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Computer Science Machine Learning

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Tuesday 11 August

Machine Learning · Cross-listed from cs.AI

MobileMem: Learning from a Year of Mobile Experiences

The next generation of AI agents is increasingly moving beyond systems that answer isolated questions toward persistent personal assistants that can understand, remember, and continuously learn from users' experiences. Such assistants require long-term memory to accumulate and leverage user-specific experiences over time, yet existing benchmarks remain inadequate for realistic mobile settings, where experiences are heterogeneous, multimodal, evolving, and deeply personal. We introduce MobileMem, a benchmark and framework for studying on-device long-term memory, grounded in a year-scale collection of mobile experiences. MobileMem employs a knowledge-grounded synthesis pipeline to construct coherent and temporally consistent long-horizon trajectories from user-app sessions. It provides complementary text and multimodal settings covering multi-hop and temporal reasoning, knowledge updating, and implicit preference inference. Specifically, MobileMem enables agents to remember the past, understand the present, and adapt to the future. By modeling experiences rather than isolated facts, MobileMem moves memory beyond information retrieval toward experiential intelligence for continuous personal learning.
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All authors Xinle Deng, Yida Xue, Xiangyuan Ru, Yijun Chen, Buqiang Xu, Mingjun Mao, Xinjie Liu, Haoming Xu, Shuofei Qiao, Mengru Wang, Chen Jiang, Yuchen Eleanor Jiang, Lizhong Wang, Jason Wang, Li Zeng, Haofen Wang, Guilin Qi, Huajun Chen, Ningyu Zhang

Machine Learning · Cross-listed from q-bio.NC

Evaluation Resolution Confounds Learning-Rule Comparisons in Model-Brain RSA of Early Visual Cortex

Studies of biologically plausible learning rules (feedback alignment, predictive coding, STDP) train small networks on $32\times32$ images and compare them with brain responses to naturalistic stimuli presented at much higher resolution. We find that a common result in this setting, that untrained or locally trained networks rival or beat backpropagation at early visual cortex, depends on the resolution at which networks are evaluated. In representational similarity analysis (RSA) against human V1, the gap between an untrained and a backprop-trained network grows monotonically from $-0.001$ (95% CI $[-0.011, 0.009]$) at the 32 px training resolution to $+0.030$ $[0.018, 0.042]$ at 224 px (six resolutions, 5 seeds; per-subject RSA on cross-run stimulus pairs). The growth reproduces for three further learning rules, directionally in single-seed macaque electrophysiology, along training, and for an ImageNet ResNet-50 and a Swin-Tiny transformer, which also align best at low resolution although trained at 224 px. Gabor and pixel structure, the normalization state of the untrained baseline, and a global brightness statistic do not account for it. Against a criterion fixed before the analysis, limiting image content to 32 px while the input still grows does not shrink the V1 gap ($+0.035$ $[0.023, 0.046]$ vs. $+0.030$ at 224 px; ratio 1.14 $[1.03, 1.34]$): it arises once the input exceeds the training resolution, through a decline of backprop. A single luminance value per image reaches $\rho = 0.054$ against V1, matching the untrained network (0.053), which bounds what RSA on globally pooled features can resolve at V1 in this dataset. The one learning effect that holds across resolution is backprop above untrained at LOC. Comparisons of learning rules or architectures at early visual cortex need to control, and report, the evaluation resolution.
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Machine Learning

Let it Cook: Learning to Wait in Sequential Decision Making

In sequential decision making, an agent typically observes its environment and acts at every timestep. However, such active participation may not always be necessary; tasks such as brewing coffee include periods that are served equally well by letting the environment evolve without constant monitoring and control. During such periods, the agent could simply wait to conserve its resources, or redirect its attention to another task. We capitalize on these opportunities by training a "waiting policy" that decides where and how long to wait. This involves forgoing sensing to commit to a wait action, representing a deliberate pause for a set number of timesteps. We formalize "learning to wait" as minimizing the frequency of sensing and decision making without sacrificing task performance (e.g., the total amount of time to complete a task). To train a waiting policy, we propose an approach that employs reinforcement learning with lexicographically ordered objectives. In experiments across 4 discrete-state household tasks and 3 continuous-state environments, we show that our approach successfully learns waiting behaviors, and can adapt pre-trained policies to wait where appropriate. While different tasks permit different amounts of waiting without sacrificing task performance, our approach consistently finds solutions with significant waiting, sometimes waiting for over 50 percent of the task duration.
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All authors Christopher Watson, Arjun Krishna, Dinesh Jayaraman, Rajeev Alur

