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Computer Science Machine Learning

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Wednesday 29 July

Machine Learning · Cross-listed from stat.ML

An analysis of binary isotonic regression: degrees of freedom and implications for calibration

Raphael Rossellini, Rina Foygel Barber, Zhimei Ren et al. (+1 more)

Isotonic regression is a canonical tool for estimating monotone functions and calibrating probabilistic predictors. We provide a fully sharp finite-sample characterization of its worst-case degrees of freedom on binary samples. Specifically, we identify the binary sequences that maximize the number of distinct fitted values produced by isotonic regression. We develop a sharp bound on the degrees of freedom with a leading term of $\frac{3}{(4\pi^2)^{1/3}} n^{2/3}$ using analytic number theory, improving on previous bounds. We then apply this result to calibration. Calibration is a central requirement for probabilistic prediction, and isotonic regression is a widely used post-processing method for improving calibration. Building on deterministic degrees-of-freedom bounds, we derive, to our knowledge, the first nontrivial distribution-free guarantee on the Expected Calibration Error (ECE) of isotonic regression. This ECE bound is fully model-free and distribution-free, only assuming $Y \in \{0,1\}$.
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All authors Raphael Rossellini, Rina Foygel Barber, Zhimei Ren, Jake A. Soloff

Machine Learning · Cross-listed from cond-mat.mtrl-sci

MatCreatioNN: Machine learning-guided computational discovery of photocatalysts for environmental applications

Satya Kokonda

The rational design of photocatalysts for environmental remediation and CO2 conversion remains limited by the high computational cost and sparse experimental data describing multi-parameter photocatalytic behavior. This work presents an integrated machine-learning framework that couples reinforcement learning-based metal-organic framework (MOF) generation with a multi-stage Crystal Graph Convolutional Neural Network (CGCNN) prediction funnel to identify photocatalysts optimized across multiple electronic and structural features. 120,000 MOF candidates were generated and screened using 13 key descriptors, including band-gap suitability, CO2/H2O selectivity, adsorption energy, and structural stability. The funnel approach reduced computational cost by 4.13-fold while maintaining predictive robustness. Two top candidates, a Cr-based and a Zn-based MOF, exhibited predicted photocatalytic fitness values of 1.70 +/- 0.25 and 1.20 +/- 0.05 fold higher respectively than benchmark materials such as PCN-224(Zr), demonstrating simultaneous improvements in light absorption, redox energetics, and framework durability. Simulated X-ray diffraction patterns confirmed strong structural agreement with experimentally synthesized MOFs, indicating high synthesizability. Post-hoc analysis revealed recurring structural motifs, such as the N262 metal cluster, that correlated strongly with high predicted photocatalytic activity. These results highlight the potential of data-driven methods to accelerate discovery of efficient and durable photocatalysts for environmental and energy-related transformations, providing a foundation for experimental realization and large-scale implementation of computationally designed MOFs.
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Machine Learning

EvoCause: LLM-Guided Evolution of Causal Graphs for Root Cause Analysis

Lei Zan, Keli Zhang, Shifeng Xie et al. (+7 more)

Modern telecommunication, cloud, and microservice systems emit correlated alarm cascades when components fail. Root cause analysis (RCA) aims to identify the small set of alarms that initiate each cascade. A common approach learns a causal graph from observational logs and predicts all zero-in-degree alarms in each incident-induced subgraph. However, the learned graph remains fixed and cannot benefit from expert diagnoses of historical incidents. We close this loop with EvoCause. Expert labels constrain which alarms should be source nodes but do not specify the edge edits needed to satisfy those constraints. EvoCause uses a large language model (LLM) to propose semantically plausible graph edits, while deterministic code validates node identities and acyclicity and retains the best graph on a labeled alignment set. At test time, the refined graph alone produces transparent predictions without an LLM call. We also release TeleRCA, an expert-annotated benchmark from a production telecommunication network containing $485{,}681$ alarm events spanning $194$ alarm types over $5{,}621$ resources. On synthetic data, EvoCause initialized with the PC causal discovery algorithm outperforms the unrefined PC baseline, raising Node F1, Case EM, and Graph F1 by $11.59$, $9.40$, and $4.59$ percentage points, respectively, while reducing nSHD by $0.2379$. On TeleRCA, replacing human-readable alarm titles with anonymous identifiers lowers Node F1 and Case EM by $6.12$ and $8.04$ percentage points, respectively, indicating that alarm-name information contributes to graph refinement.
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All authors Lei Zan, Keli Zhang, Shifeng Xie, Jiale Zheng, Zehao Xiao, Zhiwei Dong, Ke Zhang, Ruichu Cai, Malik Tiomoko, Lujia Pan

Machine Learning

TIER-MoE: Trust-Informed Expert Routing via Conditional Modality Risk for Multimodal Fusion in Biomedical Classification

Yu Chang, Anzhe Cheng, Chenwei Wu et al. (+7 more)

The promise of multimodal fusion lies in combining complementary sources of evidence, yet more evidence does not always yield a better prediction. Recent multimodal models have advanced fusion through richer cross-modal interaction and sample-adaptive fusion. However, the influence assigned to a modality during fusion does not reveal whether that source is unreliable, redundant, or poorly matched to a specialized expert. To address this limitation, we introduce TIER-MoE, a risk-guided subspace mixture-of-experts model that defines sample-specific modality reliability as the prediction loss its unimodal predictor is expected to incur. This risk is learned from out-of-fold predictions generated by models that were not trained on the corresponding sample. TIER-MoE combines the estimated risk with expert-specific subspace compatibility for sparse modality-expert routing, while an always-active shared path preserves multimodal complementarity. We evaluate TIER-MoE on four public multimodal biomedical datasets spanning Alzheimer's disease status, skin-lesion malignancy, and retinal classification. Results demonstrate its superiority over state-of-the-art methods in predictive performance and probability calibration, with consistent improvements in Macro-F1 and Brier score and strong zero-shot generalization to an external cohort.
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All authors Yu Chang, Anzhe Cheng, Chenwei Wu, Zhuoran Wang, Jiahao Chen, Tamoghna Chattopadhyay, Sophia I. Thomopoulos, Paul M. Thompson, Liyue Shen, Paul Bogdan

