution with varying numbers of agents, providing a roadmap for scaling offline MARL effectively.

Generative retrieval has demonstrated significant success by unifying representation learning and search into a single sequence-to-sequence generation task. However, extending this paradigm to cross-modal retrieval reveals a critical challenge arising from the inherent information asymmetry across different modalities, such as the gap between concise text queries and dense visual candidates. This structural mismatch causes the autoregressive decoder to suffer from forced hallucination when generating identifiers via standard trie-constrained beam search, where the model is severely penalized for failing to guess fine-grained details absent from the query, allowing irrelevant candidates to hijack top rankings. To address this issue, we propose Wildcard Inference with Dynamic Expansion (WIDE). WIDE employs Adaptive Entropy Thresholding (AET) to calibrate layer-specific uncertainty boundaries offline. During the decoding generation phase, Asymmetry-aware Wildcard Decoding (AWD) detects semantic blind spots and emits wildcards instead of forced deterministic identifiers, dynamically expanding the search space without incurring log-probability penalties. Finally, Blind-Spot Re-ranking (BSR) evaluates the expanded candidate pool using a hybrid scoring mechanism that combines discrete generation confidence with continuous semantic similarity. Extensive experiments on the M-BEIR benchmark demonstrate that WIDE outperforms state-of-the-art generative retrieval methods, effectively suppressing forced hallucination while maintaining compact index structures.

Proteins are fundamental to biological processes, with their function determined by the complex interplay between the amino acid sequence and the three-dimensional structure. Developing generative models capable of understanding this intrinsically multi-modal relationship is crucial for fields like drug discovery and protein engineering. Existing models often rely on a multi-stage training process where autoencoders that tokenize data into latent representations are trained in a first stage. Secondly, a generative model is trained on the latent representation of the autoencoder(s), i.e., generative modeling in a latent space. We hypothesize that this multi-stage training is not necessary to obtain performant co-design models and thus present SimpleDesign, an effective multi-modal protein design model trained directly in the data space. SimpleDesign leverages a single-stage end-to-end objective that combines discrete cross-entropy for sequences and a regression objective for structures. In order to effectively model the difference in sequence and structure modalities, we develop a Mixture-of-Transformer architecture that allows modality-specific processing while keeping global self-attention over both modalities. We train SimpleDesign on over 2M sequence-structure pairs achieving strong performance across co-design and unconditional sequence/structure generation benchmarks.

Long-context reasoning for large language models (LLMs) is becoming increasingly important, but training over long sequences remains challenging due to massive memory and communication requirements. Sequence parallelism has emerged as an essential technique for addressing bottlenecks in long sequence LLM training. However, we observe that existing sequence parallelism methods are batch-agnostic and apply uniform sequence partitioning across all batch sizes, resulting in inefficient communication. In this paper, we introduce Batch- Aware Sequence Parallelism (BASP), a sequence parallelism approach that leverages batch structure to reduce communication overhead. BASP exploits batch structure by partitioning GPUs into disjoint sequence-parallel groups according to the micro- batch size. This design reduces the all-to-all communication group size, thereby localizing communication and improving training efficiency. Experimental results on an NVIDIA A100 cluster show that BASP improves end-to-end training time by up to 1.17 - 1.31x in Llama and Qwen models compared to standard sequence parallel baselines, while preserving identical model accuracy and memory usage.

This article presents SSAKG 2.0, an open-source software package for constructing and operating Structural Sequential Associative Knowledge Graphs (SSAKGs). An SSAKG represents objects as graph vertices and ordered sequences as structural patterns of graph connections. The resulting sparse graph is used as an associative memory in which complete sequences can be reconstructed from a partial, unordered context. Version 2.0 introduces new algorithms that exploit individual bits of computer memory to efficiently search graph connections. The package is implemented in Python, while performance-critical graph operations are implemented in C and exposed through a Python interface. This hybrid implementation provides a flexible high-level programming environment while reducing the memory and computational overhead associated with large sparse graphs. The algorithms were evaluated using randomly generated numerical sequences, sequences derived from sentences in the NLTK corpus, and mRNA sequences. The experiments demonstrate the ability of the package to store and reconstruct sequences from partial contexts and provide a basis for evaluating the effects of graph density, sequence length, and memory size on retrieval performance. SSAKG 2.0 is distributed under the Apache 2.0 open-source license. The package includes documentation and reproducible examples and is publicly available through GitHub and the Python Package Index (PyPI).

Protein inverse folding aims to recover amino acid sequences for a given 3D protein structure, underpinning broad applications such as enzyme engineering and drug discovery.Current methods often follow a serial pipeline, in which a structure encoder predicts a coarse sequence, which is then refined by protein language models (PLMs). However, because PLMs only perform post-hoc sequence edits, the refinement is bounded by the quality of upstream predictions.Thanks to recent multimodal protein language models (MPLMs), we could directly encode structure to generate sequences with pretrained structural knowledge, but we observe that they are not effective for inverse folding. Therefore, we introduce a symmetric dual-path architecture that both leverages PLMs for pretrained sequence evolution knowledge and MPLMs for pretrained structural knowledge to iteratively guide protein sequence generation.Through extensive experiments across standard protein inverse folding benchmarks, our method achieves state-of-the-art performance, surpassing prior approaches, and ablation studies validate the rationale of our symmetric design, revealing a promising direction for the community.