Machine Learning

RelShap: Relationally Consistent Shapley Explanations

Machine learning pipelines commonly flatten relational data into single-table representations, discarding structural constraints. Widely used Shapley value-based feature attributions then rely on feature independence, evaluating the model on combinations that could never arise in the underlying data, producing misleading explanations. We propose RelShap, a framework that incorporates relational constraints and data provenance into Shapley value computation, restricting both background data and coalition evaluation to relationally valid configurations. The framework is estimator-agnostic and composes with Kernel SHAP, Monte Carlo, and Leverage SHAP without altering their sampling or weighting properties. Functional dependencies further induce equivalence classes over feature coalitions, which RelShap exploits to reduce runtime without changing Shapley values; we provide a combinatorial characterization of the expected speedup. Experiments across multiple datasets, models, and estimators show that RelShap produces explanations that are more faithful to the data-generating process, correctly identifying the dominant feature in controlled settings where existing methods, including Conditional SHAP and ManifoldShap, do not. Our code is available at: https://github.com/duneag2/relshap.
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Machine Learning · Cross-listed from cs.NE

Predictive Allostatic Organization in Recurrent and Spiking Agents Under Partial Observability

Adaptive behavior under partial observability depends on internal organization that carries information beyond the current observation. Drawing on Barrett and Miller's account of categorization as predictive, compressive, functionally organized, and allostatically constrained, we test whether recurrent and spiking agents develop internal states with corresponding computational properties. Agents operate in an energy-constrained foraging task requiring resource acquisition, threat avoidance, contact-dependent consumption, and regulation of an internal energy variable. In a frozen benchmark, learned agents outperform random and heuristic baselines; the trace-augmented recurrent policy is strongest overall, while spiking variants show stress-specific differences. Early internal dynamics predict later full-safe-efficient success above permutation baseline, reaching a maximum ROC-AUC of 0.802. Reduced PCA subspaces retain behaviorally relevant information. Feature-family controls show that predictive signal is distributed across trace, policy-head, internal-dynamics, observation, and allostatic variables, and low-energy state remains strongly decodable after explicit energy-related features are removed. Evaluation-time perturbations to temporal state, sensory information, operating conditions, and allostatic mechanisms alter behavior and/or internal prediction. Seed-balanced event probes show weaker but measurable information about future contact, successful consumption, and threat events, alongside strong low-energy decoding. We interpret this pattern as a computational analogue of predictive allostatic organization: distributed control regimes that are predictive, energy-sensitive, action-relevant, and partly causally involved, without claiming biological validation or discrete symbolic categories.
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Machine Learning

HyperFix: Combinatorial Nonlinear Correction for Task Vector Merging

Task vectors enable model merging without joint retraining. In practice, the subset of task vectors to be merged may vary, but many existing methods use scalar tuning for a particular subset, requiring repeated tuning across subsets and restricting task vector merging to linear rescaling. We therefore formulate merging across varying task subsets as a combinatorial correction problem and introduce HyperFix, a lightweight hypernetwork that predicts subset-conditioned nonlinear corrections in weight space. Trained once on singleton, pair, and triple subsets from a task bank, HyperFix generalizes to larger subsets without per-subset optimization. Our local perturbation analysis bounds the residual correction beyond linear merging and motivates learning it from small task updates. Experiments across diverse benchmarks show that HyperFix outperforms existing task vector merging methods while reducing tuning cost.
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Machine Learning · Cross-listed from cs.CV

Language-Structured Relational Q-Learning for Threat-Aware Control in Safety-Critical Driving

Natural-language-based scenario generation offers an intuitive means of describing rare and complex driving interactions, yet it is still uncertain whether training with language-structured data leads to truly adaptive control policies. We propose Language-Structured Relational Q-Learning, instantiated through an Ego-Centric Relational Q-Network (ERQ-Net), which jointly learns inter-vehicle relevance and action values from dynamic traffic graphs. Language descriptions define surrounding-vehicle behaviours during training, while prompts and semantic actor roles are hidden from the policy. ERQ-Net must therefore infer threat relevance solely from observable kinematics and interactions. Across 2,500 safety-critical scenarios, language-structured training improves test success from 49-52% to 55-58% and increases adversary-focused attention from 1.2x to 2.1x, demonstrating emergent threat awareness. However, this representational gain does not consistently translate into adaptive control: trained policies perform similarly to the best constant action, while a portfolio of simple policies solves 76% of scenarios. We formalise this discrepancy as a recognition-control gap and show that reward reweighting and margin shaping do not eliminate the resulting policy collapse. Evaluations of realism, criticality, semantic accuracy, and transfer of state-interface representations to CARLA further highlight both the strengths and the constraints of language-structured relational policy learning in safety-critical driving scenarios.
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Machine Learning