Machine Learning

Benchmarking the Residual: What Long-Horizon Evaluations Add Beyond Matched Short-Task Performance

Chao Peng, Zhiheng Lyu, Peijie Dong et al. (+2 more)

Long-horizon benchmarks often show that agents fail more as tasks become longer. This observation is useful for deployment, but it does not by itself explain why failure occurs. More stages create more opportunities for ordinary errors to compound; longer tasks may also contain harder individual decisions or become harder as conversation history, tool outputs, and environment changes accumulate. We use trajectory-induced degradation to mean this last possibility: earlier execution makes later work harder. When the harmful accumulation is specifically the text visible to the model, it is often called context rot. In this position paper, we argue that to claim a "long-horizon failure", benchmarks must compare actual full-task success against a baseline prediction built from short, individual stages. We call the log-ratio between this prediction and actual success the horizon residual. The comparison must use the same agent configuration and specify in advance how stages, checkpoints, information, and budgets will be chosen. The residual shows that the full rollout differs from the chosen baseline; targeted experiments are still needed to explain why.
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All authors Chao Peng, Zhiheng Lyu, Peijie Dong, Hande Dong, Qiang Lin

Machine Learning

The Kinetics of Training: A Driven-Nucleation Rate Law for Emergence, Plasticity Loss, and Circuit Control in Language Models

Lei Dong

A capability appears in a language model when the last parts of its circuit align in one stochastic attempt, and getting all but one right is worth nothing. We show this no-partial-credit joint alignment is the rate-limiting step of capability formation. Two fingerprints: in a shortcut-free apparatus a five-part circuit missing three waits as long as a three-part circuit missing three (1.19-1.37), so the wait counts missing parts, not size; and on Pythia across seven capabilities and three scales, ablating one part leaves a median 17% of the capability in 32 of 32 discriminating cells, where partial credit predicts 50-83% (p = 2e-10), while a random non-part head leaves 100%. One rare event whose barrier grows with missing parts yields a rate equation – sites x attempts x drive x exp(-beta*K), minus destruction – read three ways, each preregistered with frozen constants. Forward: a capability flat at baseline ignites at a step of our choosing once the mix passes a concentration floor (10/10 above, 0/12 below), and while still flat its arrival is datable from its precursor to 5% median error on six held-out models. Backward: the delay to learn a withheld capability grows with waiting until, past a critical step, it never ignites – yet validation loss falls smoothly throughout, so standard monitors are blind to it. We locate the damage (heads commit to the base data) and isolate the cure: re-initializing only the query-key slices restores learnability (6/6) while the value slices do nothing (0/6). We prove the mechanism in a controlled gated-attention model: occupation forces a deadline whose consequences need no mixing assumption. Completed: SGD's noise fails the fluctuation-dissipation test, so we install one and anneal, melt and pin circuits on schedule. Scope: conjunction circuits in transformers to 1.4B.
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Machine Learning · Cross-listed from stat.ML

Expected Survival-Time Bounds for Robust Optimization Over Time under Isotropic Gaussian Dynamics

Pavel Novoa-Hernández

Robust Optimization Over Time (ROOT) is a recent branch of evolutionary dynamic optimization that seeks solutions capable of remaining effective across multiple consecutive environments. Unlike the traditional track-the-moving-optimum (TMO) paradigm, which reoptimizes after every environmental change, ROOT explicitly values persistence. Although the field has grown considerably, most contributions remain algorithmic and empirical, leaving several fundamental properties poorly understood from a theoretical perspective. One such property is survival time, defined as the number of future environments in which a deployed solution continues to satisfy a prescribed quality threshold. While survival time is widely used as a measure of temporal robustness, little is known about how its expected value depends on environmental dynamics, deployment quality, or problem characteristics. This paper studies expected survival time for a fixed deployed solution under isotropic Gaussian environmental dynamics. Modeling survival as a discrete first-exit problem, we derive a rigorous lower bound and a computable multi-step upper bound. The analysis shows that expected survival scales as ${\Theta}({\sigma}^-{2})$ in slowly varying environments and approaches its minimum value of one future change in high dimensions. A comprehensive Monte Carlo study validates the theoretical predictions, examines sensitivity to modeling assumptions and parameter uncertainty, and illustrates how the bounds can support deployment decisions after optimization. The resulting framework provides an analytical characterization of deployment lifetime and identifies when a required deployment horizon can be guaranteed, ruled out, or remains analytically unresolved.
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Machine Learning

Flat Score, Amplified Failures: How the Error Budget Masks Damage in Quantized LLM Agents

Jiwon Jang, Kisu Yang, Heuiseok Lim et al. (+1 more)

Post-training quantization to 4-bit weights is widely reported to be nearly lossless. We test this claim for multi-turn, tool-calling agents, where it now matters most. On $\tau^2$-bench, across two open-weight model families in dense and MoE variants and two domains (eight cells, 456 episodes each, at 16-, 8-, and 4-bit weights), quantization indeed looks free on the standard metric. No cell shows a score change that survives multiple-comparison correction, and in the cell that carries the largest process damage, equivalence testing bounds the change within $\pm$7.5 points. The process tells a different story. Quantization amplifies the failure the model already exhibits at full precision (tool-name hallucination in telecom, with the same directional trend in retail entity errors) by up to 2.5$\times$ in volume (+17.6 points per task), while creating essentially no new failures. The failure set is the same at every precision (rank correlation $\geq$ 0.94, 0.18% novel events). The score stays flat because the benchmark's ten-error budget absorbs the extra failures. Shrinking the budget to two errors re-exposes a score gap of 17 points, and it does so only in the one cell where quantization added error volume, exactly as the masking account predicts. A targeted error-repair prompt, run for five telecom models at every precision, removes the damage exactly and only where it lives. Both diagnostics, the per-channel error rate and success under a shrinking budget, come from logs benchmarks already collect; we suggest reporting them alongside task reward.
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All authors Jiwon Jang, Kisu Yang, Heuiseok Lim, Hyunwoo Park

