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Nov 6

Static Recovery Is Not Dynamic Stability: Dynamics-Aware Benchmarking of Protein Motif Scaffolding

Protein motif scaffolding benchmarks assess whether generative models can build scaffolds around functionally important residues. Their conclusions depend on which motifs are tested and which criteria define success. Existing benchmarks typically use small hand-curated motif sets and static refolding criteria, but protein function often depends on conformational ensembles and transitions. Here, we address both benchmark scope and success criteria. We introduce BILBY-PRO, a systematically derived benchmark of structurally conserved functional motifs from PROSITE-linked experimental structures, comprising 220 cases from 174 PROSITE motif-pattern entries. Evaluating six recent scaffold-generation models reveals distinct patterns in target coverage and unique-solution yield: RFDiffusion and Proteina solve more targets, whereas ESM3 produces more unique successful scaffolds on the targets it solves. We further introduce BILBY-MD, a reference-based all-atom molecular dynamics evaluation framework. Applied to statically solved designs from the original MotifBench benchmark, it compares motif drift, scaffold drift, motif-contact preservation, and motif-dihedral free-energy landscapes against reference simulations. Of 55 statically solved model-problem pairs, 31 satisfy our MD-supported criterion and only 8 pass all checks. Compact, self-contained motifs are often MD-supported, whereas interface-like or context-dependent motifs fail more frequently. Static refolding success therefore provides useful evidence of local motif recovery but does not establish dynamical fidelity of the full scaffold. BILBY highlights three complementary axes of motif-scaffolding evaluation: target coverage, unique-solution yield, and MD-supported dynamical fidelity.

HFMI-PROFOUND PROFOUND
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Nov 5

AnE: Pushing the Reasoning Frontier of Multimodal LLMs via Anchor Evolution

Post-training via Supervised Fine-Tuning (SFT) and Reinforcement Learning (RL) is crucial for enhancing reasoning in Multimodal Large Language Models (MLLMs), yet existing paradigms often reach a performance bottleneck due to the limitations of static data. While current methods leverage self-reflection or self-evolution to push these boundaries, they still suffer from cognitive drift and hallucinated reasoning paths caused by low-quality synthetic data. To address these challenges, we propose Anchor Evolution (AnE), a new paradigm that integrates truth-anchored data curation and model evolution, achieving faithful and steady performance gains at the reasoning frontier. Specifically, we propose Truth Anchor Expansion, which pinpoints the model failing frontier via trajectory rollouts and leverages ground-truth databases to retrieve high-fidelity anchors for faithful data curation. Subsequently, we introduce the Scaffold-Stripping Mechanism to internalize reasoning capabilities. This mechanism first anchors reasoning paths via scaffold-augmented supervision to mitigate the learning complexity and distribution drift of direct SFT on raw data, then leverages RL to strip the scaffold template, thereby effectively transitioning the reasoning paths into intrinsic model capabilities. Experimental results on multimodal reasoning benchmarks show that our method substantially advances the model performance frontier, improving the base model by 10.3\% across eight multimodal benchmarks and achieving state-of-the-art results. The code will be made publicly available.

  • 8 authors
·
May 24

Momentum Benefits Non-IID Federated Learning Simply and Provably

Federated learning is a powerful paradigm for large-scale machine learning, but it faces significant challenges due to unreliable network connections, slow communication, and substantial data heterogeneity across clients. FedAvg and SCAFFOLD are two prominent algorithms to address these challenges. In particular, FedAvg employs multiple local updates before communicating with a central server, while SCAFFOLD maintains a control variable on each client to compensate for ``client drift'' in its local updates. Various methods have been proposed to enhance the convergence of these two algorithms, but they either make impractical adjustments to the algorithmic structure or rely on the assumption of bounded data heterogeneity. This paper explores the utilization of momentum to enhance the performance of FedAvg and SCAFFOLD. When all clients participate in the training process, we demonstrate that incorporating momentum allows FedAvg to converge without relying on the assumption of bounded data heterogeneity even using a constant local learning rate. This is novel and fairly surprising as existing analyses for FedAvg require bounded data heterogeneity even with diminishing local learning rates. In partial client participation, we show that momentum enables SCAFFOLD to converge provably faster without imposing any additional assumptions. Furthermore, we use momentum to develop new variance-reduced extensions of FedAvg and SCAFFOLD, which exhibit state-of-the-art convergence rates. Our experimental results support all theoretical findings.