Defending against Model Extraction for GNNs with Model Reprogramming

Graph Neural Networks (GNNs) serve as the backbone for high-stakes applications in Machine-Learning-as-a-Service (MLaaS). Still, their black-box deployment exposes them to Model Extraction (ME) attacks, in which adversaries steal intellectual property by querying APIs. Existing defenses suffer from a critical ”Euclidean bias”: they transfer image-based strategies (e.g., random noise) to graphs, ignoring the complex topological dependencies between nodes, which often results in severe utility degradation. Passive methods like watermarking also fail to prevent theft in real time. To bridge this gap, we propose GraphRP (Graph Reprogramming Protection), a proactive defense framework that repurposes Model Reprogramming for security. Unlike static perturbations, GraphRP introduces a Structure-Aware Gating Mechanism driven by learnable topological prototypes. This creates a dynamic ”structural firewall” that selectively modulates the model's decision boundary: it preserves fidelity for benign queries residing on the training manifold, while maximizing the Fisher Information along the perturbation direction for adversarial queries. Under standard assumptions (bounded loss, optimal attacker, and local second-order approximation), we prove a lower bound on the attacker's estimation error that increases with the structural sensitivity of the reprogramming noise. Extensive experiments on both hard-label and soft-label ME attacks demonstrate that GraphRP significantly degrades attack effectiveness while preserving benign utility.
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Machine Learning · Cross-listed from cs.AI

From Prompting to Behavioral Alignment: Personalized LLM Judges for Recommendation Evaluation

Traditional offline recommendation evaluation relies heavily on complex, manually maintained feature pipelines that are difficult to scale. While Large Language Models (LLMs) offer a promising alternative by predicting user engagement directly from raw text logs, empirical analysis in this study identifies a critical failure mode termed bidirectional rationalization. In a zero-shot setting, LLMs are found to convincingly argue for both positive and negative user engagement outcomes on the exact same item with identical evidence, highlighting the unreliability of off-the-shelf LLMs in predicting user engagement. To resolve this, we develop and apply a sequential behavioral alignment framework pairing fine-tuning with preference optimization over paired correct and counterfactual rationales. Evaluated on real-world homepage interaction logs, this aligned reasoning approach achieves a 32.19% lift in Macro-F1 score over the zero-shot baseline and matches the production feature-engineered baseline. The results demonstrate that behavioral alignment mitigates bidirectional rationalization while delivering human-interpretable reasoning traces without manual pipeline overhead.
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All authors Alireza S. Ziabari, Kat Ellis, Colleen Chan, Ding Tong

Machine Learning · Cross-listed from cs.CR

Cross-Corpus Evaluation of Generalizable Vulnerability Detection in IoT Firmware

IoT firmware vulnerability detection is constrained by ecosystem heterogeneity, resource-limited platforms, and benchmark quality limitations. Existing datasets are often synthetic or general-purpose and lack human-verified, contamination-screened annotations, leaving cross-corpus generalization across training sources, architectures, and curriculum design underexplored. In this study, we have introduced IoTVulBench, a human-verified benchmark for cross-corpus firmware vulnerability detection. IoTVulBench was built from GitHub repositories, validated by three expert reviewers, and evaluated on a contamination-screened held-out target across five architectures, two tuning methods, and three curriculum strategies, with ensemble, distillation, and robustness analyses. Models trained on IoTVulBench reached the highest Matthews Correlation Coefficient (MCC) among undersampling-matched single-source datasets, at 0.58 versus 0.44 for PrimeVul and 0.39 for D2A. Staged curriculum learning raised MCC to 0.69, and a diversity-optimized ensemble reached 0.73. This gain represents a 0.42 MCC improvement over the strongest reference comparator, a static analyzer with an MCC of 0.31, and a 0.29 MCC improvement over the strongest single-source dataset, PrimeVul. At a 0.5% false-positive rate, the model missed only 21% of vulnerabilities versus 71% for the comparator. The model also retained 86% of its performance under identifier renaming, with strong calibration. These results indicate that domain-matched training data and curriculum design, rather than model scale alone, drive generalization in firmware vulnerability detection, and yield both a benchmark and deployment-ready configurations for IoT security.
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Machine Learning · Cross-listed from cs.AI

A Modular Agentic Framework for Synthetically Constrained Multi-Objective Hit-to-Lead Optimization

Hit-to-lead optimization requires iterative design of hit analogs across competing potency, selectivity, physicochemical, pharmacokinetic, safety, and synthetic constraints. We present SABLE (Synthetically-accessible Agentic Bayesian Ligand Exploration), an open-source framework that employs natural-language orchestration to guide chemical structure optimization. SABLE uses an LLM to interpret user-defined goals and route tasks, while specialized tools perform reaction-templated analog enumeration, physicochemical and ADMET property prediction, structure-based affinity scoring, and Bayesian optimization. The resulting workflow is a computational twin of the analytical and prioritization stages of the design-make-test-analyze cycle, providing provenance of each numerical output. Across single, and multi-objective optimization studies, SABLE enriches candidate sets for user-defined computational objectives while evaluating only a subset of the enumerated search space. Its modular architecture allows tools and characterization backends to be replaced by editing a simple config file, without modifying operational logic. SABLE provides an extensible decision-support framework for prioritizing synthetically constrained analogs in early-stage drug discovery.
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All authors Kelvin P. Idanwekhai, Enes Kelestemur, Benjamin Strickland, Matthew Hart, Steini Davidsson, Angelos Angelopoulos, Ron Alterovitz, Marcello DeLuca, Alexander Tropsha