Machine Learning

Rethinking EEG-Based Disease Diagnosis: Decoupling Instance Representation Learning from Subject-Level Supervision

Zhiyuan Ma, Zeyuan Li, Zhiyi Lu et al. (+7 more)

EEG-based disease diagnosis requires one prediction per subject, yet common pipelines segment recordings into short instances, inherit the subject label for every instance, and train instance-level classifiers. This assumes that all instances provide equally reliable diagnostic evidence. Multiple instance learning (MIL) avoids inherited labels by treating each subject as a bag. However, EEG datasets contain far fewer subjects than instances, which can limit the quality of the representations learned by end-to-end MIL. We propose BridgeMIL, a two-stage framework that decouples instance representation learning from subject-level supervision. Stage 1 pretrains the encoder without inherited instance labels by aligning temporally nearby windows and independently sampled within-subject sub-bags. Variance and covariance regularization prevent collapse and reduce redundancy without negative pairs. Stage 2 transfers the encoder to an attention-based MIL aggregator, applies supervision only to subject predictions, and limits representation drift through feature retention. Across three EEG disease datasets and five representative backbones, BridgeMIL attains the highest mean accuracy in 14 of 15 dataset-backbone settings and an overall mean accuracy of 76.57%, 4.28 percentage points higher than the strongest baseline. Further analyses reveal substantial variation in inherited-label reliability across instances, greater performance sensitivity to subject scarcity than to instance scarcity, and a more structured representation space with distinct subject-wise clusters and improved separation between diagnostic classes. Together, these findings underscore the importance of aligning supervision with the subject-level prediction objective while learning from abundant EEG instances without assigning disease labels to individual instances.
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All authors Zhiyuan Ma, Zeyuan Li, Zhiyi Lu, Jiacheng Hao, Youlang Du, Zhen Jiang, Xinche Zhang, Yuhao Sun, Xinke Shen, Sen Song

Machine Learning

SDO: Structure-Aware Data Organization for Efficient LLM Post-Training

Jinliang Gao, Ning Yang, Hai Wang et al. (+2 more)

Post-training of large language models is expensive, and existing efficiency improvements mainly focus on selecting informative samples or designing training schedules. However, data organization itself is usually treated as a static preprocessing step: embedding-based grouping methods construct fixed partitions before training and cannot adapt to the evolving sample exposure during optimization. As a result, all samples receive similar exposure despite their different optimization needs, leading to redundant updates for some samples while leaving others under-optimized. To address this problem, we propose SDO (Structure-Aware Data Organization), a plug-and-play data organization framework with an exposure-driven feedback mechanism that organizes mini-batch composition and sample exposure according to representation-space structure. SDO operates epoch by epoch on frozen external embeddings, avoiding model warm-up training overhead: within each epoch, locality-aware batching forms coherent mini-batches via KNN neighborhood traversal; across epochs, exposure-balanced scheduling records per-sample participation and reduces the sampling probability of over-exposed samples to preserve long-term coverage. Across SFT, DPO, and GRPO, SDO accelerates convergence, with the largest gains observed in the early-to-mid phase, producing more coherent gradients and more balanced accuracy across question types without permanently excluding training samples.
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All authors Jinliang Gao, Ning Yang, Hai Wang, Baili Xiao, Pin Lyu

Machine Learning

RLPF: Reinforcement Learning from Performance Feedback for Code Generation

Huihao Jing, Haozhe Cui, Wenbin Hu et al. (+9 more)

Code models are increasingly trained with execution feedback, but most training signals still stop at correctness. This leaves an important gap for systems code: two programs can pass the same tests while differing greatly in runtime. We study how to train code agents to prefer faster correct implementations, rather than treating efficiency only as an evaluation metric. The key difficulty is that runtime is a fragile reward. It is meaningful only after a program is correct, varies across tasks, and gives little guidance when most sampled programs fail to compile or run. We propose RLPF, reinforcement learning from performance feedback, which turns execution outcomes into a staged reward. Failed programs are ordered by execution progress, while correct programs are ranked by their relative improvement from the baseline toward the expert reference. This gives useful feedback before correctness and performance-sensitive feedback after correctness. Fine-tuning Qwen3-32B with RLPF on PerfCodeBench raises correct-and-runnable solutions from $11.1\%$ to $54.6\%$ and improves relative efficiency from $8.1\%$ to $38.6\%$. The trained model becomes competitive with stronger open-weight systems, and its optimization behavior transfers modestly to EffiBench-X. Additional studies show that model-generated references provide useful but weaker supervision, and that the full composite reward is more reliable than correctness-only or runtime-only baselines. These results suggest that code agents can be trained not only to pass tests, but also to optimize the programs they write.
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All authors Huihao Jing, Haozhe Cui, Wenbin Hu, Shaojin Chen, Haochen Shi, Changxuan Fan, Yuxuan Liu, Hanyu Yang, Sirui Zhang, Ziyi Chen, Haoran Li, Yangqiu Song

Machine Learning

Beyond KV Reconstruction: Functional Reconstruction for MLA Draft Models in Speculative Decoding