  • 4 authors
·
Jun 28, 2023

Don't Blame the Large Language Model: How Scaffolding Evolution Shapes Coding Agent Quality

Coding agents, autonomous systems that use large language models (LLMs) to resolve software engineering tasks, rely on agentic scaffolding: a middleware layer in between a developer and a large language model that orchestrates system prompts, tool execution, context management, and iterative reasoning loops. While these scaffoldings evolve at extreme velocities, no study has examined how this evolution affects agent quality (i.e., effectiveness and efficiency) over time. Practitioners regularly report quality regressions after scaffolding updates, yet consistently attribute them to the underlying model rather than the scaffolding itself. In this paper, we address this gap by conducting the first controlled longitudinal study that isolates the scaffolding's contribution. Unlike prior work that fixes the scaffolding and varies the model, we fix the model and vary only the scaffolding, evaluating 35 sequential releases to measure their impact on agent effectiveness and efficiency. We first empirically study the development and release evolution of five major open-source scaffoldings (i.e., Codex, Qwen Code, Gemini, OpenCode, and OpenHands), revealing extreme release velocities exceeding two releases per day and thousands of issues within months. We then perform a controlled deep dive into 35 sequential releases of the Qwen Code CLI, evaluating each against 50 stratified SWE-bench Verified tasks while holding the underlying LLM constant. We trace the resulting quality fluctuations to specific development patterns and architectural components, and illustrate our findings with concrete qualitative evidence linking individual pull requests to measured quality shifts.

  • 4 authors
·
Jul 3

DCAS: Decoupling CLI Agent Scaffolding to Internalize Planning across Scaffolds

CLI-based software-engineering agents have matured rapidly, yet the open ecosystem has converged on a single training environment: trajectory datasets used to fine-tune open models are collected almost exclusively under OpenHands. Models fine-tuned on this data score well under OpenHands but degrade substantially when deployed under any non-training scaffold. Untrained base models do not show this divergence, indicating the gap is fine-tuning-induced and tied to the conventions of the training scaffold. We argue that a load-bearing scaffold-specific behavior is planning structure, in two senses this paper distinguishes: explicit planning, a pre-execution plan produced as a first-class artifact, and implicit planning, the structural conventions that shape execution throughout the agent loop. Under this hypothesis, closing the gap requires moving planning from a fixed scaffold artifact to a learned model capability. We introduce Decoupling CLI Agent Scaffolding (DCAS), a backend-substitution interception layer that routes API traffic between any CLI scaffold and any backend model without modifying the scaffold, enabling cross-scaffold evaluation and planning-aware trajectory collection. Using DCAS, a controlled plan-source intervention confirms planning quality is a high-leverage component, with gains exceeding the cross-scaffold drops we observe. A model fine-tuned on a small set of DCAS-collected planning-aware trajectories under a single scaffold gains consistently across non-training scaffolds, and the two senses of planning are empirically separable in training data.

Steady-Forcing: Balancing Spatial Persistence and Motion Continuity in Long-Horizon Nature Video Diffusion

Autoregressive video diffusion models enable streaming generation but often degrade over long rollouts: static scene layouts drift, while mechanisms that improve spatial stability tend to suppress motion, causing natural flows such as water, fire, or smoke to stagnate. We study this stability-motion trade-off in fixed-camera long-horizon nature video generation, where the two failure modes can be more clearly separated than in moving-camera settings. We propose Steady-Forcing, a memory and training framework combining a persistent visual anchor (V-Sink), an exponential moving-average motion memory (EMA-Sink), block-relative temporal encoding, periodic cache purification, and distillation from a Wan2.1-14B teacher with motion-rewarded priors under task-focused configurations. Together, these components are designed to preserve background identity while sustaining visually plausible fluid dynamics over multi-minute autoregressive rollouts. Evaluations across seven baselines show that Steady-Forcing improves long horizon background consistency and imaging quality, while a blind user study indicates stronger perceived stability and motion continuity. The benchmark evaluation further suggest that generic VBench aggregate scores under-penalize fixed-camera artifacts as well as rewarding drift-induced optical flow as Dynamic Degree while not directly penalizing texture hardening or flow stagnation - motivating future task-specific benchmarks for static-camera nature-flow evaluation. Project page: https://minar09.github.io/steadyforcing/