Solving problems through repeated attempts is a sequential modeling task: at each step, the solver receives feedback and decides how to revise their solutions. Predicting whether performance improves, plateaus, or regresses across attempts is central to understanding any iterative problem-solving process in both human learners and autonomous agents. Beyond outcomes, modeling what errors persist and how strategies shift across attempts provides deeper insight into the mechanics of sequential learning. Studying these dynamics requires observing many solvers as they attempt, receive feedback, and revise. Programming courses with automated grading provide this setting, as students iteratively submit code to test suites and receive feedback on every attempt. We therefore curate CodeInsight, a large-scale dataset of over 3 million submissions from 3,286 undergraduates across 2 introductory C++ courses in 2 academic years, with test-case-level outcomes, timestamps, and source code. On this dataset, we build a benchmark that evaluates models spanning parametric, sequential, and generative traditions under a shared calibration-and-scoring protocol, including a Recurrent State Space Model (RSSM) adapted to track solver characteristics through discrete latent variables and an LLM-based predictor that generates explicit solutions. The adapted RSSM achieves the strongest predictive accuracy on three of the four courses. The LLM predictor is less accurate but produces full submissions at each attempt, enabling direct analysis of failure modes. We find that the model's coding proficiency is inversely related to predictive performance in this setting, with the LLM better understood as a generative solver conditioned on context rather than a faithful predictor of solver behavior. We publicly release our code and the dataset on request to facilitate future research.

We consider the problem of sequential prediction of an $m$-ary sequence, where at each epoch, (i) the environment selects an outcome from an $m$-ary alphabet, (ii) the learner selects a probability distribution over the same alphabet (unaware of the outcome generated by the environment), and finally, (iii) the learner incurs a cost that depends on the probability assigned to the outcome. The cost function we consider captures the complexity of predicting the outcome generated by the environment, in a scenario where the aforementioned prediction is performed via comparative queries to a lying oracle. We consider both stochastic and adversarial environments, propose algorithms for both settings, and establish logarithmic upper bounds on their regret.

Existing predictive models in learning analytics often treat student academic history as a simple sequence, overlooking the concurrent nature of courses taken within a semester. This simplification can lead to inaccurate performance predictions, particularly for students with heavy or challenging course loads. This paper introduces a TRansformer for Academic Course-grade Estimation (TRACE) that addresses this limitation by jointly predicting both the set of courses a student will take and their corresponding grades for an upcoming semester. Our approach encodes courses on a per-semester basis to capture the effects of course concurrency and utilizes a novel loss function combining course-set prediction with grade prediction. We demonstrate that predicting courses taken in addition to the grades in those courses leads to significant improvements in prediction quality. Trained on ten years of institutional data, our joint prediction model reduces mean absolute error by nearly 50% compared to an identical architecture that predicts grades alone. The model also outperforms traditional LSTM-based sequential models, as well as graph neural network-based approaches, and offers natural ways to incorporate student attribute data. This work demonstrates the utility of modern neural architectures for creating interpretable models that can be adapted to new institutions via retraining and recalibration, as well as the importance of key techniques, such as predicting courses taken during training. We discuss how this model could be incorporated into early detection systems at institutions of higher education.

AlphaFold3-class structure predictors pair a representational trunk, which processes sequence and context, with a diffusion module, which generates atomic coordinates. How biological information changes as it crosses this architectural boundary remains poorly understood. We analyze per-residue activations from the Pairformer trunk and diffusion module of Boltz-1 using linear probes, sparse autoencoders (SAEs), and causal interventions. From the trunk, both geometry (secondary structure, disorder) and sequence chemistry (amino-acid identity, signal peptides, disulfide-bond annotations) are linearly decodable. In the diffusion module, the two diverge. Secondary structure transfers essentially unchanged, whereas sequence chemistry is strongly attenuated. We then test whether decodable directions can steer the model, intervening on the final trunk single representation that conditions the diffusion module. Helix and coil directions change predicted structure dose-dependently against matched-norm random controls, but a beta-strand direction that is highly predictive (F1 =0.82) produces no measurable increase in strand content: linear decodability does not imply causal influence at the site we tested. The same probes also score markedly lower against sparse SwissProt annotations than against dense DSSP labels, because unannotated residues that the model gets right are charged as false positives; such scores are therefore lower bounds. Finally, supervised probes outscore single SAE features wherever a label already exists. We release the trained trunk and diffusion SAEs, Boltz-1 per-residue activations, and the analysis code.

Methods for text-based generation of hand-object interaction (HOI) sequences primarily focus on producing smooth, physically plausible trajectories. A truly utilitarian method should additionally support variable-length generation, composite motion sequences, motion completion and infilling, and reliable termination without compromising physical plausibility. Standard diffusion models for HOI generation are typically trained only for text-to-motion generation on atomic motions and require the motion length to be specified a-priori. Autoregressive (AR) methods provide greater sequence-level flexibility, but commonly depend on discrete motion codes, which can lose contact-sensitive motion detail. To address these key limitations, we present a model performing Masked Autoregression with Diffusion for HOI generation (MAD-HOI). Our method starts by encoding hand and object motions in a continuous latent space while keeping them disentangled to maintain stream-wise control. This is followed by a masked autoregressive transformer to predict context features that condition a flow-matching head. MAD-HOI is capable of motion generation for atomic and composite articulated sequences, conditioned motion completion and infilling, as well as EOM (End of Motion) prediction from a single training objective. We provide comprehensive evaluations for these capabilities and benchmark our method on the ARCTIC and GRAB datasets. Our experiments demonstrate that our method generates more diverse and physically plausible interactions compared to other open-sourced baseline methods.

Modern sequence models, from Transformers to State Space Models, have enabled powerful generative modeling across diverse domains, yet they are typically trained to predict what happens while treating when it happens as a secondary concern. In data-mining settings where events are associated with explicit timing information, this separation can limit temporal reasoning, anomaly detection, and faithful reconstruction of event chronology. A common strategy is to treat timing as an auxiliary signal, training a separate timing model using representations learned solely for event prediction. However, this two-stage approach implicitly assumes that representations optimized for event prediction already contain sufficient temporal structure. We introduce ChronoSSM, an autoregressive State Space Model (SSM) that jointly models events and timestamps with a shared backbone trained using combined token and temporal generation objectives. We compare the joint regime, where temporal supervision updates the backbone, with the two-stage regime, where timing is learned only using the frozen event representations. Across four domains spanning dense and partial timestamp supervision, joint training consistently makes inter-arrival information more recoverable from frozen representations without any systematic degradation in content-generation quality overall. Our results show that temporal supervision can produce more temporally informative representations without materially degrading autoregressive event modeling.

