Targeted AMP generation through controlled diffusion with efficient embeddings

Deep learning-based antimicrobial peptide (AMP) discovery faces critical challenges such as low experimental hit rates as well as the need for nuanced controllability and efficient modeling of peptide properties. To address these challenges, we introduce OmegAMP, a framework that leverages a diffusion-based generative model with efficient low-dimensional embeddings, precise controllability mechanisms, and novel classifiers with drastically reduced false positive rates for candidate filtering. OmegAMP enables the targeted generation of AMPs with specific physicochemical properties, activity profiles, and species-specific effectiveness. Moreover, it maximizes sample diversity while ensuring faithfulness to the underlying data distribution during generation. We demonstrate that OmegAMP achieves state-of-the-art performance across all stages of the AMP discovery pipeline, significantly advancing the potential of computational frameworks in combating antimicrobial resistance.

Accurate Ab-initio Neural-network Solutions to Large-Scale Electronic Structure Problems

We present finite-range embeddings (FiRE), a novel wave function ansatz for accurate large-scale ab-initio electronic structure calculations. Compared to contemporary neural-network wave functions, FiRE reduces the asymptotic complexity of neural-network variational Monte Carlo (NN-VMC) by $\sim n_\text{el}$, the number of electrons. By restricting electron-electron interactions within the neural network, FiRE accelerates all key operations -- sampling, pseudopotentials, and Laplacian computations -- resulting in a real-world $10\times$ acceleration in now-feasible 180-electron calculations. We validate our method's accuracy on various challenging systems, including biochemical compounds, conjugated hydrocarbons, and organometallic compounds. On these systems, FiRE's energies are consistently within chemical accuracy of the most reliable data, including experiments, even in cases where high-accuracy methods such as CCSD(T), AFQMC, or contemporary NN-VMC fall short. With these improvements in both runtime and accuracy, FiRE represents a new `gold-standard' method for fast and accurate large-scale ab-initio calculations, potentially enabling new computational studies in fields like quantum chemistry, solid-state physics, and material design.

Prior2Former -- Evidential Modeling of Mask Transformers for Assumption-Free Open-World Panoptic Segmentation

In panoptic segmentation, individual instances must be separated within semantic classes. As state-of-the-art methods rely on a pre-defined set of classes, they struggle with novel categories and out-of-distribution (OOD) data. This is particularly problematic in safety-critical applications, such as autonomous driving, where reliability in unseen scenarios is essential. We address the gap between outstanding benchmark performance and reliability by proposing Prior2Former (P2F), the first approach for segmentation vision transformers rooted in evidential learning. P2F extends the mask vision transformer architecture by incorporating a Beta prior for computing model uncertainty in pixel-wise binary mask assignments. This design enables high-quality uncertainty estimation that effectively detects novel and OOD objects enabling state-of-the-art anomaly instance segmentation and open-world panoptic segmentation. Unlike most segmentation models addressing unknown classes, P2F operates without access to OOD data samples or contrastive training on void (i.e., unlabeled) classes, making it highly applicable in real-world scenarios where such prior information is unavailable. Additionally, P2F can be flexibly applied to anomaly instance and panoptic segmentation. Through comprehensive experiments on the Cityscapes, COCO, SegmentMeIfYouCan, and OoDIS datasets, we demonstrate the state-of-the-art performance of P2F. It achieves the highest ranking in the OoDIS anomaly instance benchmark among methods not using OOD data in any way.

LipShiFT: A Certifiably Robust Shift-based Vision Transformer

Deriving tight Lipschitz bounds for transformer-based architectures presents a significant challenge. The large input sizes and high-dimensional attention modules typically prove to be crucial bottlenecks during the training process and leads to sub-optimal results. Our research highlights practical constraints of these methods in vision tasks. We find that Lipschitz-based margin training acts as a strong regularizer while restricting weights in successive layers of the model. Focusing on a Lipschitz continuous variant of the ShiftViT model, we address significant training challenges for transformer-based architectures under norm-constrained input setting. We provide an upper bound estimate for the Lipschitz constants of this model using the $l_2$ norm on common image classification datasets. Ultimately, we demonstrate that our method scales to larger models and advances the state-of-the-art in certified robustness for transformer-based architectures.