Agent Evaluation Reliability: More Tasks Won't (Always) Fix An Agent Leaderboard

Agent evaluations are increasingly used to compare LLMs and inform deployment decisions, yet ranks can reflect not only the model but also the effects of the evaluation conditions such as the scaffolds or tasks. This makes reliability claim-dependent: an evaluation that reliably ranks deployed systems may not reliably rank underlying models. We ask which conclusions current agent evaluations reliably support and what additional evaluation would improve them. We develop a Bayesian variance-decomposition framework for sparse, imbalanced agent leaderboards and apply it to 22 benchmarks from the Holistic Agent Leaderboard and Harbor Index. The framework separates signal, performance differences relevant to the intended claim, from noise, irrelevant variation that can still change rankings. We find: (1) Reliability depends on the measurement goal. Fixed model-scaffold systems are ranked reliably (0.935-0.994), while underlying-model reliability is substantially lower (0.148-0.841). (2) Scaffold choice can change conclusions. Inter-scaffold reliability measures whether scaffolds preserve model rankings, showing that scaffold effects vary substantially across evaluations. (3) More tasks cannot resolve all uncertainty. Even infinitely many similarly constructed tasks improve model-ranking reliability of a benchmark by at most 0.097 when uncertainty is dominated by limited scaffold coverage. (4) Pooling diverse benchmarks can improve cross-task rankings at lower cost. For rankings across diverse agentic tasks, pooling benchmarks raises projected reliability from 0.44 to 0.75 at the same task budget and can reduce projected cost by up to 83\%. Evaluation design should follow the intended claim: identify what a score or ranking should mean, diagnose what limits its reliability, and spend evaluation budget on the sources of uncertainty that matter.

  • 5 authors
·
Sep 29

On the Collapse of Generative Paths: A Criterion and Correction for Diffusion Steering

Inference-time steering enables pretrained diffusion/flow models to be adapted to new tasks without retraining. A widely used approach is the ratio-of-densities method, which defines a time-indexed target path by reweighting probability-density trajectories from multiple models with positive, or in some cases, negative exponents. This construction, however, harbors a critical and previously unformalized failure mode: Marginal Path Collapse, where intermediate densities become non-normalizable even though endpoints remain valid. Collapse arises systematically when composing heterogeneous models trained on different noise schedules or datasets, including a common setting in molecular design where de-novo, conformer, and pocket-conditioned models must be combined for tasks such as flexible-pose scaffold decoration. We provide a novel and complete solution for the problem. First, we derive a simple path existence criterion that predicts exactly when collapse occurs from noise schedules and exponents alone. Second, we introduce Adaptive path Correction with Exponents (ACE), which extends Feynman-Kac steering to time-varying exponents and guarantees a valid probability path. On a synthetic 2D benchmark and on flexible-pose scaffold decoration, ACE eliminates collapse and enables high-guidance compositional generation, improving distributional and docking metrics over constant-exponent baselines and even specialized task-specific scaffold decoration models. Our work turns ratio-of-densities steering with heterogeneous experts from an unstable heuristic into a reliable tool for controllable generation.

  • 9 authors
·
Dec 10, 2025

Label-Free Detection of Governance Evidence Degradation in Risk Decision Systems

Risk decision systems in fraud detection and credit scoring operate under structural label absence: ground truth arrives weeks to months after decisions are made. During this blind period, model performance may degrade silently, eroding the governance evidence that justifies automated decisions. Existing drift detection methods either require labels (supervised detectors) or detect statistical change without distinguishing harmful degradation from benign distributional evolution (unsupervised detectors). No existing framework integrates drift detection with governance evidence assessment and operational response. This paper presents a label-free governance monitoring extension to the Governance Drift Toolkit that produces governance alerts rather than statistical alarms. The monitoring architecture applies composite multi-proxy monitoring across four proxy monitors (score distribution, feature drift, prediction entropy, confidence distribution), with governance-calibrated thresholds. Empirical evaluation on the Lending Club credit scoring dataset (1.37M loans, 11 years) demonstrates three findings. First, raw proxy metrics (Feature PSI delta up to 1.84, Score PSI delta up to 0.92) distinguish injected covariate degradation from natural temporal drift in an offline evaluation setting. Second, pure concept drift in P(Y|X) produces exactly zero delta across all proxy metrics in all windows, confirming the irreducible blind spot of label-free monitoring as a structural verification. Third, the composite score provides monotonic severity progression as more monitors trigger (0.583 to 0.833 to 1.000), enabling graduated governance response. Cross-domain comparison with IEEE-CIS fraud detection results shows the detectable/undetectable boundary is consistent across both domains. The toolkit and evaluation code are available as open-source artifacts.