Recurrent neural networks (RNNs) are widely used for sequence learning, yet their application is commonly associated with temporal data, although recurrent computation fundamentally operates on ordered sequences rather than on time itself. Building on this observation, we introduce the Ordered Structural Dependency Hypothesis (OSDH), which proposes that multiple admissible orderings of the same observations may reveal complementary structural dependencies inaccessible through a single sequential organization. To operationalize this hypothesis, we propose the Independent Structural Expert Principle (ISEP), whereby projection-specific sequence models are trained independently before their learned representations are integrated through a dedicated fusion model. As a concrete realization, we present Structural Evolution RNNs (SE-RNNs), which employ conventional RNNs as projection-specific structural experts while preserving the underlying recurrent computation unchanged. Proof-of-concept experiments on three synthetic datasets with substantially different levels of structural complexity demonstrate that the proposed architecture consistently benefits from multiple ordered projections when hidden structural dependencies are present, while remaining competitive on simpler datasets. Since OSDH is independent of the underlying sequence-processing model, the proposed framework naturally extends beyond recurrent networks and may be instantiated using alternative architectures. The results suggest a general computational perspective for exploiting complementary ordered representations across diverse structured learning problems.

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.

Graph neural networks typically propagate information through repeated message-passing layers, coupling the distance over which information travels with the number of nonlinear transformations applied. This coupling can make deep architectures difficult to optimize and can lead to over-smoothing, over-squashing, and the loss of long-range information. Linearized Graph Sequence Models (LGSMs) address this issue by separating information depth from processing depth and treating the successive propagation states of each node as a sequence. However, existing LGSMs construct these sequences using fixed graph operators, limiting their ability to adapt propagation to the input graph, node features, and downstream task. We introduce HOPPER, an end-to-end learnable extension of LGSM that learns how hop sequences should be extracted before they are processed by a modern state-space model. Our framework supports feature-conditioned, structure-aware, graph- and hop-adaptive propagation mechanisms while preserving permutation equivariance. Standard adjacency-based and non-backtracking LGSM sequences arise as special cases of our proposed extractor family. We show that HOPPER is state-of-the-art or competitive across the ECHO-Synth benchmark, and that varying the maximum neighborhood size of message backtracking cancellation (i.e. structural memory window) can optimize accuracy on the LRIM physics-based long-range dependency benchmark. These results demonstrate that learnable sequence extraction provides a flexible and effective approach to long-range graph representation learning.

Organic photovoltaic (OPV) materials are promising candidates for distributed solar energy in tropical regions, yet existing virtual screening tools report static power conversion efficiency (PCE) values at standard testing conditions (STC) that fail to capture the temperature-driven performance degradation experienced under real deployment conditions. Here we introduce a Climate-Native computational framework that forecasts the annual PCE profile of OPV donor molecules under geographically realistic operating conditions. The framework combines GFN2-xTB molecular dynamics with an equivariant graph neural network surrogate ($268$ Neyman-stratified CEP molecules; $120,600$ training geometries; $\sim 1050\times$ speedup over explicit quantum chemistry) and sequential deep learning models trained on annual time series anchored in NASA POWER climate data for Douala, Cameroon, and validated by zero-shot transfer to Yaoundé and Maroua. Applied to $\sim 30,000$ molecules from the Harvard Clean Energy Project (CEP) and validated against $350$ HOPV15 experimental device measurements, the framework demonstrates that sequential models trained on full molecular dynamics trajectories outperform time-averaged baselines ($35\%$-$48\%$ relative MAE improvement over static baselines), confirming that thermal conformational dynamics carry information beyond mean geometry. We further introduce a seasonal stability score that reranks OPV candidates by performance consistency under tropical conditions, identifying molecules whose deployment suitability differs substantially from their static PCE ranking.

Test-time training (TTT) views sequence modeling as an online learning problem in which fast weights are updated by an internal learning rule. Despite the growing number of TTT variants, existing approaches typically hard-code each variant separately, which makes it difficult to design new TTT methods and to isolate the role of each component. To address this, we propose Modular TTT, a framework that represents the inner learner as a directed acyclic graph and exposes the fast-weight network, loss function, learning rate, weight decay, and normalization as explicit design dimensions. Modular TTT automatically composes primitive-level train-view forward, train-view backward, and causal query-view rules into the full graph-level TTT computation, including the fast-weight state transition. Using Modular TTT, we systematically ablate the components of TTT and find that small learning-rate initialization, weight decay, and a single-layer nonlinearity improve performance, while MSE and inner-product losses perform similarly. Deeper fast-weight networks and normalization tend to hurt performance because they induce excessively large activations, while residual connections and gating provide little measurable benefit. Guided by these findings, we train the best resulting variant as 410M- and 1.45B-parameter models on 100B tokens, and observe training loss and benchmark performance comparable to Gated DeltaNet.

Merchant risk control at large payment platforms screens tens of millions of merchants daily, where false positives harm legitimate merchants and false negatives leave harmful activity undetected. The hardest cases require jointly understanding a merchant's textual profile and long behavioral sequence. Large language models (LLMs) excel at text but cannot natively model such sequences, while adapting them often causes catastrophic forgetting. We present SeqLLM, a framework that adds behavioral-sequence modeling to a pretrained LLM while preserving its language ability. SeqLLM combines three components: a compact discrete vocabulary that represents behavioral events as native tokens; a lightweight projector, trained with a two-stage alignment curriculum, that grounds these tokens in the LLM's semantic space; and prefix-guided capability injection, which acquires sequence-modeling ability through task-prefixed supervised fine-tuning rather than continual pre-training. SeqLLM is deployed at WeChat Pay, screening millions of merchants daily. Against the production DeepSeek-based LLM baseline, it raises screening precision from 92.0% to 97.5%. Its pretrained behavior-token embeddings also improve Precision@Top-0.01% by 26.8 percentage points in a production fraud detector serving billion-scale transaction traffic. Beyond payments, SeqLLM achieves state-of-the-art results on public recommendation benchmarks. On MovieLens and Amazon, it surpasses the strong User-LLM baseline by up to 32% relative Recall@5 while retaining markedly stronger language ability. On RecIF, it improves Pass@32 by 14.2% over the full OneRec-8B pipeline using only one-fifth of its GPU-days.