Weiye Shi, Fanxu Meng and Muhan Zhang

Multi-head latent attention (MLA) is increasingly important for long-context LLM inference because compact latent states replace the growing key-value (KV) cache and reduce decoding memory traffic. Yet most capable open checkpoints use multi-head or grouped-query attention (MHA/GQA), so conversion is needed to obtain MLA's cache efficiency without retraining from scratch. Speculative decoding offers complementary acceleration, but its speedup depends on agreement between draft proposals and target verification. We find that direct MHA/GQA-to-MLA conversion can sharply reduce this agreement: low-rank factorization and RoPE handling introduce attention-function errors that may be tolerable for standalone generation but substantially lower draft-token acceptance. We therefore formulate MLA draft construction as functional reconstruction rather than cache compression. Our end-to-end (E2E) method optimizes each converted MLA attention module to reproduce the post-output-projection response of its original MHA/GQA counterpart on calibration hidden states. This converter-agnostic post-conversion procedure preserves the converted cache and inference graph and requires neither verifier logits nor verifier supervision. We evaluate 192 model-converter-backend-method-task configurations spanning four Llama/Qwen draft-target pairs, TransMLA and MHA2MLA, HF and vLLM, and four 200-prompt tasks. With a 0.5-percentage-point reporting tolerance, Functional Reconstruction materially improves acceptance in 37 of 64 matched task cells, leaves 26 practically unchanged, and materially decreases one. Code and evaluation artifacts are available at https://github.com/swyhahaha/FunctionalMLA.
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Machine Learning · Cross-listed from cs.CV

Theatre Chapbooks At Scale: A Statistical Comparative Analysis of Typography

Diego Belzarena, Seginus Mowlavi, Paula Casariego Castiñeira et al. (+3 more)

We propose a statistical methodology that quantifies the similarity of typefaces between printed historical books. This provides a tool that accelerates philological analysis. Using character prototypes derived from clustering and aligning automatically extracted character images, the method defines a typeface distance between any two books. To produce actionable outputs, we develop an a contrario statistical framework to interpret the significance of the computed typeface distances. We apply the method to the philological study of 17 th -century Spanish printed theatre chapbooks in a quantity that exceeds the capabilities of systematic visual inspection by human experts. Our method enables the automatic comparison of Roman and Italic types extracted from different books. After validation by human experts, our method has led to new printer attributions being discovered, and former printer attributions being revised. This success strongly suggests that our method has the potential to enable digital bibliography on a larger scale than was previously possible.
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All authors Diego Belzarena, Seginus Mowlavi, Paula Casariego Castiñeira, Alejandra Ulla Lorenzo, Gregory Randall, Jean-Michel Morel

Machine Learning

PlatformBid: An Auto-Bidding Benchmark from a Unified Advertising Platform's Perspective

Shengtian Yang, Yewen Li, Peng Jiang et al. (+5 more)

Real-time bidding is central to computational advertising, comprising three elements: Supply Side Platform (SSP) selling ad impressions, Demand Side Platform (DSP) bidding for advertisers, and Ad Exchange conducting auctions between them. Traditional auto-bidding algorithms focus solely on the DSP side, maximizing advertiser conversions by adjusting bids against competitors. However, current big ad platforms, such as social media and e-commerce companies, now integrate SSP, DSP, and Ad Exchange functions internally. From such ad platforms' perspective, the goal of the auto-bidding algorithms is not only to maximize the advertisers' conversions, but also the total revenue of the platform. Given the lack of platform-centric evaluation frameworks and the pressing need to advance auto-bidding research, we propose PlatformBid - the first comprehensive benchmark designed from a unified ad platform's perspective. To accurately reflect the real-world auto-bidding scenarios, we define three representative settings: (1) homogeneous competition with identical algorithms across advertisers, (2) heterogeneous competition with diverse algorithmic strategies, and (3) promotional competition where some advertisers surge budgets for boosting sales during promotional events like Black Friday. We systematically evaluate a broad spectrum of existing auto-bidding methods across these settings, encompassing classical control methods, RL-based methods, and recent generative methods. Besides these methods, we further propose a novel auto-bidding method based on flow-matching, termed BidFlow, which leverages the flow-matching method's expressive policy representation to effectively handle dynamic competitive environments. Online experiments on Kuaishou further show a +0.68% improvement in target cost, providing deployment evidence for the offline-online consistency of PlatformBid.
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All authors Shengtian Yang, Yewen Li, Peng Jiang, Zhiyi Lyu, Bo An, Peng Jiang, Qingpeng Cai, Lei Feng

Machine Learning

DoTime: A Synthetic Benchmark Generator for Interventional and Counterfactual Time Series

Dennis Thumm, Billy Tim Anthony and Ying Chen

Most benchmarks for causal inference over time series are observational, small, or domain-specific, leaving interventional and counterfactual estimation under-served exactly where it matters most, such as in healthcare, policy evaluation, and climate science. We introduce DoTime, an open, scalable, and theoretically grounded generator of multivariate temporal structural causal models (TSCMs) with interventions, released as the \code{dotime} PyPI package together with four frozen evaluation suites. Beyond existing work, it adds capabilities absent from prior generators: continuous-time intervention windows, counterfactual sampling modes with a positivity guard, regime-switching SCMs as a strict generalization of interrupted time series, non-stationary dynamics by construction with switching SCM parameters, and deterministic ramp and sinusoidal intervention profiles that place trends and structural breaks inside the evaluation window. Moreover, it demonstrates the suitability of the generator as a prior for a causal foundation model reference implementation. The released suites span a training-scale snapshot of $100{,}000$ trajectories and eight named identification structures, each with exact ground truth: paired interventional trajectories from the same SCM throughout, and shared-noise counterfactuals in the continuous-time suite. We ship reference baseline implementations with an evaluation harness, and pose a falsifiable claim: interventional training buys a measurable direction-accuracy advantage over an observational model of identical capacity. It is tested across three training seeds per arm. Under structure-matched evaluation on held-out episodes, the interventional prior-fitted network's (PFN) gap is positive in every structure, trajectory length, and seed tested.
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Machine Learning · Cross-listed from quant-ph

