In-silico prediction of protein mutant stability, measured by the difference in Gibbs free energy change ( G), is fundamental for protein engineering. Current sequence-to-label methods typically employ the two-stage pipeline: (i) encoding mutant sequences using neural networks (e.g., transformers), followed by (ii) the G regression from the latent representations. Although these methods have demonstrated promising performance, their dependence on specialized neural network encoders significantly increases the complexity. Additionally, the requirement to individually compute latent representations for each mutant site negatively impacts computational efficiency and poses the risk of overfitting. This work proposes the Venus-MAXWELL framework, which reformulates mutation G prediction as a sequence-to-landscape task. In Venus-MAXWELL, mutations of a protein and their corresponding Gvalues are organized into a landscape matrix, allowing our framework to learn the G landscape of a protein with a single forward and backward pass during training. Besides, to facilitate future works, we also curated a large-scale G dataset with strict controls on data leakage and redundancy to ensure robust evaluation. Venus-MAXWELL is compatible with multiple protein language models and enables these models for accurate and efficient G prediction. For example, when integrated with the ESM-IF, Venus-MAXWELL achieves higher accuracy than ThermoMPNN with 10 faster in inference speed (despite having 50 more parameters than ThermoMPNN).

We present a novel enhanced cyclic coordinate descent (ECCD) framework for solving generalized linear models with elastic net constraints that reduces training time in comparison to existing state-of-the-art methods. We redesign the CD method by performing a Taylor expansion around the current iterate to avoid nonlinear operations arising in the gradient computation. By introducing this approximation we are able to unroll the vector recurrences occurring in the CD method and reformulate the resulting computations into more efficient batched computations. We show empirically that the recurrence can be unrolled by a tunable integer parameter, s, such that s > 1 yields performance improvements without affecting convergence, whereas s= 1 yields the original CD method. A key advantage of ECCD is that it avoids the convergence delay and numerical instability exhibited by block coordinate descent. Finally, we implement our proposed method in C++ using Eigen to accelerate linear algebra computations. Comparison of our method against existing state-of-the-art solvers show consistent performance improvements of 3 in average for regularization path variant on diverse benchmark datasets. Our implementation is available at https://github.

Vision-language models (VLMs) have shown strong performance on text-to-image retrieval benchmarks. However, bridging this success to real-world applications remains a challenge. In practice, human search behavior is rarely a one-shot action. Instead, it is often a multi-round process guided by clues in mind. That is, a mental image ranging from vague recollections to vivid mental representations of the target image.

Robust verbal confidence generated by large language models (LLMs) is crucial for the deployment of LLMs to help ensure transparency, trust, and safety in many applications, including those involving human-AI interactions. In this paper, we present the first comprehensive study on the robustness of verbal confidence under adversarial attacks. We introduce attack frameworks targeting verbal confidence scores through both perturbation and jailbreak-based methods, and demonstrate that these attacks can significantly impair verbal confidence estimates and lead to frequent answer changes. We examine a variety of prompting strategies, model sizes, and application domains, revealing that current verbal confidence is vulnerable and that commonly used defence techniques are largely ineffective or counterproductive. Our findings underscore the need to design robust mechanisms for confidence expression in LLMs, as even subtle semantic-preserving modifications can lead to misleading confidence in responses.

Increasing demand for Large Language Models (LLMs) services imposes substantial deployment and computation costs on providers. LLM routing offers a cost-efficient solution by directing queries to the optimal LLM based on model and query features. However, existing works primarily focus on offline scenarios and struggle to adapt to online settings with high query volume and constrained token budgets. In this work, we introduce the first training-free algorithm for online routing scenarios. Our algorithm leverages approximate nearest neighbor search to efficiently estimate query features and performs a one-time optimization over a small set of initial queries to learn a routing strategy that guides future routing. We provide theoretical guarantees demonstrating that our algorithm achieves a competitive ratio of 1 o(1)under natural assumptions, which is further validated by extensive experiments across 3 benchmark datasets and 8 baselines, showing an average improvement of 3.55 in overall performance, 1.85 in cost efficiency, and nearly 4.25 in throughput. Our code is available at https://github.com/fzwark/PORT.

Adversarial optimization algorithms that explicitly search for flaws in agents' policies have been successfully applied to finding robust and diverse policies in multi-agent settings. However, the success of adversarial optimization has been largely limited to zero-sum settings because its naive application in cooperative settings leads to a critical failure mode: agents are irrationally incentivized to selfsabotage, blocking the completion of tasks and halting further learning. To address this, we introduce Rationality-preserving Policy Optimization (RPO), a formalism for adversarial optimization that avoids self-sabotage by ensuring agents remain rational--that is, their policies are optimal with respect to some possible partner policy. To solve RPO, we develop Rational Policy Gradient (RPG), which trains agents to maximize their own reward in a modified version of the original game in which we use opponent shaping techniques to optimize the adversarial objective. RPG enables us to extend a variety of existing adversarial optimization algorithms that, no longer subject to the limitations of self-sabotage, can find adversarial examples, improve robustness and adaptability, and learn diverse policies. We empirically validate that our approach achieves strong performance in several popular cooperative and general-sum environments.

Diffusion Transformers (DiTs) deliver state-of-the-art image quality, yet their training remains notoriously slow. A recent remedy--representation alignment (REPA) that matches DiT hidden features to those of a non-generative teacher (e.g., DINO)--dramatically accelerates the early epochs but plateaus or even degrades performance later. We trace this failure to the capacity mismatch: once the generative student begins modeling the joint data distribution, the teacher's lower-dimensional embeddings and attention patterns become a straitjacket rather than a guide. We then introduce HASTE (Holistic Alignment with Stage-wise Termination for Efficient training), a two-phase schedule that keeps the help and drops the hindrance. Phase I applies a holistic alignment loss that simultaneously distills attention maps (relational priors) and feature projections (semantic anchors) from the teacher into mid-level layers of the DiT, yielding rapid convergence. Phase II then performs one-shot termination that deactivates the alignment loss, once a simple trigger such as a fixed iteration is hit, freeing the DiT to focus on denoising and exploit its generative capacity.

Graph Transformers (GTs), which effectively capture long-range dependencies and structural biases simultaneously, have recently emerged as promising alternatives to traditional Graph Neural Networks (GNNs). Advanced approaches for GTs to leverage topology information involve integrating GNN modules or modulating node attributes using positional encodings. Unfortunately, the underlying mechanism driving their effectiveness remains insufficiently understood. In this paper, we revisit these strategies and uncover a shared underlying mechanism--Cross Aggregation--that effectively captures the interaction between graph topology and node attributes. Building on this insight, we propose the Universal Graph Cross-attention Transformer (UGCFormer), a universal GT framework with linear computational complexity. The idea is to interactively learn the representations of graph topology and node attributes through a linearized Dual Cross-attention (DCA) module. In theory, this module can adaptively capture interactions between these two types of graph information, thereby achieving effective aggregation. To alleviate overfitting arising from the dual-channel design, we introduce a consistency constraint that enforces representational alignment. Extensive evaluations on multiple benchmark datasets demonstrate the effectiveness and efficiency of UGCFormer.

Flow-based latent generative models such as Stable Diffusion 3 are able to generate images with remarkable quality, even enabling photorealistic text-to-image generation. Their impressive performance suggests that these models should also constitute powerful priors for inverse imaging problems, but that approach hasnot yet led to comparable fidelity. There are several key obstacles: (i) the datalikelihood term is usually intractable; (ii) learned generative models cannot be directly conditioned on the distorted observations, leading to conflicting objectives between data likelihood and prior; and (iii) the reconstructions can deviate from theobserved data.

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