Pretrained large language models (LLMs) have demonstrated in-context learning (ICL) capabilities for numerical inference over sequences serialized as text. Prior work has identified and characterized this form of numerical inference primarily through output-level evaluations such as prediction error. However, how numerical information is organized within LLM representations remains much less understood. To study this internal organization, we adopt a graph signal processing perspective in which attention induces a weighted graph over tokens, while token hidden states define signals on its nodes. Quantitative graph-spectral diagnostics and qualitative token-graph visualizations reveal that representations become more clearly differentiated by input dynamical complexity as context length increases. Simpler inputs produce attention-induced token graphs with stronger global connectivity and smoother, spectrally concentrated hidden-state signals, whereas more complex inputs produce more localized graphs and hidden-state signals with broader spectral support and greater high-frequency energy. Together, these findings point to systematic, context-dependent internal signatures associated with numerical ICL that are conserved across model families.

Recurrent linear attention models (RLAs) such as Mamba offer efficient linear-time sequence modeling as an alternative to Transformers, yet their fixed-capacity recurrent states limit long-sequence modeling. Drawing inspiration from hierarchical human memory, we propose Hierarchical Memory Mamba (HMM) to address this limitation. Building upon a pre-trained Mamba backbone, HMM integrates a lightweight working memory that extracts slow paragraph-level semantics (PLS) from the fast sensory memory embedded in the backbone's hidden states. The PLS is subsequently compressed into persistent long-term memory for task-relevant retrieval. The hierarchical processing of semantic information overcomes the representation bottleneck of RLAs and endows HMM cross-task generalization through parametric learning, which is not observed in other long-context enhanced Mamba variants. Evaluations on Passkey Retrieval and LongBench-E tasks demonstrate that HMM improves retrieval success by 34.3--37.1% and reasoning accuracy by 1.6--14.2% over strong Mamba-based models, while adding only 2% extra parameters and with minimal training overhead.

Player-centric ball action spotting requires temporally precise event detection together with actor attribution in crowded, partially observed multi-agent sports videos. Existing Denoising Sequence Transduction (DST) baselines treat the player-role dimension as part of a flattened frame-level representation, which weakens the inductive bias for modeling player-specific temporal evolution and inter-player interactions. To address this limitation, we propose Multi-Entity Denoising Sequence Transduction (ME-DST). ME-DST keeps the role-slot dimension throughout encoding. It uses temporal attention to model the history of each role slot, and spatial attention to exchange information across role slots at each frame. This factorized design gives the model a direct structure for separating within-player evolution from inter-player context. We also add learnable role embeddings, tracking-derived tactical features, and fused visual predictions from X3D-L and Swin3D-S. Experiments on the FOOTPASS dataset show that ME-DST reaches a Micro F1 of 0.778. This improves the strongest official TAAD+DST baseline by 10.3 percentage points. Controlled ablations show that preserving the entity axis and encoding role identity are central to this gain. These results suggest that explicit entity modeling is an effective inductive bias for player-centric sports event understanding.

Solomonoff Induction, or SolInd, provides an ideal unbounded model of a priori sequence prediction but cannot naturally describe extrapolation from a given training dataset, as performed by Large Language Models. We apply de Finetti's theorem on exchangeable distributions to SolInd to produce what we call Hierarchical Solomonoff Induction, or HSI, which maintains a hyperprior over all Solomonoff priors that can be conditioned on previously observed sequences. We extend Wood et al.'s proof that universal mixtures of semimeasures are equivalent to SolInd to show that universal mixtures of these mixtures are also equivalent, proving that HSI=SolInd. We also prove that HSI's excess error on any distribution, compared to its true generator, is bounded by that generator's complexity in the hyperprior. This result is directly comparable to SolInd's prediction error being bounded by the Kolmogorov complexity of the sequence being predicted, and forces HSI's average excess error to converge to 0 as a dataset grows, leading to optimal prediction in the limit. We claim that HSI is an ideal unbounded model of sequence prediction given a dataset in the same way that SolInd is ideal over individual sequences.

This study addresses the Variable Gapped Longest Common Subsequence Problem (VGLCSP), a variant of the classical longest common subsequence problem with additional gap constraints and applications in sequence alignment and time-series analysis. While the two-sequence version has been widely studied using dynamic programming, the generalized multi-sequence form is usually solved with beam search-based heuristics, whose hand-crafted designs often lack robustness. To overcome this limitation, we propose a learning-based approach for automatically designing more effective data-driven heuristics. The heuristics are represented by a neural network with predefined architecture, whose weights are optimized by a genetic algorithm within a neuro-evolutionary framework. The learning process alternates between weight optimization and evaluation within an iterative multi-source beam search procedure, a state-of-the-art method for the problem. Rather than constructing solutions directly, the neural network learns to guide the search process, producing a neuro-evolved heuristic. We further introduce an ensemble heuristic that combines the scores of learned and the best-performing hand-crafted heuristic. Integrated into the iterative multi-source beam search framework, the resulting hybrid approach outperforms existing methods on both synthetic benchmark instances and newly introduced real-world instances with data-driven gap constraints.