Machine Learning · Cross-listed from eess.SY

Forward Trajectory Steering for Hamilton-Jacobi Reachability Analysis

Hamilton-Jacobi (HJ) reachability provides a mathematically rigorous framework for safe control of dynamical systems, but its practical application is bottlenecked by the computational complexity of solving Hamilton-Jacobi-Isaacs variational inequality PDEs in high dimensions. Physics-informed neural networks (PINNs) have recently emerged as a promising alternative to classical mesh-based solvers, yet their performance is highly sensitive to the choice of collocation sampling. In order to learn accurate safety value functions, existing PINNs-based HJ reachability solvers must rely on complex training pipelines and auxiliary supervision. In this work, we propose STEER2REACH (S2R), a PINNs-based HJ reachability solver that requires minimal modification on top of standard PINNs training. S2R's key contribution is a lightweight, low-overhead adaptive collocation sampling distribution constructed by steering forward trajectories using a combination of the optimal control and disturbance signals induced by the current value function, with injected stochastic exploration noise. We demonstrate that despite its simplicity, S2R achieves competitive–and in some cases improved–performance on safety metrics while reducing relative L2 error across a range of reachability benchmarks compared with SoTA MPC-guided HJ reachability solvers, all without requiring multi-stage training or MPC-based supervision.
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Machine Learning

Convergence Guarantees of Gradient Descent for Neural Networks via Generalized Lipschitz Smoothness

We establish the first convergence guarantees of gradient descent for general feedforward neural networks of any width or depth, with any initialization or dataset. We only assume that the activation functions are linearly bounded, Lipschitz continuous, and Lipschitz smooth—properties that hold for linear, tanh, softplus, sigmoid, and smoothed ReLU functions—and that the loss function is Lipschitz smooth in the model outputs, a mild condition satisfied by mean squared error and binary cross-entropy loss. By relating the Lipschitz properties of one layer to the next, we obtain a novel generalized Lipschitz smoothness condition for an $L$-layer neural network where the change in gradient is upper bounded by the change in the parameter space, multiplied by a polynomial of the parameter norms at both endpoints of degree $2L - 2$. This yields a descent lemma where the loss decreases as long as the learning rate is small enough with respect to the parameter norms. By ensuring that the leading term of the polynomial grows at a controlled rate, we prove that the minimum squared gradient norm converges to zero in $T$ iterations at rate $O(1/T^{1/L})$.
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Machine Learning · Cross-listed from q-bio.QM

Probing and steering biology across Boltz-1s trunk-diffusion boundary

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.
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All authors Piotr Jedryszek, Tongmeng Xie, Adam Winnifrith, Alexander Hasson, Weronika Ślesak, George Wicks, Toby Winnifrith, Oliver M. Crook

Machine Learning

Dual-Primal Graph VAEs for Noisy Label Aggregation

Inferring the ground-truth from noisy crowdsourced labels is an important theoretical and practical problem. Neural network-based methods offer an alternative to classical Bayesian models which require specifying a family of generative models used for inference. However, current models either still rely on fairly simple generative models for inference or require pseudo-labels or synthetic data to train the aggregate classifier. We propose a graph VAE architecture in which the decoder and encoder use GAT-based message passing on the adjacency graph of a crowdsourced dataset and its dual, respectively. The ground-truth labels are treated as latent variables, enabling unsupervised representation learning without needing to train a separate classifier. We show our model achieves state of the art performance on crowdsourcing benchmarks. We then demonstrate the generality of our approach by showing how the original crowdsourcing graph can be augmented to incorporate side information such as representations from neural network classifiers trained on the noisy labels to substantially boost their classification performance at test time.
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Machine Learning · Cross-listed from cs.CV

Gaussian Meta-Space Augmentation for Stacking Ensembles in Multimodal IPMN Risk Stratification