LLM-Guided Initialization for Accelerated Hybrid Quantum-Classical Medical Image Classification

Riza Alaudin Syah, Irwan Alnarus Kautsar and Haza Nuzly Bin Abdull Hamed

Variational quantum algorithms often encounter barren plateaus, where cost gradients decay rapidly with increasing circuit depth, undermining the trainability of parameterized quantum circuits. This paper evaluates AdaInit (Adaptive Initialization), proposed by Zhuang and Cunningham, which uses large language models to propose initial parameters for quantum neural networks. We study a simplified single-query AdaInit variant paired with GPU-accelerated simulation in NVIDIA CUDA-Q and apply it to binary classification on the DMR-IR mammography dataset. AdaInit delivers 14.6 times higher gradient variance at initialization than random initialization (0.0095 vs. 0.0006), producing 160 times faster convergence (1.1s vs. 176 s) while maintaining the same classification accuracy of 61.4 percent. We provide theoretical analysis grounded in the geometry of parameterized circuit landscapes and show empirically that LLM-guided initialization places the optimizer in trainable regions of parameter space. Beyond performance, our results indicate that a single LLM query can yield informative parameters without iterative refinement, suggesting a low-overhead path to improved trainability. The findings validate AdaInit in a medical imaging setting and demonstrate its compatibility with GPU-accelerated quantum backends for practical speedups.
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Machine Learning

Regularizing modality contribution drift in multimodal continual learning

Zhen Zhang, Jielei Chu, Wenjie Ban et al. (+5 more)

Multimodal continual learning (MMCL) aims to acquire new knowledge from multimodal data while retaining previously learned knowledge. Existing MMCL methods primarily mitigate forgetting by aligning cross-modal representations or preserving feature-level semantic similarity. However, different tasks may rely on different modalities, and learning new tasks can alter how modalities contribute to predictions on previously learned tasks. It remains underexplored how modality contributions evolve across incremental stages and how such changes relate to forgetting in MMCL. We term such changes Modality Contribution Drift (MCD) and introduce an MCD score based on controlled modality-subset interventions. Our theoretical and empirical analyses show how contribution drift can lead to forgetting, while existing MMCL and conventional CL methods do not effectively mitigate MCD. To address this issue, we propose Continual Modality Contribution Drift Regularization (CMCDR) to preserve the modality contribution profiles of previously learned tasks in both replay-based and replay-free settings. In the replay-based setting, CMCDR estimates modality contributions from stored old samples and regularizes their drift relative to a frozen previous model. In the replay-free setting, CMCDR uses current-task samples as probes to match old-class contribution profiles between the current and frozen models without storing old exemplars. Across six benchmarks covering multimodal class-incremental learning and continual multimodal question answering, CMCDR substantially reduces modality contribution drift, improves average accuracy by 0.88-7.66 percentage points, and reduces average forgetting by 0.85-11.55 percentage points over the corresponding baselines.
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All authors Zhen Zhang, Jielei Chu, Wenjie Ban, Tian Sang, Yuxiao Li, Bin Liu, Fengmao Lv, Tianrui Li

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

PlantBGC: Transformer for Plant BGC Discovery via Label-Free Domain Adaptation and Weak Supervision

Yuhan Zhao, Nidhi Grover, Zhishan Guo et al. (+1 more)

Plant biosynthetic gene clusters (BGCs) encode specialized-metabolite pathways, yet curated plant BGC labels remain scarce, hindering supervised discovery at genome scale. Existing plant BGC mining tools are largely signature- and rule-driven and do not fully leverage recent advances in contextual representation learning for modeling long-range domain context and controlling false positives under strong domain shift. We seek an AI-assisted workflow that narrows experimental search space by transferring supervision from well-annotated microbial BGCs to plant genomes. We present PlantBGC, representing genomes as ordered Pfam-domain sequences and learning BGC-likeness with an encoder-only Transformer trained on MIBiG microbial BGCs and adapted to plants via label-free masked language modeling. On microbial benchmarks, PlantBGC achieves token-level AUC = 0.988 (10-fold CV) and 0.979 (leave-class-out). On plants, adaptation improves known-BGC recovery on n = 34 curated loci under strict 100% coverage, increasing recovery from 29.4% to 67.6% and indicating more complete boundaries. GO/KEGG-derived weak supervision reduces proxy primary-like ratio by 48.40% (GO) and 45.20% (KEGG), with consistent per-species reductions (paired Wilcoxon p = 1.53e-5). Compared to plantiSMASH, PlantBGC yields more compact loci on matched regions (median length ratio = 0.278; 93.8% of pairs are shorter).
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All authors Yuhan Zhao, Nidhi Grover, Zhishan Guo, Ning Sui

Machine Learning

Do You Really Need to Pretrain Q-Functions for Online RL Fine-Tuning?