Accurate ICU mortality prediction requires modeling irregular clinical observations across heterogeneous entity types. Existing sequence models handle irregular sampling but ignore typed relational structure; existing graph models assume fixed-interval inputs. We introduce the Continuous-Time Heterogeneous EHR Graph (CT-HEG) schema and evaluate which architectural choices drive predictive performance. CT-HEG encodes each ICU stay as a typed, timestamped graph with three node types (visit, vital, lab_event) and 2D edge attributes (t_hours/48, value_norm) encoding timing and value without imputation. We instantiate CT-HEG as CHIRP-Net, a four-layer heterogeneous GATv2Conv network, evaluated on MIMIC-IV v3.1 (31,142 ICU stays, LOS>=48h, 13.4% mortality) with five seeds and bootstrapped confidence intervals, against logistic regression, mTAND, a Transformer, and GRU-D, plus an ablation study. CHIRP-Net achieved 5-seed mean AUROC 0.8449+/-0.0071 (AUPRC 0.4958+/-0.0209); the ensemble achieved AUROC 0.8618 (95% CI: 0.8485-0.8745). Removing reverse edges disconnected observation nodes from the visit readout, cutting AUROC by 0.1968+/-0.0073. Time-attentive edge features contributed 0.0247+/-0.0093 AUROC. Collapsing heterogeneous edge types into one relation (7x fewer parameters) outperformed the full model on all seeds. Post-calibration ECE was 0.0307. Temporal and demographic subgroup analyses were explored but not reported here, pending follow-up work. Bidirectional connectivity was necessary for the model to use its inputs at all, and CT-HEG was reasonably well calibrated after validation-fitted temperature scaling. These results support CT-HEG for irregular EHR data, while external validation, a pre-specified temporal evaluation, and a demographic fairness audit remain necessary before any claim of robustness. Code: https://github.com/nasiruddinstudents-ctrl/chirp-net-mimic-iv.

Variational autoencoders (VAEs) trained on multiple sequence alignments (MSAs) have emerged as powerful generative models for biological sequences, with applications ranging from disease variant prediction to functional RNA design. However, standard biological VAE training treats all sequences as exchangeable, ignoring the rich evolutionary structure that organizes homologous sequences from evolutionarily close to highly divergent. We propose Evolutionary Curriculum Learning (ECL), a training strategy that exploits this structure by progressively exposing the model to sequences of increasing evolutionary distance from sampled anchors, following a power-law expansion schedule. Applied to two architecturally distinct VAE models and two biological domains--protein variant effect prediction with EVE and RNA family sequence generation with RfamGen--ECL improves downstream task performance across five random seeds per configuration. Mean ClinVar classification AUROC rises from 0.981 to 0.989 for p53; for PTEN, ECL attains 1.000 in every seed whereas the baseline is unstable (mean 0.905, falling as low as 0.54). For RNA, ECL raises mean covariance-model bit scores on all three families tested and exceeds its seed-matched baseline in 12 of 15 training runs, though with only three families the effect cannot be established as significant at the family level. Ablation experiments show that progressively expanding the sampled sequences by evolutionary distance outperforms fixed-size neighborhood sampling in addition to uniform random sampling. Evolutionary distance is therefore a useful inductive bias for ordering the training curriculum in biological sequence modeling.

Large language models (LLMs) generate text by auto-regressively sampling the next token. This inherently leads to a many-to-many mapping between prompts and responses, complicating the task of inferring prompts from observed outputs. Prior work on LLM inversion frames prompt recovery as a semantic reconstruction task. They rely on fine-tuning pretrained sequence-to-sequence models on large external datasets--and requiring access to model weights or logits--to generate semantically plausible prompts. In contrast, we present a functional approach to inverting a given LLM in a black-box setting, without auxiliary aids. We train an explicit inverse language model entirely from scratch on data synthetically generated from the target LLM itself. Analogous to forward next-token prediction, our inverse model is trained using previous-token prediction, establishing a generative link between the forward and inverse processes that enables faithful prompt reconstruction. Moreover, it naturally supports diverse prompt reconstructions through sampling, whereby all such prompts induce similar responses under the forward, target LLM. Our approach generalises across datasets and exhibits transferability in reconstructing prompts from responses generated by different LLMs. Further, across the set of token based evaluation metrics for prompt and response reconstructions, our approach outperforms prior work.

We introduce PhiZero, a physical world model built around physical language, a compact discrete representation of world-state transitions. Existing physical world models typically predict future videos directly in pixel space, leaving the underlying world dynamics implicit within high-dimensional visual predictors. Motivated by humans' ability to abstract predictive structure from visual experience and organize it in natural language for explicit reasoning, we learn physical language from in-the-wild videos through self-supervision and use it to explicitly reason about how the physical world evolves. Accordingly, PhiZero adopts a reason-then-render paradigm: it first infers future world evolution as a physical-language sequence and then renders the inferred transitions into videos. Extensive experiments across generation and understanding benchmarks validate the ability of PhiZero to model physically coherent world evolution. We further show its potential for realistic and interactive world modeling, fine-grained action-conditioned simulation, and zero-shot motion transfer.

Predictive process monitoring (PPM) leverages event logs to forecast the future of running process instances, for instance, predicting the next activity, the remaining time until case completion, or the time to the next event. While PPM research in recent years has been dominated by deep sequence models trained from scratch, such as Long Short-Term Memory (LSTM) models, foundation-model approaches---particularly large language models (LLMs)---are increasingly explored for PPM. At the same time, tabular foundation models with in-context learning capabilities offer a promising alternative but have not yet been systematically benchmarked for PPM. Thus, it remains unclear whether classical sequence-based models remain competitive in this evolving landscape. This paper compares the three modeling paradigms both conceptually and empirically through a controlled benchmark across multiple datasets and prediction tasks. The results show that sequence models consistently perform best for next activity prediction, whereas tabular foundation models are competitive on temporal tasks, with LLMs usually lagging behind despite higher cost.

Sybil bots are Ethereum actors that imitate legitimate users to extract airdrop rewards or influence governance. Recent Sybil detection methods increasingly use deep learning and treat blockchain activity as a quasi-linguistic sequence. However, complex sequence models are computationally expensive for real-time monitoring, and their reported performance may be inflated by label leakage from high-signal smart contracts. We ask whether and how organic users, Sybil bots, and MEV bots differ in the structural complexity of their transaction histories; whether sequential models outperform tree-based tabular models once leakage is reduced; whether transaction order or timing provides the stronger behavioral signal; and whether the resulting models are practical for low-latency deployment. Our approach to leakage-aware Sybil bot detection consists of a Blind-Spot protocol and a Transaction Grammar representation of wallet behavior. The former eliminates shortcuts associated with high-signal contracts, whereas the latter models wallets using rhythm, EVM execution structure, and intent. We evaluate this approach on Ethereum actor classification by comparing Transformer and BiLSTM sequence models against XGBoost and SVM baselines. We contribute a framework for leakage-aware Ethereum actor classification and a Transaction Grammar representation of wallet behavior. Our results demonstrate that, under leakage-aware evaluation, XGBoost outperforms Transformer-based sequence models while providing lower latency and estimated energy use.