Pancreatic cancer is among the most lethal malignancies; risk stratification of intraductal papillary mucinous neoplasms (IPMNs) offers a crucial opportunity for early intervention but typically requires invasive tissue biopsy. Dominant vision-based approaches, including radiomics and deep learning, provide promising but initially separate discrimination opportunities. Similarly, multisequence MRI (T1W/T2W) and anatomically decomposed (head, body and tail) analysis of the pancreas provide additional and potentially complementary signals. Effective fusion of this information is crucial in ordinal IPMN dysplasia risk prediction and can be accomplished via a meticulously regularized and calibrated ensemble stacking combiner. We present cUPMI, a class-conditional Gaussian augmentation of a combiner's log-probability meta-features, and test it on various prediction paradigms. In our multi-center analysis, we find cUPMI adds limited value to properly regularized L2-logistic binary classification stacks, but consistently regularizes higher-capacity tree combiners in the binary and radiomics-only setting (RF +0.015 and XGBoost +0.024 binary AUC, positive in all seeds). Its cleanest ordinal benefit appears for XGBoost on an 8-stream radiomics task (3-class no < low < high, +0.022 QWK in all seeds). Separately, fold-locked fusion of radiomics and 2.5D CNN streams yields the strongest overall model, an RF stack reaching QWK 0.595 (95% CI [0.54, 0.64]) and binary AUC 0.839, surpassing radiomics, 2.5D ResNet, and 3D DenseNet-121 baselines.
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All authors Max A. Nelson, Eminenur Sen Tasci, Zhixiang Wang, Zongwei Zhou, Halil Ertugrul Aktas, Andrea M. Bejar, Elif Keles, Ziliang Hong, S{\i}tk{\i} Safa Taflan, Muhammed Enes Tasci, Frank H. Miller, Michael B. Wallace, Rajesh N. Keswani, Gorkem Durak, Ulas Bagci

Machine Learning

PAC-Bayes Beyond Parameter Space: Behavioral Equivalence, Z-Information, and Exact Complexity Decomposition

PAC-Bayes theory provides generalization guarantees by controlling the Kullback–Leibler (KL) divergence between posterior and prior distributions over a chosen hypothesis representation. However, predictive risk depends only on the predictive behavior induced by a hypothesis, not on the particular internal realization that implements that behavior. In over-parameterized systems, many distinct configurations induce identical predictive behavior, yet the classical PAC-Bayes KL divergence does not distinguish uncertainty over predictive behavior from variation among behaviorally equivalent realizations. We show that this distinction induces an exact structural decomposition of classical PAC-Bayes complexity. We formalize behavioral equivalence through a measurable behavior map and use measure disintegration to decompose probability measures on the configuration space into a distribution over predictive behaviors and conditional distributions over behavioral fibers. This yields an exact decomposition of the classical PAC-Bayes KL divergence into a behavior-selection term and a realization-level term given by an expected conditional KL within fibers. We define Z-information as the negative of this realization-level contribution: the exact gap between the KL divergence and the complexity of uncertainty over predictive behavior alone. We further show that the behavior-selection term admits an exact variational characterization: it is the minimum KL divergence among all posteriors inducing the same distribution over predictive behaviors, attained by a canonical fiber-symmetrized representative. Finally, we show that symmetry, behavior-preserving directions, fiber geometry, and invariance under fiber-preserving perturbations arise naturally from the same behavior-map structure. Together, these results identify predictive behavior as the natural object of PAC-Bayes complexity.
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All authors Vasant G. Honavar, Satish Kumar Keshri, Neil Ashtekar, Zehao Liu

Machine Learning

XGBoost "is all you need": the case of forecasting transmitted heat energy in District Heating Systems

This paper presents a comparative study of two distinct approaches, XGBoost and Long-Short Term Memory (LSTM), for forecasting transmitted heat energy in District Heating Systems (DHS). The objective is to explore scenarios in which conventional ML algorithms demonstrate better performance over deep learning networks in time series forecasting and the associated benefits in terms of computational cost and environmental impact. The study focuses on a real-world DHS dataset. Through experimentation and analysis, it is demonstrated that XGBoost consistently outperforms LSTM in this specific forecasting task. The difference is explained by the error distribution illustrating that LSTM makes more significant errors in the intervals of less data availability. The reduced computational demands of conventional ML approaches not only result in cost savings but also minimize the carbon footprint associated with data analysis tasks in energy systems.
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Machine Learning · Cross-listed from q-bio.QM

Large-scale AI-Ready Data for Anti-Cancer Drug Response Modeling

Drug response prediction (DRP) models are an active area of research in pharmacogenomics, with growing potential to accelerate the identification of effective anticancer drugs. However, their predictive performance is often constrained by limited dataset scale and insufficient coverages of cancer and chemical spaces. In addition, inconsistent benchmarking practices hinder reliable comparison across models. Standardized frameworks, such as the Innovative Methodologies and New Data for Predictive Oncology Model Evaluation (IMPROVE) project, provide unified data schemas and evaluation protocols for consistent benchmarking, but improving model generalizability requires larger and more diverse training data. In this work, we substantially expand the IMPROVE benchmark through large-scale integration of pharmacogenomic data, primarily from PharmacoDB, together with additional smaller data sources. The expanded resource includes millions of drug response measurements, broader multi-omics coverage, and a major increase in chemical diversity, adding more than 50,000 compounds. To evaluate the impact of the new dataset compared to the original IMPROVE benchmark dataset, we trained DRP models using the two datasets and assess their prediction performance using a common test set and several evaluation strategies, including drug-blind, cancer-blind, and disjoint data splits. While cancer-blind performance remained comparable to the original benchmark, models trained on the expanded dataset showed consistent improvements in drug-blind and disjoint settings, indicating enhanced generalization to previously unseen compounds. These results position the expanded dataset as a community resource that provides a richer foundation for developing DRP models intended to aid in the discovery of novel anticancer drugs.
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All authors Vincent Lavelle, Yitan Zhu, Kaitlyn Marlor, Thomas Brettin, Rick Stevens