  • 1 authors
·
Apr 19

Agent Drift: Quantifying Behavioral Degradation in Multi-Agent LLM Systems Over Extended Interactions

Multi-agent Large Language Model (LLM) systems have emerged as powerful architectures for complex task decomposition and collaborative problem-solving. However, their long-term behavioral stability remains largely unexamined. This study introduces the concept of agent drift, defined as the progressive degradation of agent behavior, decision quality, and inter-agent coherence over extended interaction sequences. We present a comprehensive theoretical framework for understanding drift phenomena, proposing three distinct manifestations: semantic drift (progressive deviation from original intent), coordination drift (breakdown in multi-agent consensus mechanisms), and behavioral drift (emergence of unintended strategies). We introduce the Agent Stability Index (ASI), a novel composite metric framework for quantifying drift across twelve dimensions, including response consistency, tool usage patterns, reasoning pathway stability, and inter-agent agreement rates. Through simulation-based analysis and theoretical modeling, we demonstrate how unchecked agent drift can lead to substantial reductions in task completion accuracy and increased human intervention requirements. We propose three mitigation strategies: episodic memory consolidation, drift-aware routing protocols, and adaptive behavioral anchoring. Theoretical analysis suggests these approaches can significantly reduce drift-related errors while maintaining system throughput. This work establishes a foundational methodology for monitoring, measuring, and mitigating agent drift in production agentic AI systems, with direct implications for enterprise deployment reliability and AI safety research.

  • 1 authors
·
Jan 6

DRIFT-Net: A Spectral--Coupled Neural Operator for PDEs Learning

Learning PDE dynamics with neural solvers can significantly improve wall-clock efficiency and accuracy compared with classical numerical solvers. In recent years, foundation models for PDEs have largely adopted multi-scale windowed self-attention, with the scOT backbone in Poseidon serving as a representative example. However, because of their locality, truly globally consistent spectral coupling can only be propagated gradually through deep stacking and window shifting. This weakens global coupling and leads to error accumulation and drift during closed-loop rollouts. To address this, we propose DRIFT-Net. It employs a dual-branch design comprising a spectral branch and an image branch. The spectral branch is responsible for capturing global, large-scale low-frequency information, whereas the image branch focuses on local details and nonstationary structures. Specifically, we first perform controlled, lightweight mixing within the low-frequency range. Then we fuse the spectral and image paths at each layer via bandwise weighting, which avoids the width inflation and training instability caused by naive concatenation. The fused result is transformed back into the spatial domain and added to the image branch, thereby preserving both global structure and high-frequency details across scales. Compared with strong attention-based baselines, DRIFT-Net achieves lower error and higher throughput with fewer parameters under identical training settings and budget. On Navier--Stokes benchmarks, the relative L_{1} error is reduced by 7\%--54\%, the parameter count decreases by about 15\%, and the throughput remains higher than scOT. Ablation studies and theoretical analyses further demonstrate the stability and effectiveness of this design. The code is available at https://github.com/cruiseresearchgroup/DRIFT-Net.

Progression as Latent Drift: Generative Forecasting of Slow-Evolving Pathologies

Forecasting the future anatomy of slow-evolving neurodegenerative diseases could enable earlier, more targeted intervention and improve clinical trial design, but it remains challenging because true progression signals are subtle in longitudinal MRI. In this low-signal regime, transferring modern generative sequence models directly is unreliable: training is dominated by stable baseline anatomy and confounded by dense, sample-specific nuisance variation. We first provide a theoretical analysis that explains these failures through two modes. Identity collapse occurs when optimization is driven toward reproducing the current anatomy, which prevents the model from learning faint temporal change. The continuous interpolation trap arises when standard smooth networks cannot separate localized biological drift from pervasive noise, which leads to spurious changes that diffuse across the volume. To address both issues, we propose Latent Drift, a progressive generative framework that learns change in a compressed semantic representation rather than synthesizing full-resolution anatomy. This design removes pixel-level identity from the prediction target and concentrates model capacity on progression-relevant dynamics. We further apply Finite Scalar Quantization to the learned change representation, which suppresses small, high-frequency nuisance fluctuations while preserving consistent structural drift. Experiments on longitudinal 3D brain MRI show that Latent Drift improves patient-specific neuro-forecasting over diffusion and autoregressive transformer baselines across generative fidelity and clinically relevant evaluation metrics. Project page: https://cutepkq.github.io/latent-drift{https://cutepkq.github.io/latent-drift}.

