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arXiv

PRISM: A Predictive Protocol for Permutation Optimization via Landscape Diagnostics

Blessings Mambwe

Permutation optimization arises whenever the components of a system are fixed but their ordering affects performance. We introduce PRISM, a predictive protocol for permutation optimization that measures a fitness landscape before selecting a search strategy. PRISM uses inexpensive landscape diagnostics, including one-step move autocorrelation and fitness-distance correlation, to predict useful mutation operators, identify when structured search is likely to outperform random sampling, and detect regimes in which search provides little advantage. Across synthetic permutation landscapes, neural architecture benchmarks, scientific machine learning pipelines, and large-language-model instruction ordering, the protocol makes testable predictions about search behavior before optimization begins. Exhaustive instruction-ordering experiments reveal substantial performance variation induced solely by permutation, while cross-model experiments show that useful ordering structure can transfer across model families and task difficulty. Additional experiments demonstrate that instruction ordering remains consequential after prompt wording is optimized, indicating that content optimization and ordering optimization are complementary. The results position PRISM not as a universally superior optimizer, but as a framework for determining when permutation search is useful, which representation and operator should be used, and when simpler alternatives are preferable.

arXiv

Eikonal Regularisation in Physics-Informed Neural Networks for Three-Dimensional Level-Set Advection: Transferability of Two-Dimensional Design Principles

Muhammad Akbar Khan

Physics-informed neural networks applied to the level-set formulation of interface advection commonly augment the residual and initial-condition losses with an eikonal regulariser, penalising the deviation of $\|\nablaϕ\|$ from unity. A previous two-dimensional study identified this weight as the dominant hyperparameter and found its optimum shifts by four orders of magnitude between rigid-body and deforming flows, but left open whether these principles transfer to three dimensions and whether single-seed results survive run-to-run variability. We answer both by repeating the weight selection across four 3D benchmarks (translating sphere, rotating sphere, slotted sphere, reversed vortex), sweeping six weights with three seeds at full training budget under a pre-registered selection rule. The ordering transfers: the selected weight tracks how far the exact solution departs from the signed-distance property, spanning four decades from $10^{-1}$ where it holds exactly to $10^{-5}$ where the interface is stretched. Values transfer only benchmark by benchmark; two of four carry over unchanged and two do not, so inheritance must be verified. The multi-seed protocol reveals that at small weights the seed-to-seed standard deviation equals the error itself, and the regulariser reduces it by more than an order of magnitude, buying reproducibility as well as accuracy. We benchmark against a fifth-order WENO solver on identical grids and error measures; the classical scheme is more accurate on all four problems, by two orders of magnitude on smooth rigid advection, with a margin that narrows with geometric difficulty and is smaller in volume conservation than in the field norm. Finally, we show that the relative $L_2$ error cannot certify the preservation of thin features, and report a feature-restricted measure that can.

arXiv

Spatial Heterogeneity-Aware Multi-Hazard Susceptibility and Risk Mapping at Regional Scale

Aswathi Mundayatt, Siddharth Anil, Hitanshu Seth, Jaya Sreevalsan-Nair

Floods and landslides often co-occur, but their relationships with environmental controls vary spatially. This study develops a spatial heterogeneity-aware framework for flood-landslide susceptibility and relative-risk mapping in Kerala, India, and Nepal. It combines 15 km x 15 km grid cells with region-specific contextual zones and compares proximity-gated cross-zone training (S1) and ecology-gated zone-constrained training (S2). S1 permits geographically nearby models to be assigned across contextual boundaries, whereas S2 restricts model development and assignment to the same zone. Random Forest models for each hazard use strategy-specific predictor sets and are evaluated on spatially held-out test samples. Susceptibility surfaces are integrated with CRITIC-weighted exposure and vulnerability indices to produce hazard-specific and nine-class bivariate relative-risk maps. S1 achieved higher mean accuracy, precision, recall, F1-score, AUC-ROC, and PR-AUC for both hazards and regions. The largest difference occurred for Nepal flood susceptibility, where AUC-ROC increased from 0.728 under S2 to 0.886 under S1 and PR-AUC from 0.512 to 0.823. S2 produced lower Brier scores for both Nepal hazards and retained zone-specific differences in predictor selection, SHAP rankings, and response patterns, particularly in Kerala. Both strategies reproduced flood-prone lowland and landslide-prone upland patterns but differed in susceptibility and risk classes. Bivariate risk-map agreement was 0.521 in Kerala and 0.711 in Nepal, with allocation disagreement exceeding quantity disagreement in all S1-S2 comparisons. Susceptibility-to-risk correspondence remained below 0.350, showing that exposure and vulnerability changed priority locations. Overall, cross-zone learning strengthens regional discrimination, while zone-constrained learning preserves environmental differences, supporting their integration.

