Sequence Modeling

Latest papers 265

Mar 16, 2026cs.LG

Training-Free Generation of Protein Sequences from Small Family Alignments via Stochastic Attention

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.
Mar 11, 2026cs.LG

Beyond Pairwise Attention: Higher-Order Modular Attention for Efficient Sequence Learning

Sequence modeling tasks can involve intrinsic higher-order dependencies, while standard self-attention assigns scores to token pairs and does not explicitly parameterize such interactions. We introduce Higher-Order Modular Attention (HOMA), which fuses pairwise attention with an explicit triadic attention pathway made tractable through overlapping blocks, local windows, and a low-rank projection. We compare HOMA with matched pairwise and purely triadic baselines on controlled PARITY and MATCH3 tasks, as well as TAPE benchmarks. HOMA is competitive with or outperforms the baselines, with its clearest advantages when the underlying dependencies extend beyond the explicitly modeled triadic order. These advantages are accompanied in several settings by faster convergence and improved parameter efficiency, with the learned nonlinear fusion providing an effective mechanism for combining the pairwise and triadic representations. Overall, our results provide empirical evidence that HOMA is an effective attention design when task structure extends beyond pairwise interactions.
Mar 3, 2026cs.AI

Retrievit: In-context Retrieval Capabilities of Transformers, State Space Models, and Hybrid Architectures

Transformers excel at in-context retrieval but suffer from quadratic complexity with sequence length, while State Space Models (SSMs) offer efficient linear-time processing but have limited retrieval capabilities. We investigate whether hybrid architectures combining Transformers and SSMs can achieve the best of both worlds on two synthetic in-context retrieval tasks. The first task, n-gram retrieval, requires the model to reproduce an n-gram that succeeds the query within the input sequence. The second task, position retrieval, presents the model with a query token and requires it to perform a two-hop lookup: first locating the corresponding element in the sequence, and then outputting its positional index. Under controlled conditions, we assess data efficiency, length generalization, robustness to out of domain training examples, and learned representations across Transformers, SSMs, and hybrid architectures. We find that hybrid models outperform SSMs and match or exceed Transformers in terms of data efficiency and extrapolation for tasks that require precise information retrieval from the input context. However, Transformers maintain superiority in position retrieval tasks. Through representation analysis, we discover that SSM-based models develop locality-aware embeddings where tokens representing adjacent positions become neighbors in embedding space, forming interpretable structures. This property is absent in Transformers as causal attention is sufficient for acquiring positional associations, and the introduction of positional encoding amplifies this behavior, leading to improvement in data efficiency. SSMs on the other hand update their internal representations incrementally and without positional encodings, are required to learn these associations. Our findings reveal fundamental differences in how Transformers and SSMs, and hybrid models learn positional associations.
Feb 24, 2026cs.IR

HiSAC: Hierarchical Sparse Activation Compression for Ultra-long Sequence Modeling in Recommenders

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.
Feb 20, 2026cs.LG

Adaptive Time Series Reasoning via Segment Selection

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.
Feb 16, 2026cs.LG

Learning State-Tracking from Code Using Linear RNNs

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.
Feb 11, 2026cs.LG

PRISM: Parallel Residual Iterative Sequence Model

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-LL accumulation, structurally expanding the update scheme beyond the single-step Rank-11 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/.
Feb 6, 2026quant-ph

Quantum Attention by Overlap Interference: Predicting Classical and Many-Body Quantum Sequences

We propose a variational quantum implementation of self-attention (QSA)-the core operation in transformers and large language models-which predicts future elements of a sequence by forming overlap-weighted combinations of past data. At variance with previous approaches, our QSA realizes the required nonlinearity through interference of state overlaps and a degree-kk polynomial kernel, and estimates a loss based on Rényi-1/21/2 entropic functionals via two observables' expectation values, avoiding the decoding of amplitude-encoded predictions into classical probabilities. QSA also accommodates a constrained, trainable data-embedding tying state overlaps to data-level similarities. Its dominant end-to-end training complexity scales as O(μ−1k2Td)O\left(μ^{-1}k^2Td\right), versus O(Tdk+1)O\left(T d^{k+1}\right) of the fairest classical comparison, with μμ a training signal; we show numerically that this allows a complexity advantage in the regime where sequence length TT dominates the embedding size dd. In simulations, our QSA-based quantum transformer learns sequence prediction on classical data and on many-body transverse-field Ising trajectories-establishing trainable attention as a practical primitive for quantum dynamical modeling.
Feb 5, 2026cs.LG

Two Stages of Folding: Convergent Mechanisms in AI Protein Folding Trunks

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.
Feb 2, 2026cs.LG

Efficient Neural Controlled Differential Equations via Attentive Kernel Smoothing

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.
Jan 17, 2026cs.CV

Learning Language-Driven Sequence-Level Modal-Invariant Representations for Video-Based Visible-Infrared Person Re-Identification

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.
Jan 12, 2026cs.CL

From Word Sequences to Behavioral Sequences: Adapting Modeling and Evaluation Paradigms for Longitudinal NLP

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 behavioral sequences\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 (cross-sectional\textit{cross-sectional}) and/or time (prospective\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 coarseness\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 behavior-sequence\textit{behavior-sequence} paradigms for NLP.
Dec 26, 2025cs.LG

DuaDeep-SeqAffinity: Dual-Branch Deep Learning for Tri-Stream Sequence-Based Antibody--Antigen Affinity Prediction