Sequence labeling is a fine-grained information extraction task, yet existing large language model-based approaches suffer from insufficient domain alignment and low inference efficiency. To address these issues, we propose DIRECT, a framework that addresses these issues through training-time optimization and inference-time rectification. Specifically, DIRECT performs Direct Preference Optimization (DPO) after supervised fine-tuning to strengthen task alignment with human preferences, and introduces a controlled decoding process that enforces fixed output formats and restricts predictions to candidate sets. To further improve efficiency, a template-filling mechanism requires the model to generate only label tokens while reusing prefixed content through the KV Cache, thus reducing redundant computation. Experimental results on eight datasets demonstrate that DIRECT achieves significant improvements in both performance and efficiency compared to existing methods.

Rotary Position Embedding (RoPE) has been widely adopted in transformer-based large language models. However, its log-linear frequency schedule, originally designed to produce long-term attention decay, limits its adoption in domains with more complex distance-correlation patterns, such as temporal periodicity in sequential recommendation. We investigate the expressiveness of general query/key rotations and find that any normalized continuous positive-definite attention modulation function can be approximated by random rotations induced by its own Fourier transform, which we term Random Fourier Rotations. Building on this theory, we propose ClockRoPE for routine modeling in sequential recommendation, where rotation frequencies are derived from periodic attention modulation functions. In online A/B tests, ClockRoPE demonstrates consistent improvements in valued engagement metrics, and has been successfully deployed in production-scale generative retrieval system at a major video-sharing platform.

Long-context recall in linear-time sequence models highlights a tradeoff in how they write to memory. State-based linear models, such as state-space models (SSMs) and linear Transformers, write densely, updating the entire state for each newly arrived token, which leads to interference and makes specific past tokens hard to recover. Sliding-window attention (SWA) exhibits the opposite behavior: it writes sparsely by storing explicit token representations, but only within a fixed window, so recall drops once the relevant token is evicted. Interpolating between these models, we introduce Raven, a linear-time sequence model that maintains a fixed set of memory slots and, at each step, decays and updates only a selected subset via learned, input-dependent routing. This lets Raven mitigate SWA's position-based overwriting and hard eviction while reducing interference from dense state updates in SSMs, thereby preserving long-range content much more effectively. Across recall-intensive benchmarks, Raven is competitive with or outperforms prior linear-time baselines, achieving strong long-context recall where both SWA and SSMs sharply degrade. It remains effective when extrapolating to context lengths as large as 16x its training length, with similar gains in hybrid architectures.

The rapid evolution of generative models has unlocked new potentials in protein binder design, a pivotal task in structural biology, by facilitating end-to-end generation via joint sequence-structure modeling or hallucination. However, existing approaches are predominantly implemented under a single-target, single-state assumption, limiting their ability to model multi-target or multi-state interactions required for advanced function-oriented protein design. Here, we introduce Chamaileon, which unifies multi-target and multi-state binder design by formulating the problem as cross-context binding landscape modeling. The framework is underpinned by a training paradigm termed In-Context Complex Co-Design (I3CD) for context-aware sequence-structure co-modeling. During inference, we employ Mixture-of-Paths Sampling (MoPS), a scalable strategy that optimizes a single sequence across contexts while alleviating the scarcity of high-quality multi-conformational paired data. Extensive evaluation on our newly constructed benchmark, CROSS, demonstrates that Chamaileon effectively generates sequences adaptable to diverse conformational landscapes and multi-target requirements. The code is available on https://github.com/caohengyuan/Chamaileon.

Multiple Sequence Alignments (MSAs) provide protein language models with explicit evolutionary context, but their large depth makes subsampling unavoidable under limited token budgets. Existing strategies, including random selection, identity-based filtering, and diversity-driven sampling, are effective heuristics, yet provide limited control over the evolutionary signals retained in the subset. In this work, we recast MSA subsampling as an explicit optimization problem, where key evolutionary measures, including query identity and diversity, are treated as controllable objectives. Building on this view, we introduce AP-REASONER, an Affinity-Propagation-based factor-graph approach. With evolution-aware unary factors, exemplar-consistency factors, and two control knobs, AP-REASONER performs factor-graph reasoning through message passing to infer a fixed-budget MSA subset. Experiments on long-range contact prediction and conformational ensemble prediction show that AP-REASONER outperforms baseline subsamplers on structure-sensitive downstream tasks and enables controllable recovery of alternative protein conformations. These results highlight the value of modeling MSA subsampling as a controllable optimization problem, where factor-graph reasoning offers an effective alternative to heuristic selection.

Protein language models learn transferable sequence representations. However, because they primarily model contextual dependencies along amino-acid sequences, their training objectives do not explicitly constrain the model to learn three-dimensional residue contacts formed after folding . Here, we introduce LC-SEPLM (Long-range Contact-supervised ESM Protein Language Model), which adapts ESM2 with LoRA and long-range residue-pair contact supervision while retaining sequence-only downstream inference. Pair-specific queries use cross-attention over the complete sequence to extract global sequence context associated with long-range spatial contacts. To expose the model to diverse structural information, we trained LC-SEPLM on 500,000 AlphaFold Swiss-Prot proteins. In downstream evaluation, LC-SEPLM improved all eight protein-level tasks relative to ESM2. The largest gain occurred in remote-homology recognition, where macro-F1 increased from 0.6122 to 0.6769 (+0.0647, or 6.47 percentage points). On the official ESM-S EC benchmark, LC-SEPLM also outperformed ESM-S with a maximum absolute gain of 0.1771. These results support residue-pair contact supervision as a bounded route for introducing structural information into protein sequence representations while preserving sequence-only inference.

