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Steering Generative Models with Experimental Data for Protein Fitness Optimization

Neural Information Processing Systems

Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent advances in steering protein generative models (e.g., diffusion models and language models) with labeled data offer a promising approach. However, most previous studies have optimized surrogate rewards and/or utilized large amounts of labeled data for steering, making it unclear how well existing methods perform and compare to each other in real-world optimization campaigns where fitness is measured through low-throughput wet-lab assays. In this study, we explore fitness optimization using small amounts (hundreds) of labeled sequencefitness pairs and comprehensively evaluate strategies such as classifier guidance and posterior sampling for guiding generation from different discrete diffusion models of protein sequences. We also demonstrate how guidance can be integrated into adaptive sequence selection akin to Thompson sampling in Bayesian optimization, showing that plug-and-play guidance strategies offer advantages over alternatives such as reinforcement learning with protein language models. Overall, we provide practical insights into how to effectively steer modern generative models for next-generation protein fitness optimization.


d61819e9b4a607b8448de762235148c4-Paper-Conference.pdf

Neural Information Processing Systems

Leveraging the lottery ticket hypothesis, novel training GMV pipeline, activates which diverse includes sub-net mix works ed-vie within w generation, a single GNN and multi-vie through w a decomposition and learning. This approach simultaneously broadens "views" from the data, model, and optimization perspectives during training to enhance the generalization additional prediction capabilities heads of into GNNs.


AMultimodal BiMamba Network with Test-Time Adaptation for Emotion Recognition Based on Physiological Signals

Neural Information Processing Systems

Emotion recognition based on physiological signals plays a vital role in psychological health and human-computer interaction, particularly with the substantial advances in multimodal emotion recognition techniques. However, two key challenges remain unresolved: 1) how to effectively model the intra-modal long-range dependencies and inter-modal correlations in multimodal physiological emotion signals, and 2) how to address the performance limitations resulting from missing multimodal data. In this paper, we propose a multimodal bidirectional Mamba (BiMamba) network with test-time adaptation (TTA) for emotion recognition named BiM-TTA.


Class-wise Balancing Data Replay for Federated Class-Incremental Learning

Neural Information Processing Systems

Federated Class Incremental Learning (FCIL) aims to collaboratively process continuously increasing incoming tasks across multiple clients. Among various approaches, data replay has become a promising solution, which can alleviate forgetting by reintroducing representative samples from previous tasks. However, their performance is typically limited by class imbalance, both within the replay buffer due to limited global awareness and between replayed and newly arrived classes. To address this issue, we propose a class-wise balancing data replay method for FCIL (FedCBDR), which employs a global coordination mechanism for class-level memory construction and reweights the learning objective to alleviate the aforementioned imbalances. Specifically, FedCBDRhas two key components: 1) the global-perspective data replay module reconstructs global representations of prior task in a privacy-preserving manner, which then guides a class-aware and importance-sensitive sampling strategy to achieve balanced replay; 2) Subsequently, to handle class imbalance across tasks, the task-aware temperature scaling module adaptively adjusts the temperature of logits at both class and instance levels based on task dynamics, which reduces the model's overconfidence in majority classes while enhancing its sensitivity to minority classes. Experimental results verified that FedCBDR achieves balanced class-wise sampling under heterogeneous data distributions and improves generalization under task imbalance between earlier and recent tasks, yielding a 2%-15% Top-1 accuracy improvement over six stateof-the-art methods.


Truthful Aggregation of LLMs with an Application to Online Advertising

Neural Information Processing Systems

The next frontier of online advertising is revenue generation from LLM-generated content. We consider a setting where advertisers aim to influence the responses of an LLM, while platforms seek to maximize advertiser value and ensure user satisfaction. The challenge is that advertisers' preferences generally conflict with those of the user, and advertisers may misreport their preferences. To address this, we introduce MOSAIC, an auction mechanism that ensures that truthful reporting is a dominant strategy for advertisers and that aligns the utility of each advertiser with their contribution to social welfare. Importantly, the mechanism operates without LLM fine-tuning or access to model weights and provably converges to the output of the optimally fine-tuned LLM as computational resources increase. Additionally, it can incorporate contextual information about advertisers, which significantly improves social welfare. Via experiments with publicly available LLMs, we show that MOSAIC leads to high advertiser value and platform revenue with low computational costs. While our motivating application is online advertising, our mechanism can be applied in any setting with monetary transfers, making it a general-purpose solution for truthfully aggregating the preferences of selfinterested agents over LLM-generated replies.


d607a260b3bc0b9a704a1a04dd64040a-Paper-Conference.pdf

Neural Information Processing Systems

We introduce PlayerOne, the first egocentric realistic world simulator, facilitating immersive and unrestricted exploration within vividly dynamic environments. Gi the ven corresponding an egocentric w scene orld and image generate from the egocentric user, PlayerOne videos can that accurately are strictly construct aligned with the real-scene human motion of the user captured by an exocentric camera. PlayerOne is trained in a coarse-to-fine pipeline that first performs pretraining on ing, lar follo ge-scale wed by egocentric finetuning text-video on synchronous pairs for coarse-le motion-video vel egocentric data extracted understandfrom egocentric-exocentric video datasets with our automatic construction pipeline.


