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 Deep Learning


Understanding protein function with a multimodal retrieval-augmented foundation model

Neural Information Processing Systems

Protein language models (PLMs) learn probability distributions over natural protein sequences. By learning from hundreds of millions of natural protein sequences, protein understanding and design capabilities emerge. Recent works have shown that scaling these models improves structure prediction, but does not seem to improve mutation understanding and representation quality for protein function prediction. We introduce PoET-2, a multimodal, retrieval-augmented protein foundation model that incorporates in-context learning of family-specific evolutionary constraints with optional structure conditioning to learn generative distributions over protein sequences. PoET-2 uses a hierarchical transformer encoder that is equivariant to sequence context ordering and a dual decoder architecture with both causal and masked language modeling objectives, allowing PoET-2 to operate in both fully generative and bidirectional representation learning modes. PoET-2 achieves stateof-the-art performance on zero-shot variant effect prediction, excelling at scoring variants with multiple mutations and challenging indel mutations. In supervised settings, PoET-2 embeddings outperform previous methods for learning sequencefunction relationships, especially with small datasets. This work highlights the benefits of combining retrieval augmentation with multimodal, family-centric modeling for advancing protein foundation models. 1


AR AutoRegressive Any to Image Generation

Neural Information Processing Systems

Autoregressive (AR) models have demonstrated strong potential in visual generation, offering superior performance with simple architectures and optimization objectives. However, existing methods are typically limited to single-modality conditions, e.g., text, restricting their applicability in real-world scenarios that demand image synthesis from diverse controls.


Activated LoRA: Fine-tuned LLMs for Intrinsics

Neural Information Processing Systems

Low-Rank Adaptation (LoRA) has emerged as a highly efficient framework for finetuning the weights of large foundation models, and has become the go-to method for data-driven customization of LLMs. Despite the promise of highly customized behaviors and capabilities, switching between relevant LoRAs in a multiturn setting is inefficient, as the key-value (KV) cache of the entire turn history must be recomputed with the LoRA weights before generation can begin. To address this problem, we propose Activated LoRA (aLoRA), an adapter architecture which modifies the LoRA framework to only adapt weights for the tokens in the sequence after the aLoRA is invoked. This change crucially allows aLoRA to accept the base model's KV cache of the input string, meaning that aLoRA can be instantly activated whenever needed in a chain without recomputing the prior keys and values. This enables building what we call intrinsics, i.e. specialized models invoked to perform well-defined operations on portions of an input chain or conversation that otherwise uses the base model by default. We train a set of aLoRA-based intrinsics models, demonstrating competitive accuracy with standard LoRA while significantly improving inference efficiency. We contributed our Activated LoRA implementation to the Huggingface PEFT library.1


HAODiff: Human-Aware One-Step Diffusion via Dual-Prompt Guidance

Neural Information Processing Systems

Human-centered images often suffer from severe generic degradation during transmission and are prone to human motion blur (HMB), making restoration challenging. Existing research lacks sufficient focus on these issues, as both problems often coexist in practice. To address this, we design a degradation pipeline that simulates the coexistence of HMB and generic noise, generating synthetic degraded data to train our proposed HAODiff, a human-aware one-step diffusion. Specifically, we propose a triple-branch dual-prompt guidance (DPG), which leverages high-quality images, residual noise (LQ minus HQ), and HMB segmentation masks as training targets. It produces a positive-negative prompt pair for classifier-free guidance (CFG) in a single diffusion step. The resulting adaptive dual prompts let HAODiff exploit CFG more effectively, boosting robustness against diverse degradations. For fair evaluation, we introduce MPII-Test, a benchmark rich in combined noise and HMB cases. Extensive experiments show that our HAODiff surpasses existing state-of-the-art (SOTA) methods in terms of both quantitative metrics and visual quality on synthetic and real-world datasets, including our introduced MPII-Test. Code is available at: https://github.com/gobunu/HAODiff.


Consistently Simulating Human Personas with Multi-Turn Reinforcement Learning

Neural Information Processing Systems

Large Language Models (LLMs) are increasingly used to simulate human users in interactive settings such as therapy, education, and social role-play. While these simulations enable scalable training and evaluation of AI agents, off-the-shelf LLMs often drift from their assigned personas, contradict earlier statements, or abandon role-appropriate behavior. We introduce a unified framework for evaluating and improving persona consistency in LLM-generated dialogue. We define three automatic metrics--prompt-to-line consistency, line-to-line consistency, and Q&A consistency--that capture different types of persona drift and validate each against human annotations. Using these metrics as reward signals, we apply multiturn reinforcement learning to fine-tune LLMs for three user roles: a patient, a student, and a social chat partner. Our method reduces inconsistency by over 55%, resulting in more coherent, faithful, and trustworthy simulated users.