Temporal point processes (TPPs) provide a general and flexible framework for modeling sequences of events in continuous time. Neural networks have been successfully employed to model TPPs in a highly expressive and data-driven way. Neural TPPs are typically trained via Maximum Likelihood Estimation (MLE) by minimizing the negative log-likelihood (NLL), which depends on both the conditional intensity function (CIF) and its integral over time, the compensator. Recent neural TPP approaches enable exact evaluation of the NLL without numerical integration. However, these methods typically model the compensator rather than the CIF directly, impose constraints on the neural network architecture, and are computationally expensive during training, as event contributions to the NLL are evaluated sequentially rather than in parallel. In this work, we propose a novel neural TPP model that directly parametrizes the CIF as a non-negative combination of B-spline basis functions, whose coefficients are predicted by a neural network. This formulation enables exact evaluation of the NLL, preserves full flexibility in the neural architecture, allows efficient parallelization during training, and naturally supports CIF smoothness regularization through the integrated squared second derivative. Experiments on both synthetic and real-world datasets show improved computational efficiency and predictive accuracy compared to the reference neural TPP baseline.

We propose a hybrid approach for user-centric modeling of transactional event sequences that combines contrastive representation learning (CoLES) with State Space Models (SSMs). While contrastive methods yield high-quality compressed user representations, existing encoders -- RNNs and Transformers -- suffer from vanishing gradients or quadratic complexity, respectively. Mamba, a selective SSM, efficiently handles long-range dependencies but remains underexplored for personalized user analysis. We investigate two integration strategies: (1)~initializing the Mamba hidden state with a CoLES embedding, and (2)~prepending the projected CoLES embedding as a prefix token to the input sequence. Both approaches supply the model with an informative user prior from the first step. Experiments on three public datasets -- Age (multiclass age-group prediction), MBD (multi-label product acquisition), and Taobao (binary purchase prediction) -- demonstrate consistent improvements over standalone Mamba and CoLES with a linear classifier, with the hybrid models converging 2--3$\times$ faster than the plain SSM baseline. Explainability analysis via discretization-step maps and Integrated Gradients reveals selective event filtering on behavior-rich datasets and identifies the most informative transaction features.

Knowledge distillation (KD) is a standard approach for compressing sequence-to-sequence models, but its per-sample effects are rarely examined. On the BanSum Bangla summarization benchmark, we find that standard KD improves ROUGE-L by only +0.0003 over a cross-entropy baseline, and that approximately 51.3% of training samples are estimated to actively harm student validation loss under standard KD. We propose two complementary reliability-aware distillation methods. CHAD (Counterfactual Harm-Aware Distillation) measures per-sample KD usefulness via gradient alignment with the validation loss direction and trains a lightweight gate that generalizes this counterfactual judgment to the full training set. EWAD+CPDP combines token-level entropy-weighted adaptive distillation with a capacity-proportional geometric constraint from a second, vocabulary-incompatible teacher. On BanSum, both methods substantially outperform standard KD: CHAD by +0.0173 ROUGE-L and EWAD+CPDP by +0.0219 ROUGE-L, where standard KD itself improves ROUGE-L by only +0.0003; despite using only 60M parameters, both outperform a fine-tuned Qwen 2.5-3B model (50x larger). We further evaluate the stronger method, EWAD+CPDP, across 15 typologically diverse XL-Sum languages organised into three sets, beating the CE-only baseline on 10/15 languages; gains are most reliable where the two teachers contribute complementary signal, and weakest where they have saturated or jointly weak target-language coverage. We release code and trained models to support reproducibility and further research on selective distillation.

User modeling is a critical task in a variety of personalized systems. Recognizing their effectiveness in learning from graph-structured data, Graph Neural Networks (GNNs), particularly Graph Convolutional Networks (GCNs), are increasingly employed for user modeling. However, existing approaches typically treat different relation types in a graph as homogeneous, limiting their ability to capture richer semantics and construct more informative user models. While multi-relational GNNs (MR-GNNs) have been adopted for representation learning and recommendation, their application for user modeling remains unexplored. Moreover, existing GNN-based user modeling approaches ignore the user interaction sequence. To address these research gaps, in this work we propose MR-ConceptGCN, a novel fully unsupervised approach focused on concept-based sequential learner modeling using multi-relational GCNs (MR-GCNs). MR-ConceptGCN effecively combines Personal Knowledge Graphs (PKGs), MR-GCNs, and the pre-trained language model SBERT to obtain enhanced relation- and semantic-aware representations of the PKG items. The enriched embeddings of the knowledge concepts that a learner did not understand when interacting with learning materials in CourseMapper are then used to construct a sequential learner model that combines long-term and short-term learner interactions. We report the results of an online user study (n = 31), demonstrating the benefits of MR-ConceptGCN in terms of several important user-centric aspects including accuracy, usefulness, diversity, and satisfaction with an educational recommender system.

Cross-domain sequential recommendation (CDSR) aims to model users' dynamic interest transitions and sequential patterns across multiple domains. Recently, generative recommendation (GR) has emerged. It first learns semantic identifiers (SIDs) from item semantics and formulates recommendation as autoregressive generation. However, existing methods face two critical issues: (1) they ignore collaborative correlations across domains during tokenization, and (2) they adopt inefficient decoding strategies, such as beam search, during generation, which hinders real-time deployment. To address these limitations, we propose GenCDSR, an effective and efficient generative framework for CDSR. Specifically, we design a cross-domain hybrid tokenization mechanism with a multi-tower architecture to jointly capture cross-domain commonalities and domain-specific distinctions through hierarchical shared-specific and fine-grained codebooks. Furthermore, we develop a cross-domain serial-parallel decoding strategy that leverages the hierarchical SID structure to partially parallelize generation, significantly reducing inference latency while preserving generation consistency. Experiments on three public datasets show that GenCDSR achieves an average accuracy improvement of 1.5 percent and an average inference latency reduction of 85.1 percent compared with state-of-the-art baselines. The implementation code and datasets are available online: https://github.com/Applied-Machine-Learning-Lab/RecSys2026_GenCDSR.