Perry Dong, Ron Polonsky, Dorsa Sadigh et al. (+1 more)

Pre-training followed by fine-tuning has become the dominant recipe for learning performant policies, and in value-based reinforcement learning (RL) this raises a natural question: given a pretrained policy, should the Q-function be pretrained on offline data too? Conventional wisdom suggests it should, but recent results show that online RL with a randomly-initialized Q-function can result in highly performant and reliable policies without needing to pretrain the Q-function. In this paper, we systematically study whether pretraining the Q-function actually helps when fine-tuning on top of a pretrained base policy. We find, surprisingly, that naive Q-function pretraining often provides little benefit over random initialization. We show this stems from a fundamental mismatch: the Q-function learned during pretraining targets the pretrained policy's Q-function, not the Q-function that online fine-tuning converges to, and this gap persists even after offline value maximization. Motivated by this finding, we propose Initialization via Policy Ensemble (IPE), a simple method that trains multiple diverse policies and uses their pooled rollouts to bootstrap the Q-function learning in online RL. Across a suite of challenging continuous control benchmarks, IPE yields an average 1.26x improvement in fine-tuning performance over naive Q-function pre-training.
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All authors Perry Dong, Ron Polonsky, Dorsa Sadigh, Chelsea Finn

Machine Learning

From Classification to Regression: Using a Fruitfly to Solve Equations

Shady E. Ahmed and Panos Stinis

We present a novel approach to regression tasks using classification which is motivated by the mechanism used by fruitflies to sense their environment. Specifically, we formulate a general framework for learning nonlinear input-output relationships by replacing complex global surrogate models with a finite library of representative local patterns. Since scientific data often occupy limited and recurring regions of the input space, we generate predictions by measuring similarities between a query and stored patterns, then combining their associated responses through weighted reconstruction. We apply this approach to nonlinear dynamical systems, data-driven regression, and physics-informed learning using suitable embeddings and similarity measures. For dynamical systems, our offline-online workflow extracts patterns from data or governing equations during the offline phase, while online prediction requires only similarity evaluation and response aggregation. This structure helps us reduce computational and memory demands while providing explicit control over the trade-off among accuracy, storage, and inference cost.
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Machine Learning · Cross-listed from cs.AI

Can AI agents conduct open-ended AI research? Early evidence from two case studies

Peter Kirgis, Sayash Kapoor, Andrew Schwartz et al. (+21 more)

Forecasts of explosive AI progress hinge on AI agents automating AI research. But evidence on whether agents can carry out open-ended AI research is thin. Current evaluations either test agents on narrow, verifiable tasks, which excludes open-ended research, or submit AI-generated papers to blind peer review, which is overstretched, stochastic, and suffers from poor review quality. We introduce a third way to measure progress towards AI R&D automation. An agent takes on the central, open-ended research question of a high-quality unpublished paper, and the paper's original authors grade its output. We call these shadow evaluations. We ran shadow evaluations on two unpublished NeurIPS 2026 submissions, giving frontier agents six days and thousands of dollars of compute. The agents completed all of the engineering without human help, yet could not make substantial progress towards answering the research questions. As a result, both papers were unambiguously rejected by the authors. We identify five recurring failure modes: poor judgment about the bar for publishable research, uncreative responses to shortcomings in the research design, ineffective backtracking from dead ends, poor resource awareness, and instruction drift. A robustness check with a second model and scaffold reproduced these failures. We release the expert reviews, survey responses, agent repositories, and logs. Our results provide early evidence that today's agents can do the engineering of AI research, but struggle with critical parts of the research lifecycle.
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All authors Peter Kirgis, Sayash Kapoor, Andrew Schwartz, Stephan Rabanser, David Africa, Konstantinos Voudouris, Viet Nguyen, Toby Pilditch, Magda Dubois, Harry Coppock, Cozmin Ududec, Nitya Nadgir, Matilda Orona, Tilman Bayer, Derrick Chan-Sew, Yue Ling, Abhishek Shetty, Helen Toner, Gillian Hadfield, Seth Lazar, Steve Newman, Shoshannah Tekofsky, Rishi Bommasani, Arvind Narayanan

Machine Learning

Inverse Learning of Latent Risk-Neutral Densities from Irregular Option Quotes

Lennon J. Shikhman, Michael Galarnyk, Aadi Dash et al. (+1 more)

Accurate option prices do not imply accurate recovery of the latent risk-neutral density. We study this distinction with two complementary benchmarks. A controlled benchmark exposes simulator-truth densities for latent evaluation, while a chronological NIFTY benchmark tests only held-out market prices. A two-component lognormal mixture has the lowest aggregate price, $L^1$, Wasserstein, and fixed-tail errors on the synthetic benchmark. Learned operators retain narrower strengths: DeepONet reduces 1% quantile and variance error by 39.0% and 34.6% relative to the mixture, and a quote transformer reduces $L^1$ by 16.4% on the structurally misspecified Merton family. A numerical conditioning analysis explains why these rankings can differ: after enforcing mass and forward constraints, 95 of 126 pricing directions are numerically null, and two densities separated by $L^1 = 0.061$ produce identical prices on the covered strikes. On 524 held-out NIFTY calls, validation-selected test-time adaptation reduces DeepONet RMSE by 28.3%, but per-expiry mixture and SVI fits remain much more accurate. The evidence supports target-dependent inductive bias, not a universal winner.
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All authors Lennon J. Shikhman, Michael Galarnyk, Aadi Dash, Nicholas A. Welsh

Machine Learning

When Do Learned Diffusion Proposals Help Constraint Solving? A Controlled Study on Continuous Algebraic Systems

Quang Bui, Sparsh Roy, Akash Gundimeda et al. (+1 more)