Machine Learning

Variational Parameter Calibration with Physics-Aware Latent-Space Surrogates

Forward and inverse modeling of parametric dynamical systems requires surrogate models that are not only accurate for state prediction, but also informative for parameter calibration. However, a systematic end-to-end differentiable formulation for coupling deep-learning-based reduced-order surrogates with variational parameter estimation remains underdeveloped. In this work, we introduce a physics-aware neural-network-based latent-space framework for reduced-order forward modeling and variational parameter estimation. The proposed autoencoder-based approach yields a differentiable surrogate that maps physical parameters to predicted flow fields through a latent representation. The observable supervision is used during offline training to encourage the latent variables to retain information correlated with system parameters, while the online inverse problem is solved in the parameter space through the surrogate-induced observation operator. The method is evaluated on two computational-fluid-dynamics benchmarks. The results show that reconstruction accuracy alone is insufficient for inverse modeling, owing to the lack of end-to-end differentiability or physics awareness for variational parameter calibration. Quantitative latent-space analysis further shows that observable supervision improves case-level separability and temporal organization of latent representations. Experiments with realistic measurement settings, including noisy, low-resolution, randomly masked, and block-wise partial observations, demonstrate the robustness of the proposed framework and show that it generally reduces calibration error and variability compared with the standard surrogate models.
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All authors Qiyao Zhou, Xujia Zhu, Pierre Joli, Yu Cong, Sibo Cheng

Machine Learning

AutoGrable: What Is a Good Graph for a Table?

Graph learning presupposes a graph, and tables and relational databases do not come with one. Applying a GNN to them requires deciding which entities become nodes, which of them to connect, and through which relations—a decision made by hand, by schema heuristics, or by training a model on every candidate graph and keeping the best. We give a criterion that requires no trained graph model. In the minimal table-to-graph abstraction each row is a node, so a message-passing GNN, bounded by 1-WL, sees a construction only as a partition of the rows into colour-refinement classes: a construction is good for a task when that partition separates rows with different labels and does not split rows that share one. AutoGrable turns this criterion into a construction procedure. For incidence constructions the partition is fixed by the selected columns, so building a graph reduces to choosing them, and we score a candidate subset by a label-alignment risk: the held-out risk of the best predictor constant on its blocks, penalised by an occupancy term measuring how thinly the blocks are populated. The score materialises no graph and trains no GNN, so AutoGrable can search the space of subsets greedily and cheaply, and returns the resulting grable for single tables and for foreign-key schemas alike. Our experiments show that over a space of candidate graphs the score discards a large fraction while retaining the best; that AutoGrable recovers the columns that generate the label on controlled tasks and outperforms fixed, random, and task-aware constructors on real tasks under a fixed predictor; and that it is the only method compared that can decline to build a graph when none helps.
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Machine Learning

Three Tokens Force Exponential Feature Rank in Nonnegative Kernel Attention

How much feature rank does comparison require in kernel attention? On Min-IP over $m$-bit tokens, rank one solves every sequence of length at most two exactly. At length three, the minimum feature rank of one normalized nonnegative kernel-attention head is $2^{\Theta(m)}$ for error strictly below $1/2$ on every input, even with arbitrary finite-dimensional tokenwise values and query-dependent affine readouts. Dense softmax solves this three-token task with $m$-dimensional scores and temperature constant in $m$. For every fixed number of heads $H$, the minimum total feature rank is $2^{\Theta_H(m)}$ for the same error guarantee at exact length $H+2$ in one attention layer with affine mixing. These bounds also hold with position-dependent maps and a final causal query. For one head with polynomial readout of fixed degree at most $D$, rank one suffices at exact length $D+1$, while exact length $D+2$ requires exponential feature rank. With unrestricted exact-real decoding, a scalar rank-one construction solves the task at every finite length. This motivates a separate bound on total communication for deterministic models with finite-alphabet cross-token channels and any number of heads and layers. In this setting, correctness up to length $n$ requires $\Omega(n\log m)$ bits over a range of lengths that grows exponentially with $m$.
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Machine Learning

Click2Poly: A VLM for vector mapping buildings and walls

Accurate vector mapping of buildings and walls is critical for geospatial applications but remains a labor-intensive process. While recent deep learning methods have improved automatic extraction, in order to meet cartographic standards they always require a human to perform quality control and fix complex cases in the extraction. We present Click2Poly, a human-in-the-loop AI assistant designed to speed up this manual step. Extending the Florence-2 Vision Language Model (VLM), Click2Poly responds to user clicks by editing the building or wall vector layer directly. Implemented as a QGIS plugin, Click2Poly speeds up the manual editing of building and wall vector layers in a real-world production environment.
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All authors Nicolas Girard, Jawher Ben Abdallah, Arno Gobbin, Liuyun Duan, Sacha Lepretre