arXiv

The Neural Division of Labor: Biologically-Inspired Modular Architectures for Robust Neuromorphic Computing

Maksim Bazhenov, Serafim Grubas, Vakhtang Putkaradze

Biological neural systems achieve high efficiency and robustness through compartmentalized architectures. In contrast, modern artificial neural networks rely on globally entangled structures, which obscure decision logic and suffer from catastrophic forgetting. Here, we report a Decomposable Spiking Neural Network (D-SNN) that eliminates global synaptic entanglement by structurally isolating classification pathways into independent experts. Optimized via a bio-inspired push-pull loss function, the D-SNN achieves competitive accuracies on MNIST, Fashion-MNIST, and CIFAR-10/100 benchmarks. This modular approach matches the performance of fully dense networks while utilizing an order of magnitude fewer parameters. In addition, our networks operate with up to several orders of magnitude lower firing rates and fewer synaptic operations. Furthermore, physically severing connections between experts provides inherent protection against catastrophic forgetting during sequential learning. Crucially, these isolated pathways generate auditable neural signals, increasing decision transparency. This biomimetic, verifiable architecture establishes an efficient foundation for deploying deterministic neuromorphic intelligence in resource-constrained edge environments.

arXiv

Machine-Learning-Based Diagnostic Framework for Passive Ultrasonic Detection of Railway Wheel Defects

Aashish Shaju, Steve Southward, Mehdi Ahmadian

Reliable identification of railway wheel defects is important for safety and maintenance. This study develops a machine-learning-based diagnostic framework for multi-class defect identification using passive air-coupled ultrasonic acoustic emission signals. Data were collected from eleven full-scale railway wheelsets representing nine health states. Time- and frequency-domain features were evaluated using Kruskal-Wallis statistical testing and mutual-information analysis to identify the most discriminative indicators. A Random Forest classifier was then trained using the selected features with stratified 5-fold cross-validation. The model achieved a balanced accuracy of approximately 0.66 and a Macro-F1 score of 0.65 across the nine classes. Decay rate, kurtosis, skewness, and envelope low-frequency power emerged as the most influential features, while a compact subset of features retained most of the classification performance. The results demonstrate the feasibility of combining passive ultrasonic sensing, statistical feature selection, and supervised machine learning for non-contact railway wheel defect classification and provide a foundation for future field-deployable inspection systems.