Solving a continuous algebraic constraint system requires two decisions: which values satisfy the constraints, and which structural augmentation renders an unsolvable system solvable. Classical solvers answer the first well and the second only by enumeration. On that discrete decision, a candidate-conditioned repair ranker choosing among K augmentations reaches the exhaustive-search ceiling at a fraction of the calls, outperforming random (0.997 vs 0.236 balanced nonlinear menu accuracy; p < 10^-70; 0.982 +/- 0.006 across seeds) and beating a budget-matched per-candidate probe on accuracy and cost. MARC turns such a system into a factor graph, over which a graph-neural diffusion denoiser proposes assignments, descent on an exact computer-algebra energy polishes them, and an exact symbolic checker certifies solutions. Evaluations of diffusion-based proposals rarely include one control: random multi-start under the same refinement budget. Applied to our system, it sharply curtails what the learned proposal contributes on the value decision. Does it beat random multi-start at choosing satisfying assignments? Only narrowly, in a predictable regime. Across trapped low-dimensional families it ties with random restart, but dominates in high dimension, where random search fails. Once variables couple, the advantage is gone. Since all methods share one polish and one checker, best-of-K random multi-start succeeds with probability exactly 1 - (1 - q(n))^K, where q(n) is single-start reachability; one measured constant, with no free parameters, reproduces the entire curve (mean absolute error 0.012). The favorable regime is not specific to our synthetic families: across eight real-world systems in robotics, positioning, optimization, and algebra, classical multi-start solved all eight, none in the learning-favorable regime. We map the regimes in which learned proposals improve solvers.
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All authors Quang Bui, Sparsh Roy, Akash Gundimeda, Davin Yin

Machine Learning

Skillful forecasting of offshore winds from satellite scatterometer constellations

Francesco Pinto, Luca Lanzilao, Paco Lopez Dekker et al. (+1 more)

Accurate intraday forecasts of offshore wind are becoming increasingly important for power system operation and the integration of growing shares of offshore wind energy. Operational forecasts rely predominantly on numerical weather prediction (NWP), which is not optimized for lead times of minutes to hours, where initial-condition accuracy dominates forecast skill. Although satellite scatterometer observations are routinely assimilated into NWP, they have not previously been used directly for forecasting. Here we present WindCastNet, the first satellite-based nowcasting framework for offshore wind speed and direction, introducing a new paradigm for intraday forecasting that learns from spatiotemporally irregular satellite observations. WindCastNet predicts offshore wind fields from observations acquired by satellite scatterometer constellations. WindCastNet employs a partial convolutional long short-term memory network that exploits microwave radar observations from the European, Chinese, and Indian scatterometers despite their irregular spatial coverage, asynchronous sampling, and variable revisit times. Spatial observation masks and inter-observation intervals are encoded, while a continuous temporal representation enables forecasts at arbitrary lead times. Evaluated over the North Sea, WindCastNet reduces the root-mean-square error by 23% and 7% relative to the HARMONIE MEPS model at lead times of 1 and 2 h, respectively, and outperforms persistence by 9-15% during the first three forecast hours. Forecast skill decreases under strong-wind conditions and spatially non-uniform flow. These results demonstrate that satellite scatterometer constellations can provide an independent and competitive source of short-term offshore wind forecasts, opening new opportunities for renewable energy forecasting but also broader marine weather applications, including tropical cyclone nowcasting.
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All authors Francesco Pinto, Luca Lanzilao, Paco Lopez Dekker, Angela Meyer

Machine Learning · Cross-listed from cs.SE

MindForge: Teaching Small Language Models Whole-Life-Cycle Software Engineering via Source-Free Program Synthesis

Yihao Chen, Shi Chang, Khaled Chawa et al. (+4 more)

Coding agents have made substantial progress on software engineering tasks that modify existing codebases, including bug fixing and feature implementation. However, constructing a complete program from scratch remains a major challenge: even the frontier models evaluated on ProgramBench fully resolve fewer than 1% of tasks. One obstacle is the lack of scalable training environments for this from-scratch setting, spanning the whole software engineering life cycle, as existing environment-construction frameworks focus only on a single phase in software development. To address this gap, we introduce MindForge, an automated pipeline that converts open-source command-line programs into source-free environments that expose only a compiled reference executable and its documentation. Using MindForge, we construct training environments from repositories disjoint from those in ProgramBench, and curate a high-quality data recipe consisting of program synthesis trajectories using GLM-5.2 as the teacher agent. Fine-tuning Qwen3.6-27B on these trajectories increases its ProgramBench average test pass rate from 37.98% to 49.51%, achieving performance comparable to substantially larger frontier models. Moreover, the fine-tuned model consistently improves over the base model across all seven unseen software engineering benchmarks, spanning long-horizon repository generation and translation, bug fixing, feature implementation, and cross-language issue resolution, with absolute gains of 31.00 points on RepoZero-C2Rust, 14.16 on DeepSWE, 10.70/4.56 on NL2Repo-Bench (with/without tests), 5.04 on SWE-bench Verified, 5.93 on SWE-bench Pro, 5.22 on SWE-bench Multilingual, and 4.94 on FeatBench.
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All authors Yihao Chen, Shi Chang, Khaled Chawa, Feng Lin, Boyuan Chen, Shaowei Wang, Ahmed E. Hassan

Machine Learning

Cost-Sensitive Conformal Prediction and Human-in-the-Loop Abstention for Imbalanced High-Stakes Decision Support: A Multi-Domain Benchmark

Manpreet Singh, Akshatha Srikantha and Shyamal Lakhanpal

High-stakes decision systems in credit scoring, fraud detection, healthcare, and industrial safety require reliable uncertainty quantification under severe class imbalance and asymmetric error costs. Standard marginal conformal prediction (CP) provides valid overall coverage guarantees; however, we show that it severely under-covers rare, costly minority classes, with minority-class coverage dropping to as low as 0.5% on certain datasets. To characterize and address this limitation, we conduct a comprehensive benchmark comparing marginal CP, class-conditional (Mondrian) CP, and cost-controlled abstention mechanisms across 15 real-world imbalanced tabular datasets, 7 classification models, 3 probability calibration techniques, and 10 random seeds, resulting in 3,150 experimental runs. Our results show that Mondrian CP restores valid minority-class coverage, achieving an average minority-coverage improvement of 61.7 percentage points over marginal CP (p < 1e-80). Furthermore, combining Mondrian CP with cost-controlled abstention significantly reduces expected decision cost compared with standard decision boundaries, confidence-based rejectors, and risk-controlled rejectors under realistic human review budgets. We further quantify dataset-specific break-even thresholds at which deferring ambiguous instances to human experts becomes cost-effective. These findings provide practical guidance for deploying distribution-free, cost-aware uncertainty quantification in high-stakes decision support systems.
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Machine Learning · Cross-listed from cs.AR