PSBench: a large-scale benchmark for estimating the accuracy of protein complex structural models

Neural Information Processing Systems

Predicting protein complex structures is essential for protein function analysis, protein design, and drug discovery. While AI methods like AlphaFold can predict accurate structural models for many protein complexes, reliably estimating the quality of these predicted models (estimation of model accuracy, or EMA) for model ranking and selection remains a major challenge. A key barrier to developing effective machine learning-based EMA methods is the lack of large, diverse, and well-annotated datasets for training and evaluation. To address this gap, we introduce PSBench, a benchmark suite comprising five large-scale, labeled datasets, four of which were generated during the 15th and 16th community-wide Critical Assessment of Protein Structure Prediction (CASP15 and CASP16), and one curated for new Protein Data Bank (PDB) entries deposited between July 2024 and August 2025. PSBench includes over 1.4 million structural models covering a wide range of protein sequence lengths, complex stoichiometries, functional classes, and modeling difficulties. Each model is annotated with multiple complementary quality scores at the global, local, and interface levels. PSBench also provides multiple evaluation metrics and baseline EMA methods to facilitate rigorous comparisons. To demonstrate PSBench's utility, we trained and evaluated GATE, a graph transformer-based EMA method, on the CASP15 data. GATE was blindly tested in CASP16 (2024), where it ranked among the top-performing EMA methods.


OPHR: Mastering Volatility Trading with Multi-Agent Deep Reinforcement Learning

Neural Information Processing Systems

Options markets represent one of the most sophisticated segments of the financial ecosystem, with prices that directly reflect market uncertainty. In this paper, we introduce the first reinforcement learning (RL) framework specifically designed for volatility trading through options, focusing on profit from the difference between implied volatility and realized volatility. Our multi-agent architecture consists of an Option Position Agent (OP-Agent) responsible for volatility timing by controlling long/short volatility positions, and a Hedger Routing Agent (HR-Agent) that manages risk and maximizes path-dependent profits by selecting optimal hedging strategies with different risk preferences. Evaluating our approach using cryptocurrency options data from 2021-2024, we demonstrate superior performance on BTC and ETH, significantly outperforming traditional strategies and machine learning baselines across all profit and risk-adjusted metrics while exhibiting sophisticated trading behavior.


Learning Expandable and Adaptable Representations for Continual Learning

Neural Information Processing Systems

Extant studies predominantly address catastrophic forgetting within a simplified continual learning paradigm, typically confined to a singular data domain. Conversely, real-world applications frequently encompass multiple, evolving data domains, wherein models often struggle to retain many critical past information, thereby leading to performance degradation. This paper addresses this complex scenario by introducing a novel dynamic expansion approach called Learning Expandable and Adaptable Representations (LEAR). This framework orchestrates a collaborative backbone structure, comprising global and local backbones, designed to capture both general and task-specific representations. Leveraging this collaborative backbone, the proposed framework dynamically creates a lightweight expert to delineate decision boundaries for each novel task, thereby facilitating the prediction process. To enhance new task learning, we introduce a novel Mutual Information-Based Prediction Alignment approach, which incrementally optimizes the global backbone via a mutual information metric, ensuring consistency in the prediction patterns of historical experts throughout the optimization phase.


Orient Anything V2: Unifying Orientation and Rotation Understanding

Neural Information Processing Systems

This work presents Orient Anything V2, an enhanced foundation model for unified understanding of object 3D orientation and rotation from single or paired images. Building upon Orient Anything V1, which defines orientation via a single unique front face, V2 extends this capability to handle objects with diverse rotational symmetries and directly estimate relative rotations. These improvements are enabled by four key innovations: 1) Scalable 3D assets synthesized by generative models, ensuring broad category coverage and balanced data distribution; 2) An efficient, model-in-the-loop annotation system that robustly identifies 0to N valid front faces for each object; 3) A symmetry-aware, periodic distribution fitting objective that captures all plausible front-facing orientations, effectively modeling object rotational symmetry; 4) A multi-frame architecture that directly predicts relative object rotations. Extensive experiments show that Orient Anything V2 achieves state-of-the-art zero-shot performance on orientation estimation, 6DoF pose estimation, and object symmetry recognition across 11 widely used benchmarks. The model demonstrates strong generalization, significantly broadening the applicability of orientation estimation in diverse downstream tasks.


Incentivizing Truthful Language Models via Peer Elicitation Games

Neural Information Processing Systems

Large Language Models (LLMs) have demonstrated strong generative capabilities but remain prone to inconsistencies and hallucinations. We introduce Peer Elicitation Games (PEG), a training-free, game-theoretic framework for aligning LLMs through a peer elicitation mechanism involving a generator and multiple discriminators instantiated from distinct base models. Discriminators interact in a peer evaluation setting, where utilities are computed using a determinant-based mutual information score that provably incentivizes truthful reporting without requiring ground-truth labels. We establish theoretical guarantees showing that each agent, via online learning, achieves sublinear regret in the sense their cumulative performance approaches that of the best fixed truthful strategy in hindsight. Moreover, we prove last-iterate convergence to a truthful Nash equilibrium, ensuring that the actual policies used by agents converge to stable and truthful behavior over time. Empirical evaluations across multiple benchmarks demonstrate significant improvements in factual accuracy.