Machine Learning

Analysis of Federated Aggregation under Model Poisoning and Backdoor Attacks: A Reconstructed Cross-Dataset and Cross-Architecture Benchmark

Robust comparisons of federated aggregation methods require joint consideration of predictive performance, threat definitions, metric semantics, and execution provenance. A 500-cell seed-1 evaluation matrix was reconstructed across five aggregation methods, five datasets, five architectures, and four recorded conditions: clean, sign-flipping, Gaussian, and BadNets. Successful execution logs were identified for 454 original runs and 36 repaired or rerun executions, whereas 10 clean SVHN cells were supported by summary-only provenance. Trimmed Mean achieved the highest clean macro-mean accuracy (76.02%) and the lowest mean within-task rank (1.70). Krum attained the highest recorded accuracy under both sign-flipping and Gaussian configurations. These relative rankings remained unchanged when analysis was restricted to 21 task pairs for which original successful logs were available for every method-condition combination. Audit of the supplied BadNets metric implementation established that every test input is triggered prior to target-label counting; consequently, the retained metric represents Triggered Target-Label Rate (TTLR) rather than a conventional target-excluding attack success rate. An audit of the supplied FedPARETO scaffold further identified a pathway in which predictive summaries may characterize an uncorrupted local model while the aggregation weight is applied to a separately corrupted update, introducing a potential discrepancy between reported predictive outcomes and the updates used for aggregation. The canonical matrix contains a single identified seed for each cell, and exact attack and configuration lineage is incomplete. Accordingly, the findings should be interpreted as descriptive comparisons within the recorded configurations and not as statistical estimates or universal claims regarding robustness.
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Machine Learning

Diffusion-Based Data-Driven Assortment Optimization

Assortment optimization is a fundamental problem in revenue management, typically addressed using parametric choice models such as the multinomial logit (MNL) and its variants. While these models enable tractable formulations, their performance is sensitive to model misspecification and often struggles to capture complex customer behavior. In this paper, we propose a model-agnostic framework for assortment optimization based on guided discrete diffusion. We represent assortments as binary vectors and perform stochastic search via a learned reverse diffusion process, avoiding explicit combinatorial enumeration. To incorporate decision objectives, we introduce a reward-guided mechanism that biases local transitions using estimates of expected revenue. This allows the method to effectively balance exploration and exploitation during generation. Empirically, we show that the proposed approach consistently identifies high-quality assortments and remains robust under model misspecification, often recovering near-optimal solutions in high-dimensional settings. Moreover, the generative nature of diffusion enables the production of diverse high-performing assortments, offering flexibility beyond a single deterministic solution. These results highlight the potential of generative modeling as a scalable and robust paradigm for combinatorial optimization in data-driven decision-making.
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All authors Junyi Liao, Xiaohui Jiang, Zhengwei Tong, Ethan X. Fang, Vahid Tarokh

Machine Learning

Unmasking Toxic Mimicry in Medical Offline Reinforcement Learning for ICU Sepsis Management via Counterfactual Clinical Audits

Offline reinforcement learning (RL) offers considerable promise for optimizing ICU treatment decisions, yet standard evaluation metrics Mean Squared Error (MSE) and Fitted Q-Evaluation (FQE) assess only behavioral imitation and cannot detect Toxic Mimicry, a failure mode in which agents replicate harmful patterns such as treatment withdrawal during comfort-care transitions. Using the MIMIC-III database, we propose the Counterfactual Clinical Audit (CCA) framework, which stress-tests RL agents through physiological perturbations anchored in Surviving Sepsis Campaign (SSC) guidelines. We audit a Medical Decision Transformer (MedDT) and a Historical Causal Transformer (HCT-RL), the latter employing Causal Action Shielding, propensity-based importance weighting, and Conservative Q-Learning. CCA reveals that MedDT paradoxically reduces vasopressor dosage as lactate escalates, contradicting resuscitation guidelines, while HCT-RL maintains physiologically consistent responses. These findings expose a systemic misalignment between statistical fit and clinical safety, supporting counterfactual audits as a necessary evaluation standard for medical RL.
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Machine Learning · Cross-listed from cs.AI

When Self-Consistency Backfires: Majority Vote Hurts the Majority of Hard Science Problems for Small LLMs