Investigating reservoir computing for branch prediction in pipelined processors using emerging CMOS memristor devices

Harvey Samuel George Johnson and Sendy Phang

This project aimed to develop a novel reservoir compute (RC) implementation framework targeting high-speed operation and integration with CMOS digital logic. With the target workload of branch prediction (BP) for multistage pipelined central pro-cessing unit (CPU) cores. For this, a novel memristor based RC design framework was developed within the context of the workload requirements. This was then implemented in simulation using industry standard modelling languages of System Verilog (SV) and Verilog-AMS (VAMS).The developed RC design framework was subsequently verified using a basic sequence detection task before further benchmarking for its effectiveness at BP. The developed RC framework was tested using the Dhrystone performance benchmark, while targeting the RISC-V RV64GC instruction set architecture (ISA). Conducted testing demonstrates that RC shows great promise for ap-plication to BP and is capable of achieving impressive overall prediction accuracy. However, testing also shows that further refinement of the developed RC design framework is necessary to address shortfalls in the adaptability of the proposed RC system. As comparison against the state of the art TAGE predictor showed the proposed RC design framework to be 15x slower to adapt to changes in branching behaviour.
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Machine Learning

Minimal Markovization via Stable Quotients in Holonomy-Cover Decision Processes

Zuyuan Zhang, Yongshan Chen, Mahdi Imani et al. (+1 more)

An agent acting under partial observability must retain a recursively updateable statistic of history that restores the Markov property, but the smallest such statistic is generally unknown. We characterize this minimal Markov sufficient statistic for holonomy-cover decision processes, a structured POMDP class in which the visible dynamics are Markov and every realized visible transition applies a fixed permutation to a hidden mode. In particular, we construct the stable quotient, the coarsest observation-wise abstraction preserving one-step rewards and quotient successors, and prove that the pair of the current observation and stable class forms an exact finite Markov state. When the current class is correctly initialized, exact class tracking requires exactly the minimal memory symbols, in the sense that under reachability and pairwise decision separation at a maximizing observation, no arbitrary finite-memory controller can use fewer. Under resettable diagnostics, nearest-prototype class inference has exponentially decaying error, and a calibrate-then-restart reduction transfers finite-MDP guarantees to the recovered state. The results enable Holonomy Memory Reinforcement Learning. It represents memory by the current stable class, updates it through ordered edge transports, identifies local class coordinates when diagnostics are available, and applies a standard finite-MDP RL backbone after synchronization. Experiments recover an exact compression from raw states to quotient states and achieve perfect paired-order accuracy with three decision-time memory states, matching the quotient oracle and outperforming the non-oracle baselines.
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All authors Zuyuan Zhang, Yongshan Chen, Mahdi Imani, Tian Lan

Machine Learning

Voronoi Histograms for Adaptive Vectorization of Expected Persistence Diagrams

Kaifeng Zhang and Kai Ming Ting

Persistence Diagram (PD) is known to capture point cloud topology effectively, but its computation has high time complexity. Expected Persistence Diagram (EPD) has been developed to reduce the time cost by studying the topology of multiple subsets of a point cloud and it serves as a distribution of topological features. Existing EPD vectorizations often rely on predefined point transformations, such as Gaussian or landscape functions. We study an alternative discretization based on Voronoi histograms, which trades smooth functional approximation for adaptive partition-based counting. We propose to use Voronoi Diagram-based histogram as the vectorization of EPD, without imposing an explicit smooth point transformation model. Under stated separation and normalization conditions, we establish stability bounds and characterize when the histogram representation preserves Wasserstein-scale variation. We demonstrate the effectiveness of our proposed representation on real-world datasets which have significant topological features for classification and dimensionality reduction tasks.
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Machine Learning

Hierarchical Spatio-Temporal Transformer for Coherent Emergency Department Forecasting

Filipa Lino, Bárbara Tavares, Carlos Santiago et al. (+2 more)

Emergency Departments (EDs) are critical access points in healthcare systems, yet they face persistent pressure from unpredictable patient demand, seasonal surges, and non-urgent visits. Effective ED planning requires forecasts at multiple decision-making levels: hospitals need local demand estimates for staffing and bed management, regions require forecasts to coordinate healthcare units, and national authorities need system-wide projections for capacity planning. However, most existing approaches forecast ED demand independently at a single level, ignoring the hierarchy linking hospitals, regions, and national systems. This can produce incoherent predictions, where hospital-level forecasts do not aggregate consistently to regional or national demand. We propose HierSTT, a hierarchical Transformer-based framework for coherent multi-level ED forecasting. HierSTT jointly predicts hospital, regional, and national level demand in a single end-to-end model. A Temporal Fusion Transformer captures national dynamics, while spatio-temporal Transformer encoder-decoder modules model regional and hospital demand conditioned on higher-level forecasts. A coherence-aware loss penalizes cross-level inconsistencies during training. We further introduce a nationwide Portuguese ED dataset covering 81 hospitals across 5 regional health administrations, with heterogeneous covariates at each level. Experiments show that HierSTT reduces average WAPE by 32% relative to the best non-hierarchical deep learning baseline and outperforms all classical hierarchical reconciliation methods, while producing near-coherent predictions across levels. Additional resources associated with this work are available at https://github.com/FilipaLino/HierSTT.
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All authors Filipa Lino, Bárbara Tavares, Carlos Santiago, Cláudia Soares, Manuel Marques