arXiv

Stateful CARS: Exact Cross-History Reuse for Policy-Constrained LLM Agents

Ibne Farabi Shihab, Md Najmus Swaqeeb, Abu Sa-Adat Mohamed Moon-Im Al Ahsan

Tool-using language-model agents face constraints whose meaning changes with observations and prior actions. We study exact sampling from the model distribution conditioned on a hard stateful validator while reusing invalidity certificates across histories. Stateful CARS freezes a bank of sound state--continuation schemas within each attempt and removes every trajectory containing a certified continuation at a matching abstract state. An exact residual Doob transform samples from the resulting proposal. We give a checkable future-validity bisimulation condition, prove schema soundness, adaptive exactness, i.i.d.\ outputs, almost-sure termination, monotone acceptance, and compression invariance, and characterize computation by the number of reachable full-history product states. This number can be exponential for a history-dependent language model; the evaluated method therefore makes no generic finite-trie scalability claim. On enumerable workflows, its analytic law matches the valid conditional to $10^{-16}$ at validity probability $6\times10^{-8}$, whereas state-aware local decoding can be $0.97$ away. A matched comparison is negative: observation-keyed official CARS is cheaper in sampler steps (root/Stateful ratio $0.942$ $[0.934,0.951]$), and the Qwen comparison is null ($0.99$ $[0.90,1.08]$). Cross-history transfer helps only in an internal matched-key ablation ($1.27\times$). Thus the evidence supports exact schema-induced conditioning, not a systems advantage over CARS.

arXiv

Learning under Opponent Unawareness in Linear-Quadratic Stochastic Games

Dantong Chu, Xuefeng Gao, Yufei Zhang

As firms increasingly deploy machine learning for strategic decision-making, understanding algorithmic interactions has become central to operations research and economics. This paper studies learning in infinite-horizon, nonzero-sum linear-quadratic stochastic games under a radically uncoupled information structure, where players are either unaware of opponents or strategically oblivious, observing only a common state and their own action history. Under this minimal information, we analyze an asynchronous decentralized learning process in which each player independently runs a single-agent $ε$-greedy iterated least-squares algorithm. We prove that, despite being unable to identify the system parameters, players' learning dynamics converge almost surely to the complete-information Nash equilibrium and characterize the convergence rate. We then apply the framework to a dynamic Cournot competition with sticky prices. Numerical experiments validate the theoretical results and show that learning under limited information reduces firm profits under both low and high price stickiness, while total surplus declines and market concentration increases when price stickiness is high. Publicly revealing aggregate market output substantially accelerates convergence and mitigates these welfare losses.

arXiv

On the Robustness of LLMs' Internal Representation of Code Correctness

Francisco Ribeiro, Sohaila Abdulsattar, Renata Gonzalez, Mahmoud Kassem, Sarah Nadi

Code generated by modern language models often reads naturally. Yet, it also often fails to implement what was asked. This should be no surprise, as research shows the models' own confidence signals are poorly calibrated with actual correctness. A promising way to assess correctness looks inside the model: by contrasting the hidden states of correct and incorrect programs, recent work captured an internal signal of code correctness that is able to judge candidate solutions better than the model's token-level or stated confidence, with no test execution. However, this signal was captured under one particular way, leaving open an important question: whether it reflects a robust property of the model or an artifact of that choice. We study this question systematically, varying how the signal is extracted from the model internals. Besides this, we also ask if the signal's quality is limited by the data used to extract it, by constructing program pairs that differ only in the fault that makes them incorrect. Our results show that no single configuration is best, and that isolating the fault does not help.

arXiv

Opportunity Is Not Realizability: Selection-Valid Diagnostics for Multi-LLM Routing

Ibne Farabi Shihab, Abu Sa-Adat Mohamed Moon-Im Al Ahsan, Md Najmus Swaqeeb

Oracle routing measures how much a pool of language models could gain from per-query selection, but the diagnostic has two flaws: testing against a best fixed model selected on the same examples invalidates paired inference, and a full-information oracle sees outcomes no deployable router observes. We separate three estimands (outcome-oracle opportunity, the Bayes-optimal gain from a declared pre-answer signal, and the held-out gain of a learned router) and prove selection-valid confidence intervals that survive choosing the best fixed model or the best member of a router family, a signal-information sandwich, and a $(1-1/e)$ greedy guarantee for building compact pools from submodular complementary coverage. On eight checkpoints from six families over four benchmarks, selection-valid intervals certify a population oracle gap of $9.7$--$30.7$ points on every task, yet the strongest deployable prompt router recovers only $7.5$--$14.4\%$ of it, and the simultaneous interval for the best of eleven tested policies has lower limit zero throughout. The realizable share of oracle opportunity is small and certifiable: strong routers beat the best fixed model, and most of the gap remains.