Majority-vote self-consistency (SC) lowers per-problem accuracy on most GPQA Diamond problems for small instruction-tuned models: on 56.6% of problems for Qwen2.5-7B and 65.7% for Llama-3-8B. An obvious fix is a verifier-free confidence gate that decides which problems to vote on. We report that the most natural version of that fix also fails, and we separate three signal failures that v1 treated as one. The token-entropy gate fails for a measurement reason: averaged over a chain of 602 tokens, entropy mostly measures fluency. The chain average sits 0.0005 nats from the non-answer average and 0.1695 nats from the answer token. So we measure confidence at the answer token itself. On Qwen2.5-7B-Instruct-Turbo (198 problems, 64 samples each), a sample that disagrees with its problem's plurality still emits its answer at a median margin of at least 20.4 nats, and at least 75.5% of such samples exceed 10 nats. Both quantities were pre-registered and tested once on 69 problems that no exploratory analysis had seen; both passed. The unit matters. Pooled across the benchmark, the margin does separate correct from incorrect samples: the fraction above 10 nats differs by +0.0586 [+0.0160, +0.0994]. Within a problem, paired, it does not: -0.0142 [-0.0501, +0.0215]. Token log-probabilities do carry information, but not for the within-question choice that self-consistency makes. The agreement gate's failure has no mechanism we can identify, and we leave it open. The new claims rest on one model: a registered replication on a second model was sampled but could not be evaluated, and we report that instead. Separately, three reasoning models could not be evaluated on hosted serverless inference at a small budget, each for a different measured reason. All three are downloadable, so this is a limit of metered APIs, not of what can be known.
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Machine Learning · Cross-listed from quant-ph

Generative Learning for Quantum Measurement Design

Extracting quantum information from a quantum state is a fundamental task of quantum computation, often requiring the estimation of many non-commuting observables under a finite measurement budget. For both near-term and early fault-tolerant settings, the measurement protocol must balance statistical efficiency against implementation resources such as circuit depth, connectivity, and entangling-gate count. Many existing strategies focus on two extremes: hardware-friendly product measurements with high sampling cost, and fully commuting measurements with deep circuits. Here we recast resource-constrained measurement design as a generative learning problem. We introduce FlowMeas, which uses a generative flow network to directly sample finite ensembles of shallow Clifford measurement circuits subject to a prescribed shot budget and hardware constraints. At zero entangling depth, FlowMeas learns qubit-wise commuting measurement schedules and already matches or improves leading product-measurement methods on nearly all molecular benchmarks. Allowing one or two entangling gate layers yields further reductions in energy estimation error of up to $27\%$ relative to the strongest state-independent product-measurement baseline. The learned policy can also be reused across related Hamiltonians, substantially accelerating retraining along a molecular potential-energy surface. We further obtain results for molecular Hamiltonians with up to 20 qubits and apply the framework to a compactly encoded 54-qubit interacting fermionic model, extending the demonstrated scale beyond prior molecular benchmarks. These results establish generative learning as a flexible and unified framework for quantum measurement design under practical resource constraints.
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All authors Jun Dai, Olivier Nahman-Lévesque, Guillaume Rabusseau, Hong-Ye Hu, Cunlu Zhou

Machine Learning

Mechanism Design for Generative Engines: From Exploitation toward Win-Win Outcomes

Generative engines are reshaping the web ecosystem by making citations a key mechanism for allocating attention, attribution, and downstream value. This creates a strategic tension: content providers are incentivized to optimize for model citation, while platforms must preserve answer quality and trustworthy attribution. We show that this tension can escalate into citation wars. In repeated simulations, state-of-the-art generative engine optimization (GEO) attacks adapt to conventional defenses by producing citation-seeking rewrites that degrade document quality and introduce unsupported claims. To study this problem, we formulate the supplier–platform interaction as a repeated Stackelberg game with partial monitoring. A local best-response analysis identifies when citation competition approaches an inert stationary outcome. Motivated by this finding, we propose a platform–creator mechanism called VCR based on verifiable-content rewards. Rather than only penalizing suspicious rewrites, the platform also credits rewrites that surface checkable factual substance, aligning creator incentives with answer trustworthiness. Experiments on three benchmarks show that VCR consistently achieves the largest Net defense-utility score, outperforming the strongest baseline by an average of 12.1 percentage points, and produces a win–win outcome under our empirical equivalence criterion.
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Machine Learning

Reoptimization Algorithms for Contextual Bandits with Knapsack Constraints

We study new algorithms for Contextual Bandits with Knapsack. In these problems, there are finitely many types of customers, products, and resources. Each product is made from a fixed combination of resources, and resources have finite capacity. A decision maker must assign each arriving customer one out of a set of multiple possible products. Every assignment of a customer to a product will generate a random reward, which equals an unknown linear function of customer and product features, plus a noise term. The objective is to jointly learn the mean reward function, and to make online assignments to minimize the expected revenue loss relative to an optimal policy that knows the reward function. We propose a natural and simple extension of the Upper-Confidence-Bound (UCB) family of algorithms and apply re-optimization techniques. We show that by taking advantage of re-optimization, our algorithm achieves an average regret of $O(\frac{(\ln T)^3}{T})$ where $T$ is the horizon length. Our bound significantly reduces the $O(\frac{1}{\sqrt{T}})$ bound in the literature for closely related dynamic-pricing problems that are based on re-optimization.
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