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

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

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.

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.

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.

The goal is to find representations (e.g., embeddings in Rd or a tree metric) where anchors are placed closer to positive than to negative examples. While finding global optima of contrastive objectives is NP-hard, the complexity of finding local optima--representations that do not improve by local search algorithms such as gradient-based methods--remains open. Our work settles the complexity of finding local optima in various contrastive learning problems by proving PLS-hardness in discrete settings (e.g., maximize satisfied triplets) and CLS-hardness in continuous settings (e.g., minimize Triplet Loss), where PLS(Polynomial Local Search) and CLS(Continuous Local Search) are well-studied complexity classes capturing local search dynamics in discrete and continuous optimization, respectively. Our results imply that no polynomial time algorithm (local search or otherwise) can find a local optimum for various contrastive learning problems, unless PLS P(or CLS P for continuous problems). Even in the unlikely scenario that PLS P(or CLS P), our reductions imply that there exist instances where local search algorithms need exponential time to reach a local optimum, even for d = 1(embeddings on a line).

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.

Deepfake detection models face two critical challenges: generalization to unseen manipulations and demographic fairness among population groups. However, existing approaches often demonstrate that these two objectives are inherently conflicting, revealing a trade-off between them. In this paper, we, for the first time, uncover and formally define a causal relationship between fairness and generalization. Building on the back-door adjustment, we show that controlling for confounders (data distribution and model capacity) enables improved generalization via fairness interventions. Motivated by this insight, we propose Demographic Attribute-insensitive Intervention Detection (DAID), a plug-and-play framework composed of: i) Demographic-aware data rebalancing, which employs inversepropensity weighting and subgroup-wise feature normalization to neutralize distributional biases; and ii) Demographic-agnostic feature aggregation, which uses a novel alignment loss to suppress sensitive-attribute signals. Across three crossdomain benchmarks, DAID consistently achieves superior performance in both fairness and generalization compared to several state-of-the-art detectors, validating both its theoretical foundation and practical effectiveness.

We consider the problem of certified robustness for sequence classification against edit distance perturbations. Naturally occurring inputs of varying lengths (e.g., sentences in natural language processing tasks) present a challenge to current methods that employ fixed-rate deletion mechanisms and lead to suboptimal performance. To this end, we introduce AdaptDel methods with adaptable deletion rates that dynamically adjust based on input properties. We extend the theoretical framework of randomized smoothing to variable-rate deletion, ensuring sound certification with respect to edit distance. We achieve strong empirical results in natural language tasks, observing up to 30 orders of magnitude improvement to median cardinality of the certified region, over state-of-the-art certifications.

Foundation models are increasingly becoming better autonomous programmers, raising the prospect that they could also automate dangerous offensive cyber-operations. Current frontier model audits probe the cybersecurity risks of such agents, but most fail to account for the degrees of freedom available to adversaries in the real world. In particular, with strong verifiers and financial incentives, agents for offensive cybersecurity are amenable to iterative improvement by would-be adversaries. We argue that assessments should take into account an expanded threat model in the context of cybersecurity, emphasizing the varying degrees of freedom that an adversary may possess in stateful and non-stateful environments within a fixed compute budget. We show that even with a relatively small compute budget (8 H100 GPUHours in our study), adversaries can improve an agent's cybersecurity capability on InterCode CTF by more than 40% relative to the baseline--without any external assistance. These results highlight the need to evaluate agents' cybersecurity risk in a dynamic manner, painting a more representative picture of risk.