arXiv

Control-Diverse Reinforcement Fine-Tuning: Decoupling the Shared Control Bottleneck of RL Post-Training

Binwen Tan, Jingchao Wang, Dengzhe Hou, Lingyu Jiang, Zeyuan Wu, Yunhan Shen, Fangzhou Lin, Kazunori Yamada, Atsushi Koike

Reinforcement learning post-training unlocks complex reasoning in LLMs. Yet benchmark scores reveal only whether a model improved, not what changed inside it, nor how it splits finite capability across tasks. A representative interpretability line attributes the success of RL fine-tuning to stronger and more diverse circuit activation. We challenge this activation-centered account by separating activation from control: an activated circuit need not control the post-training reward gain. Adapting Metabolic Control Analysis, we define the Post-training Control Coefficient to measure component control over reward gain and arrange these coefficients by task family into a control matrix, paired with an activation-magnitude matrix. We call cross-task control concentration the Shared Control Bottleneck and the difference between activation and control concentration the Activation-Control Gap. This reveals that highly shared activations can coexist with task-specific control, while a small gap indicates that control has collapsed onto a shared direction and lost task specificity. To reduce this collapse, we regularize the post-training loss with the Shared Control Bottleneck and propose Control-Diverse Reinforcement Fine-Tuning (CD-RFT). The exact regularizer gradient requires second-order automatic differentiation incompatible with flash attention, so we derive a first-order proxy with worst-case overhead below eight percent. On Qwen2.5-7B, CD-RFT achieves the largest control decoupling and improves multi-task capability over matched GRPO across mathematics, code, and logic. The no-KL variant leads on pass@1, and the KL-penalized variant leads on large-k pass@k coverage that KL otherwise degrades. Together, these results show that the Shared Control Bottleneck is both a mechanistic diagnostic and a training regularizer, and that control decoupling and capability gains transfer to Llama-3.2-3B.

arXiv

FreSH: Frequency-Segmented Hierarchical Multi-Expert Framework for Multivariate Time Series Classification

Pingping Liu, Muyao Wang, Zijian Zhang, Tongshun Zhang, Hao Miao, Guorui Xie, Qingliang Li, Qiuzhan Zhou

Multivariate Time Series Classification (MTSC) demands models that can effectively capture complex temporal patterns across multiple scales while remaining computationally efficient. However, existing approaches generally struggle to reconcile fine-grained representation learning, especially under class imbalance and real-world constraints. In this paper, we present FreSH, a Frequency-Segmented Hierarchical Multi-Expert Framework designed to address these challenges. FreSH introduces a new perspective for MTSC by enabling adaptive, multi-scale analysis of temporal signals, allowing different aspects of the data to be modeled in a complementary and coordinated manner. By combining localized specialization with holistic context modeling, FreSH achieves strong representational capacity without incurring excessive computational overhead. An adaptive fusion strategy further enhances flexibility, enabling the model to dynamically emphasize the most informative components of the input. In addition, we incorporate a more robust optimization objective that improves learning stability across varying sample difficulties and class distributions. Extensive evaluations on 30 UEA benchmark datasets and real-world vibration data demonstrate that FreSH consistently outperforms state-of-the-art methods in classification accuracy, while substantially reducing model size and efficiency.

arXiv

Conditional Diffusion for Nonparametric Instrumental Variable Quantile Regression