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.
Dec 22, 2025cs.LG

Lag Operator SSMs: A Geometric Framework for Structured State Space Modeling

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.
Nov 19, 2025cs.CV

Scriboora: Rethinking Human Pose Forecasting

Human pose forecasting predicts future human poses from past observations for applications including action recognition, sports analysis, and human-robot interaction. However, progress in the field is difficult to assess because reported results often rely on heterogeneous preprocessing, inconsistent metric implementations, and partially released artifacts. This paper re-examines human pose forecasting as an evaluation problem by auditing a wide range of recent forecasting methods, identifying several reproducibility issues, and introducing a unified training and evaluation pipeline for absolute pose forecasting. Under this unified protocol, mature cross-domain sequence models adapted from speech recognition provide strong baselines and obtain the lowest errors among the evaluated models. To study deployment-relevant noise, a paired clean/detector-noisy dataset variant is introduced using poses generated by a pose-estimation model. The experiments show that detector-generated poses cause substantial performance degradation compared with clean motion-capture inputs, but that part of this degradation can be recovered by adapting the forecaster on detector-generated pose sequences.
Sep 28, 2025cs.LG

HyMaTE: A Hybrid Mamba and Transformer Model for EHR Representation Learning

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.
Sep 25, 2025cs.LG

Aligning Inductive Bias for Data-Efficient Generalization in State Space Models

The remarkable success of modern AI has been closely tied to scaling laws, yet the finite supply of high-quality data makes data efficiency--learning more from less--an increasingly important frontier. A model's inductive bias is a critical lever for data efficiency, but foundational sequence models such as State Space Models (SSMs) often rely on fixed, task-agnostic biases. When this fixed prior is misaligned with the underlying structure of a task, the model may require additional samples to overcome its own bias before learning the relevant signal. In this work, we introduce a principled framework for understanding and aligning the inductive bias of linear time-invariant SSMs. We first formalize this bias through an SSM-induced kernel and show theoretically and empirically that its spectrum is governed by the model's frequency response. This characterization motivates Task-Dependent Initialization (TDI), a fast power-spectrum matching method that aligns the initial SSM bias with the task's spectral characteristics before downstream training. Across controlled synthetic experiments, trainable one-layer SSMs, and deep SSMs on diverse real-world benchmarks, TDI can improve data-efficient generalization primarily when task-relevant spectral structure is present and the default SSM bias is spectrally mismatched. Our results provide both a theoretical lens and a practical tool for task-adaptive inductive bias, suggesting a path toward more data-efficient sequence modeling.
Aug 22, 2025cs.LG

Hybrid Sequence Modeling and Reinforced Verification for Controllable Target-Conditioned Decision Making

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.
Feb 3, 2025cs.IR

Query Brand Entity Linking in E-Commerce Search

Associating user search queries with the correct brand entity is critical for e-commerce product retrieval, yet remains challenging due to the brevity of queries (three to four words on average), their lack of grammatical structure, and a catalog of hundreds of thousands of distinct brands. We formulate this as a brand entity linking task and develop two complementary solutions deployed at scale: (1) a cascaded pipeline that first detects brand mentions via sequence labeling and then disambiguates against a brand knowledge base, and (2) a single-stage approach that frames linking as extreme multiclass classification, directly mapping queries to brand identifiers. Through extensive multilingual evaluation (11 languages) and a controlled online experiment, we demonstrate that the proposed methods substantially improve brand recall while maintaining high precision, leading to measurable gains in customer engagement.
Sep 14, 2024cs.IR

Unleash LLMs Potential for Sequential Recommendation by Coordinating Dual Dynamic Index Mechanism

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 (ED2^2) 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 ED2^2, achieving an average improvement of 19.62% in Hit-Rate and 21.11% in NDCG.
Jul 9, 2024cs.LG

RotRNN: Modelling Long Sequences with Rotations

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.
Feb 26, 2024q-bio.NC

ELiSe: Efficient Learning of Sequences in Structured Recurrent Networks

Behavior can be described as a temporal sequence of actions driven by neural activity. To learn complex sequential patterns in neural networks, memories of past activities need to persist on significantly longer timescales than the relaxation times of single-neuron activity. While recurrent networks can produce such long transients, training these networks is a challenge. Learning via error propagation confers models such as FORCE, RTRL or BPTT a significant functional advantage, but at the expense of biological plausibility. While reservoir computing circumvents this issue by learning only the readout weights, it does not scale well with problem complexity. We propose that two prominent structural features of cortical networks can alleviate these issues: the presence of a certain network scaffold at the onset of learning and the existence of dendritic compartments for enhancing neuronal information storage and computation. Our resulting model for Efficient Learning of Sequences (ELiSe) builds on these features to acquire and replay complex non-Markovian spatio-temporal patterns using only local, always-on and phase-free synaptic plasticity. We showcase the capabilities of ELiSe in a mock-up of birdsong learning, and demonstrate its flexibility with respect to parametrization, as well as its robustness to external disturbances.
Aug 25, 2023eess.SY

From system models to class models: An in-context learning paradigm

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.
Date pendingcs.LG

When do cheap embeddings beat protein language models? A theoretically-grounded hashing sketch for biological sequence classification

\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 kk-mer counts into a small hash table via the deterministic MurmurHash function, and we cast it as a randomized sketch of the classical kk-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 kk-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: 0.8540.854 vs.\ 0.8070.807 accuracy; macro-F1 0.6840.684 vs.\ 0.4010.401).
Date pendingcs.CR

SIDE: Sensor Impersonation Detection at the Edge via Sequence Prediction

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.