  • 10 authors
·
Jul 8

Drift-Constrained Optimization: Only Direction Matters in Fine-Tuning Instruct Models

Fine-tuning instruct models often improves target performance while inducing behavioral drift from the reference model, which can degrade existing capabilities. Rather than treating this drift as an uncontrolled consequence of optimization, we specify a behavioral drift budget before optimization and ask how to boost the target-task performance within it. Locally, behavioral drift induces a shared geometry anchored at the reference model, with the drift budget defining a boundary within this space. In this space, drift determines distance from the reference, leaving update direction as the remaining degree of freedom. Fine-tuning updates can therefore be compared through their directional efficiency, naturally reformulating fine-tuning as a direction-selection problem. This reformulation makes a concrete prediction: changing the accessible directions can qualitatively alter the outcome of fine-tuning. We test this prediction in a stringent QA-only setting, where strong instruct models are fine-tuned only on final answers but must still generate multi-step reasoning at inference. Despite this mismatch, a coarse layer-selective probe reverses the failure of QA-only fine-tuning and reveals the existence of effective directions, with multiple neighboring configurations improving target performance while preserving reasoning and general capabilities. Across Qwen3-8B and Qwen3-14B, these directions substantially improve scientific reasoning and multilingual translation. Over more than 100 languages, the resulting models match or outperform dedicated translation systems and provide a stronger initialization for subsequent reinforcement learning. Our results suggest that fine-tuning is not just about how much a model changes, but how that change is spent. https://github.com/CONE-MT/DCO and https://huggingface.co/collections/LLaMAX/dco

  • 6 authors
·
Sep 11 2

Diffusion limits of cyclic finite-velocity random motions along vector fields

We investigate diffusion approximations for a class of multivariate inhomogeneous finite-velocity random motions motivated by models of active particles. A particle alternates cyclically among prescribed velocity fields V_1,dots,V_p with random run times and evolves according to either a flight dynamics, consisting of piecewise-linear motion, or a gliding dynamics, in which the particle follows the corresponding velocity flow. Under a Kac-type scaling that couples vanishing run times with diverging particle speed, we prove weak convergence of both processes to multidimensional diffusions. It turns out that the order of successive cyclic motions affects the diffusion limit. In addition to the second-order term generated by fluctuations of the random run times, the limiting drift contains directional derivatives DV_i[V_j] of the underlying vector fields. In Stratonovich form, part of this drift is expressed through their Lie brackets [V_i,V_j]. Thus, the generic non-commutativity of the microscopic motions survives the diffusive scaling and generates a macroscopic drift which depends on the cyclic order. The limiting drift also distinguishes the flight and gliding dynamics, despite their being driven by the same vector fields and run times. Several examples, including run-and-reverse motion and cyclic dynamics generated by multiple vector fields, illustrate how the cyclic switching protocol and the geometry of the underlying velocity fields shape the limiting diffusions.

  • 3 authors
·
Aug 30 1

FedDAA: Dynamic Client Clustering for Concept Drift Adaptation in Federated Learning

In federated learning (FL), the data distribution of each client may change over time, introducing both temporal and spatial data heterogeneity, known as concept drift. Data heterogeneity arises from three drift sources: real drift (a shift in the conditional distribution P(y|x)), virtual drift (a shift in the input distribution P(x)), and label drift (a shift in the label distribution P(y)). However, most existing FL methods addressing concept drift primarily focus on real drift. When clients experience virtual or label drift, these methods often fail to selectively retain useful historical knowledge, leading to catastrophic forgetting. A key challenge lies in distinguishing different sources of drift, as they require distinct adaptation strategies: real drift calls for discarding outdated data, while virtual or label drift benefits from retaining historical data. Without explicitly identifying the drift sources, a general adaptation strategy is suboptimal and may harm generalization. To address this challenge, we propose FedDAA, a dynamic clustered FL framework designed to adapt to multi-source concept drift while preserving valuable historical knowledge. Specifically, FedDAA integrates three modules: a cluster number determination module to find the optimal number of clusters; a real drift detection module to distinguish real drift from virtual/label drift; and a concept drift adaptation module to adapt to new data while retaining useful historical information. We provide theoretical convergence guarantees, and experiments show that FedDAA achieves 7.84% to 8.52% accuracy improvements over state-of-the-art methods on Fashion-MNIST, CIFAR-10, and CIFAR-100.

  • 2 authors
·
Jun 26, 2025