Xingdong Feng, Xinhong Jiang, Yuling Jiao, Lican Kang, Junwei Liu

This work proposes deep nonparametric Instrumental variable quantile regression (IVQR), a two-stage estimator that combines conditional diffusion modeling with a kernel-smoothed conditional moment formulation. In the first stage, we estimate the joint conditional distribution of the outcome and endogenous covariates given the instrument using a variance-preserving conditional diffusion model. In the second stage, we approximate the conditional moment operator through Monte Carlo sampling and a kernel-smoothed surrogate for the indicator function, and then estimate the structural quantile function by empirical risk minimization over deep neural networks. We establish an excess-risk bound for the proposed estimator and derive end-to-end total variation guarantees for the conditional diffusion model under unbounded support, explicitly accounting for score estimation, early stopping, and discretization errors. Our theory is developed under a polynomial-tail envelope on the data distribution and degenerates continuously to the exponential setting: as the tail index grows, the obtained excess-risk rate converges to the minimax-optimal rate of nonparametric regression, thus our heavy-tailed theory covers the classical light-tailed nonparametric guarantees as a limiting case. Simulation studies and a real-data application demonstrate that the proposed method outperforms existing nonparametric IVQR approaches, with gains that become increasingly pronounced as the dimensionality of the covariates and instruments increases.

arXiv

Beyond Aggregate Calibration: Decomposing Income-Conditional Recall Disparities in Automated Credit Default Prediction

Sai Srikar Boddupalli

Data-centric curation pipelines frequently rely on model confidence scores to flag and filter noisy or mislabeled training instances. Evaluating this filtering convention on a large-scale consumer lending sample (LendingClub, N = 1,344,936) uncovers an underlying demographic asymmetry: high-income defaulters are disproportionately classified as label noise relative to low-income defaulters (Cramer's V approximately 0.03-0.07). Re-examining this behavior through the lens of equal opportunity [Hardt et al., 2016] reveals a far more severe discrepancy: a 16.86 percentage point gap in true positive rate (recall) between high- and low-income borrowers who ultimately defaulted. Implementing a sequential feature-blinding methodology allows us to isolate the drivers of this disparity across three distinct mechanisms: (1) direct reliance on self-reported applicant income; (2) algorithmic absorption of upstream institutional bias encoded within origination interest rates; and (3) a residual disparity (3.55 percentage points in cross-validation; 2.56 percentage points on a held-out test partition, Z = -4.04, p < 0.0001) that remains even after purging both income and interest rates from the model. Out-of-sample signed SHAP valuations demonstrate that this residual gap is maintained by structural proxies, most notably loan amount and home ownership status. These empirical findings show that simply blinding an algorithm to sensitive attributes fails to ensure fairness when institutional pricing decisions and behavioral proxy variables collectively reconstruct the omitted signals. We outline the practical implications of these findings for auditing data-centric AI workflows within regulated financial institutions.

arXiv

Biologically Informed Representation Learning for Robust Cross-Center Generalization of MALDI-TOF Mass Spectrometry

Alejandro L. García-Navarro, Carlos Sevilla-Salcedo, Belén Rodríguez-Sánchez, Vanessa Gómez-Verdejo

Machine learning models for MALDI-TOF mass spectrometry have shown considerable promise for clinical microbiology tasks such as microbial identification and antimicrobial resistance prediction. However, their deployment across institutions remains limited by domain shift, as acquisition-specific variability often leads models to capture technical artifacts rather than transferable biological information. Existing representation learning approaches primarily address this problem through statistical domain alignment while largely overlooking the biological supervision naturally available in microbiology datasets. We introduce DALMA, a probabilistic representation learning framework that jointly models acquisition-specific variability and biological supervision to learn biologically structured latent representations. By combining domain-specific reconstruction with biologically guided representation learning, DALMA learns transferable representations that generalize across heterogeneous clinical centers without requiring institution-specific components at inference, enabling zero-shot deployment on previously unseen sites. We evaluate DALMA on a multi-center benchmark comprising seven datasets from three countries. DALMA consistently achieves state-of-the-art zero-shot microbial identification across two held-out clinical centers, while the learned representations also transfer effectively to antimicrobial resistance prediction. Furthermore, latent-space novelty estimation enables reliable selective prediction under previously unseen domain shifts. These results demonstrate that biologically informed representation learning provides an effective strategy for robust and transferable ML in clinical microbiology.

arXiv

Matching Supervision to the Student's Learning Capacity: A Unified Framework for On-Policy Self-Distillation