Rethinking Temporal Pattern Learning in Deep Learning Models for Time Series

Neural Information Processing Systems

Recent advances in deep learning have driven rapid progress in time series forecasting, yet many state-of-the-art models continue to struggle with robust performance in real-world applications, even when they achieve strong results on standard benchmark datasets. This persistent gap can be attributed to the blackbox nature of deep learning architectures and the inherent limitations of current evaluation frameworks, which frequently lack the capacity to provide clear, quantitative insights into the specific strengths and weaknesses of different models, thereby complicating the selection of appropriate models for particular forecasting scenarios. To address these issues, we propose a synthetic data-driven evaluation paradigm, SynTSBench, that systematically assesses fundamental modeling capabilities of time series forecasting models through programmable feature configuration. Our framework isolates confounding factors and establishes an interpretable evaluation system with three core analytical dimensions: (1) temporal feature decomposition and capability mapping, which enables systematic evaluation of model capacities to learn specific pattern types; (2) robustness analysis under data irregularities, which quantifies noise tolerance thresholds and anomaly recovery capabilities; and (3) theoretical optimum benchmarking, which establishes performance boundaries for each pattern type--enabling direct comparison between model predictions and mathematical optima. Our experiments show that current deep learning models do not universally approach optimal baselines across all types of temporal features.


Neural Tangent Knowledge Distillation for Optical Convolutional Networks

Neural Information Processing Systems

However, their adoption is limited by two main challenges: the accuracy gap compared to large-scale networks during training, and discrepancies between simulated and fabricated systems that further degrade accuracy. While previous work has proposed end-to-end optimizations for specific datasets (e.g., MNIST) and optical systems, these approaches typically lack generalization across tasks and hardware designs. To address these limitations, we propose a task-agnostic and hardware-agnostic pipeline that supports image classification and segmentation across diverse optical systems. To assist optical system design before training, we design the metasurface layout based on fabrication constraints. For training, we introduce Neural Tangent Knowledge Distillation (NTKD), which aligns optical models with electronic teacher networks, thereby narrowing the accuracy gap. After fabrication, NTKD also guides fine-tuning of the digital backend to compensate for implementation errors. Experiments on multiple datasets (e.g., MNIST, CIFAR, Carvana Image Masking Dataset) and hardware configurations show that our pipeline consistently improves ONN performance and enables practical deployment in both pre-fabrication simulations and physical implementations.


Credal Prediction based on Relative Likelihood

Neural Information Processing Systems

Predictions in the form of sets of probability distributions, so-called credal sets, provide a suitable means to represent a learner's epistemic uncertainty. In this paper, we propose a theoretically grounded approach to credal prediction based on the statistical notion of relative likelihood: The target of prediction is the set of all (conditional) probability distributions produced by the collection of plausible models, namely those models whose relative likelihood exceeds a specified threshold. This threshold has an intuitive interpretation and allows for controlling the trade-off between correctness and precision of credal predictions. We tackle the problem of approximating credal sets defined in this way by means of suitably modified ensemble learning techniques. To validate our approach, we illustrate its effectiveness by experiments on benchmark datasets demonstrating superior uncertainty representation without compromising predictive performance. We also compare our method against several state-of-the-art baselines in credal prediction.


Noisy Multi-Label Learning through Co-Occurrence-Aware Diffusion

Neural Information Processing Systems

Noisy labels often compel models to overfit, especially in multi-label classification tasks. Existing methods for noisy multi-label learning (NML) primarily follow a discriminative paradigm, which relies on noise transition matrix estimation or small-loss strategies to correct noisy labels. However, they remain substantial optimization difficulties compared to noisy single-label learning. In this paper, we propose a Co-Occurrence-Aware Diffusion (CAD) model, which reformulates NML from a generative perspective. We treat features as conditions and multilabels as diffusion targets, optimizing the diffusion model for multi-label learning with theoretical guarantees. Benefiting from the diffusion model's strength in capturing multi-object semantics and structured label matrix representation, we can effectively learn the posterior mapping from features to true multi-labels. To mitigate the interference of noisy labels in the forward process, we guide generation using pseudo-clean labels reconstructed from the latent neighborhood space, replacing original point-wise estimates with neighborhood-based proxies. In the reverse process, we further incorporate label co-occurrence constraints to enhance the model's awareness of incorrect generation directions, thereby promoting robust optimization. Extensive experiments on both synthetic (Pascal-VOC, MS-COCO) and real-world (NUS-WIDE) noisy datasets demonstrate that our approach outperforms state-of-the-art methods.