Transformers with relative positional encodings often extrapolate to sequences longer than those seen during training, whereas transformers with learned absolute encodings typically do not. This is a robust empirical regularity, and the explanations offered for it so far are chiefly about expressivity, that is, about whether a length-generalizing solution exists. We give an optimization explanation. On a minimal fixed-offset retrieval task that isolates positional selection, the gap is governed by the implicit bias of the trained attention head: among the many solutions that fit short sequences, which one gradient descent actually selects. We prove that rotary encodings make the attention logit a function of relative offset alone, an exact equivariance, so whatever selection rule is learned at training lengths is reproduced verbatim at every longer length. Learned absolute encodings instead leave out-of-range positions unconstrained, and the trained head pins to a fixed absolute position inside the training range. We characterize the learned rotary rule as a low-rank ``carrier'' kernel aligned with the target offset, and we derive the resulting graceful accuracy decay as an attention-dilution law; both predictions are confirmed across seeds and offsets. A linear-attention control shows the mechanism is specific to softmax: without normalization, training selects a min-norm interpolant that does not extrapolate. The phenomenon, the equivariance, and the carrier all transfer to a multi-layer, multi-head transformer trained on a full-sequence length-generalization task. The account connects the implicit bias of attention, implicit bias for extrapolation in recurrent models, and the learning side of the RASP-L conjecture.

In a previous paper, we began the study of sequence prediction algorithms adapted to stringological word complexity measures. One measure we considered was left-to-right (most-significant-digit-first) automaticity. Here, we show a statistically and computationally efficient algorithm adapted to the dual'' right-to-left (least-significant-digit-first) automaticity, which turns out to be substantially different for our purpose. We also demonstrate a prediction algorithm for a more expressive measure that we call arithmetic repetition complexity''. In particular, the latter can be used for predicting the so-called mix-automatic sequences.

As scalability becomes increasingly important in recommendation modeling, recent architectures have advanced the modeling of two broad sources of ranking signals along separate paths: non-sequence features, including user, item, context, and cross features; and sequence features from user behavior histories. Wukong and HSTU have emerged as representative scalable backbones for these paths: Wukong scales high-order non-sequence feature-interaction modeling, while HSTU scales long user-behavior sequence modeling. Despite their complementary strengths, practical architectures that combine these two types of feature modeling remain underexplored. We present WHALE, a scalable unified recommendation architecture that jointly models non-sequence and sequence features on top of Wukong and HSTU. Each WHALE layer contains a Wukong module, an HSTU module, and an attention-based fusion module in which Wukong-derived interaction representations query HSTU-derived behavior representations. This design keeps both backbones active throughout the network and enables progressive Wukong-HSTU exchange, allowing high-order feature crosses to repeatedly retrieve fine-grained evidence from long user histories. To make WHALE practical for industrial deployment, we introduce customized Triton kernels and other model-systems co-design techniques to improve training and inference efficiency. On large-scale industrial recommendation data, WHALE achieves consistent gains in offline experiments. Additionally, it delivers positive online gains with a modest serving-throughput trade-off. The method has been deployed in production systems. Overall, WHALE provides a practical example of how these two sources of information can be scalably unified in an industrial recommendation model.

Accurate timing prediction at the register-transfer level (RTL) is a longstanding challenge in design automation. Existing graph-based methods struggle with limited receptive fields, high complexity, and a lack of signal directionality. We present RTL-Sequencer, a novel sequence-based paradigm that enables scalable RTL timing prediction via linearizing logic cones by breadth-first traversal and applying modern linear sequence models. Furthermore, sequence models are customized by four synergistic techniques, including sequence shuffling, bidirectional modeling, differentiable modeling, and a hybrid graph-sequence architecture. Extensive experiments demonstrate significant improvements of RTL-Sequencer over state-of-the-art baselines, advancing early-stage timing optimization.

Self-attention is a ubiquitous primitive in modern sequence models, yet its operator-level geometry is only partially understood. We view a token sequence as a vector field over the token-position graph and identify attention as a connection walk: messages are aggregated by a nonnegative walk matrix while being transported along each edge by a learned linear map. Within this framework, we prove that single-head attention (SHA) is exactly a connection propagation step with constant transport, and that multi-head attention (MHA) is exactly a single edge-dependent connection walk whose effective transport is an attention-gated mixture of headwise transports. We further clarify the conditions under which the corresponding generator reduces to a random-walk connection Laplacian, highlighting the roles of stochasticity, reversibility, and metric-compatible transports. Empirically, we find that trained Transformers across scales (from 124M to 8B) and structures (encoder/decoder) exhibit geometric structure consistent with our theory: effective attention graphs converge to stable geometric operators in deeper layers, learned transports self-organize into approximate scaled isometries, and both phenomena strengthen consistently with scale. Overall, the paper provides a precise connection-walk formalism that links self-attention to classical geometric operators, along with a set of operator-level tools for analyzing transformer models from a geometric perspective.

State Space Models (SSMs) have emerged as a powerful paradigm for efficient long-sequence modeling, offering parallel training and fast linear-time recurrent inference. However, like other recurrent architectures, SSMs must compress an unbounded history into a fixed-size state, which limits context retention and makes precise retrieval over long-range context inherently difficult. To overcome this limitation, we propose Delay State Space Models (DSSMs), a delay differential equation (DDE)-inspired extension of diagonal SSMs that augments discrete SSM recurrences with explicit delayed-state feedback. Making explicit delayed feedback practical requires new stability parameterization, history management, and FFT-training tools. We address these challenges with a practical discretization and parameterization grounded in a simple delay-independent stability condition. To bypass direct time-domain kernel construction, we derive the DSSM transfer function and compute kernels in the frequency domain, using a kernel contour shift to suppress aliasing and recover accurate FFT training. Empirically, DSSMs substantially improve targeted delayed-retrieval tasks while outperforming S4D on most standard sequence metrics and remaining close on the others.