Yongkang Yang, Zhezheng Hao, Hong Zhang, Yi Liu, Xiankun Lin, Wence Ji, Fanjunduo Wei, Jiarui Yu, Qiang Lin, Xiaoyun Liang, Hande Dong

On-policy self-distillation (OPSD) improves the reasoning abilities of LLMs by internalizing privileged context into model parameters through self-distillation. Two recent research lines promote vanilla OPSD by choosing which tokens to learn from and by controlling how much privileged information the teacher receives, respectively. However, we show that each line optimizes one variable while holding the other fixed, which leads to a suboptimal solution. We argue that the two variables are coupled through the student's learning capacity: the privileged information sets the per-token divergence the teacher prescribes, while token weighting selects which of these the student must absorb. We formalize the two lines of work into a unified optimization framework, which maximizes the aggregate teacher--student divergence, subject to a budget on the aggregate learning difficulty the student can absorb. Under this modelling, we propose Unified On-Policy Self-Distillation (USD), a lightweight online algorithm to solve the Lagrangian. USD reveals that a single dual variable governs both decisions: at one price for learning difficulty, it simultaneously sets the token-selection threshold and the direction of privileged-information adjustment, keeping supervision matched to the student's evolving capacity. Through extensive experiments, USD consistently demonstrates superior performance over OPSD and token- and PI-side baselines across various model scales on various reasoning benchmarks. Code is available at https://github.com/lauvlalala/USD.

arXiv

Predicting blood clot growth from sparse post-onset measurements with latent neural differential equations

Lennon J. Shikhman, Ying Qian, He Li

Computational models of blood clotting improve understanding of thrombus formation, but their clinical application remains limited because many model inputs are difficult to measure and patient-specific data are often sparse. We present a computational framework based on latent neural differential equations that infers unknown model parameters from sparse measurements and forecasts thrombosis progression. We demonstrate the framework using data generated from a multiphysics blood-clotting model in which clot growth is governed by the coagulation cascade and diffusion. Four known biochemical inputs (fibrinogen and factors IX, VIII, and V), together with sparse early clot-size observations, are used to infer the tissue-factor parameter and predict subsequent clot growth. We compare seven probabilistic methods: stochastic neural ordinary differential equations (SNODE), stochastic neural functional differential equations (SNFDE), a latent neural-process baseline, a monotone probabilistic deep ensemble, empirical trajectory retrieval, PCA-ridge Gaussian posterior, and Gompertz-curve retrieval. SNODE achieved the best performance in inferring the unknown input and forecasting future clot-growth trajectories. SNFDE performed similarly and consistently outperformed the other non-differential models. Prediction accuracy improved as more observations became available, whereas longer forecasting horizons increased uncertainty and decreased accuracy. Latent neural differential equations thus effectively combine parameter inference and clot-growth forecasting from sparse measurements, providing a promising foundation for personalized thrombosis modeling.

arXiv

A Unified Framework for Dynamic Reward Shaping in Reinforcement Learning

Fouad Bahrpeyma

Sparse, delayed, and weakly informative rewards remain central obstacles to efficient reinforcement learning. Reward shaping addresses these limitations by supplementing the task reward with an auxiliary signal that can accelerate learning while, in the classical setting, the original objective remains the evaluation criterion. Established theory guarantees safety for fixed shaping signals: potential-based reward shaping preserves optimal policies when the auxiliary term is the discounted difference of a time-invariant potential. In contemporary reinforcement learning systems, however, both the learner and the information available for guidance evolve during training: value estimates improve, novelty diminishes, feedback shifts, and predictive models are refined. Adaptive reward mechanisms occur across exploration, Bayesian inference, human-in-the-loop learning, automated reward design, and foundation-model-based approaches. This study introduces a unified analytical framework for comparing dynamic reward shaping and neighbouring adaptive reward mechanisms. The proposed framework distinguishes parametric revision from state-dependent variation, separates additive shaping from reward replacement and reward-adjacent guidance, and organises existing methods along temporal, informational, and theoretical dimensions. Using this framework, twelve method families are comparatively analysed. The framework further highlights the conditions under which optimality guarantees survive contemporary deep reinforcement learning pipelines, replay buffers, bootstrapped critics, and reward normalisation, while exposing the unresolved relationship between adaptation rate and learner stability.

arXiv

A Hybrid Nested Harness for Decoupling Structure and Parameters in LLM-Driven Optimization

Víctor Gallego

In evolutionary algorithms powered by language models, the LLM acts as a single operator that simultaneously updates structural components (like control flow) and continuous parameters. While LLMs can be good at the first, they are not efficient at the second, wasting tokens taking discrete jumps inside a trial and error loop. We resolve this by formalizing a hybrid nested search, in which an outer loop has the LLM propose a structural sketch, with numeric gaps, and an inner numerical optimizer tunes the sketch. Both the outer and inner solvers are pluggable: any text-based optimizer can be combined with a zero-order optimizer (CMA-ES), gradient-based routines, or MCMC samplers. We validate our framework across three scientific domains: (i) meta-optimizers on closed-form test functions, (ii) code-based policies for systems research and social dilemmas; and (iii) approximate Bayesian inference tasks. Across all three, the hybrid optimizer is superior to both vanilla LLM-driven search and pure numerical optimization baselines. Code at: https://github.com/vicgalle/hybrid-nested-search

arXiv

DoGMA: A Central-Dogma-Guided Foundation Model for Multi-Omics Alignment and Multi-Task Learning in Oncology

Junfei Ling, Bangzheng Pu, Bingsen Xue, Tianle Li, Ruying Hu, Cheng Jin

Attention mechanisms have been widely utilized in modern deep learning, and many existing multi-omics models inherit their conventional use to allow unrestricted bidirectional interactions. However, the fundamental logic of life is directional. Existing designs often overlook the directionality suggested by the central dogma, potentially limiting transfer across heterogeneous cancers, downstream tasks, and incomplete modality settings.In this work, we present DoGMA, a central-dogma-guided foundation model for pan-cancer multi-omics analysis, arguing that robust transfer requires representations with domain-specific inductive bias. Concretely, we build it on a Transformer-MoE architecture where directed attention biases inter-omics communication toward central-dogma information flow. We further pretrain our model with masked hierarchical omics reconstruction to guide it toward learning central-dogma-consistent interactions. Across diverse downstream tasks, including cancer representation learning, survival prediction, and metastasis prediction, DoGMA consistently demonstrates strong predictive performance. Ablations and analyses further suggest that the performance gains arise from the synergy between central-dogma-guided directed attention and reconstruction-based pretraining, which together promote more biologically consistent cross-omics information exchange. Overall, DoGMA demonstrates that domain-specific inductive biases can improve the robustness and transferability of multi-omics foundation models, offering new insights into the design of attention mechanisms for multi-omics representation learning.

arXiv

TSDS-Toolbox: A Toolbox for Measuring Time-Series Dataset Similarity

Yen-Ku Liu, Hongjie Chen, Ryan A. Rossi, Franck Dernoncourt

The rapid advancement of artificial intelligence (AI) has significantly accelerated research in time-series analysis, particularly in forecasting, classification, and generation tasks. Recent models, especially foundation models, benefit from time-series dataset similarity due to its significant role in source dataset selection for fine-tuning. However, many existing implementations for benchmarking time-series dataset similarity methods are fragmented and difficult to extend. To address this, we present a unified framework, the Time-Series Dataset Similarity Toolbox (TSDS-Toolbox). Our work enables (1) systematic and reproducible comparisons of time-series dataset similarity methods; (2) flexible extensibility for users to add customized datasets, similarity methods, and downstream time-series tasks; and (3) consistent evaluation of both dataset-level and series-level similarity methods through integrated time-series dataset reducers. The effectiveness of TSDS-Toolbox is validated through comprehensive experiments under diverse experimental settings. Our toolbox is publicly available.

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