Joint Out-of-Distribution Filtering and Data Discovery Active Learning

As the data demand for deep learning models increases, active learning (AL) becomes essential to strategically select samples for labeling, which maximizes data efficiency and reduces training costs. Real-world scenarios necessitate the consideration of incomplete data knowledge within AL. Prior works address handling out-of-distribution (OOD) data, while another research direction has focused on category discovery. However, a combined analysis of real-world considerations combining AL with out-of-distribution data and category discovery remains unexplored. To address this gap, we propose Joint Out-of-distribution filtering and data Discovery Active learning (Joda) , to uniquely address both challenges simultaneously by filtering out OOD data before selecting candidates for labeling. In contrast to previous methods, we deeply entangle the training procedure with filter and selection to construct a common feature space that aligns known and novel categories while separating OOD samples. Unlike previous works, Joda is highly efficient and completely omits auxiliary models and training access to the unlabeled pool for filtering or selection. In extensive experiments on 18 configurations and 3 metrics, \ours{} consistently achieves the highest accuracy with the best class discovery to OOD filtering balance compared to state-of-the-art competitor approaches.

LLM-Safety Evaluations Lack Robustness

In this paper, we argue that current safety alignment research efforts for large language models are hindered by many intertwined sources of noise, such as small datasets, methodological inconsistencies, and unreliable evaluation setups. This can, at times, make it impossible to evaluate and compare attacks and defenses fairly, thereby slowing progress. We systematically analyze the LLM safety evaluation pipeline, covering dataset curation, optimization strategies for automated red-teaming, response generation, and response evaluation using LLM judges. At each stage, we identify key issues and highlight their practical impact. We also propose a set of guidelines for reducing noise and bias in evaluations of future attack and defense papers. Lastly, we offer an opposing perspective, highlighting practical reasons for existing limitations. We believe that addressing the outlined problems in future research will improve the field's ability to generate easily comparable results and make measurable progress.

The Geometry of Refusal in Large Language Models: Concept Cones and Representational Independence

The safety alignment of large language models (LLMs) can be circumvented through adversarially crafted inputs, yet the mechanisms by which these attacks bypass safety barriers remain poorly understood. Prior work suggests that a single refusal direction in the model's activation space determines whether an LLM refuses a request. In this study, we propose a novel gradient-based approach to representation engineering and use it to identify refusal directions. Contrary to prior work, we uncover multiple independent directions and even multi-dimensional concept cones that mediate refusal. Moreover, we show that orthogonality alone does not imply independence under intervention, motivating the notion of representational independence that accounts for both linear and non-linear effects. Using this framework, we identify mechanistically independent refusal directions. We show that refusal mechanisms in LLMs are governed by complex spatial structures and identify functionally independent directions, confirming that multiple distinct mechanisms drive refusal behavior. Our gradient-based approach uncovers these mechanisms and can further serve as a foundation for future work on understanding LLMs.

REINFORCE Adversarial Attacks on Large Language Models: An Adaptive, Distributional, and Semantic Objective

To circumvent the alignment of large language models (LLMs), current optimization-based adversarial attacks usually craft adversarial prompts by maximizing the likelihood of a so-called affirmative response. An affirmative response is a manually designed start of a harmful answer to an inappropriate request. While it is often easy to craft prompts that yield a substantial likelihood for the affirmative response, the attacked model frequently does not complete the response in a harmful manner. Moreover, the affirmative objective is usually not adapted to model-specific preferences and essentially ignores the fact that LLMs output a distribution over responses. If low attack success under such an objective is taken as a measure of robustness, the true robustness might be grossly overestimated. To alleviate these flaws, we propose an adaptive and semantic optimization problem over the population of responses. We derive a generally applicable objective via the REINFORCE policy-gradient formalism and demonstrate its efficacy with the state-of-the-art jailbreak algorithms Greedy Coordinate Gradient (GCG) and Projected Gradient Descent (PGD). For example, our objective doubles the attack success rate (ASR) on Llama3 and increases the ASR from 2% to 50% with circuit breaker defense.

Adversarial Alignment for LLMs Requires Simpler, Reproducible, and More Measurable Objectives

Misaligned research objectives have considerably hindered progress in adversarial robustness research over the past decade. For instance, an extensive focus on optimizing target metrics, while neglecting rigorous standardized evaluation, has led researchers to pursue ad-hoc heuristic defenses that were seemingly effective. Yet, most of these were exposed as flawed by subsequent evaluations, ultimately contributing little measurable progress to the field. In this position paper, we illustrate that current research on the robustness of large language models (LLMs) risks repeating past patterns with potentially worsened real-world implications. To address this, we argue that realigned objectives are necessary for meaningful progress in adversarial alignment. To this end, we build on established cybersecurity taxonomy to formally define differences between past and emerging threat models that apply to LLMs. Using this framework, we illustrate that progress requires disentangling adversarial alignment into addressable sub-problems and returning to core academic principles, such as measureability, reproducibility, and comparability. Although the field presents significant challenges, the fresh start on adversarial robustness offers the unique opportunity to build on past experience while avoiding previous mistakes.

Generative Modeling with Bayesian Sample Inference

We derive a novel generative model from the simple act of Gaussian posterior inference. Treating the generated sample as an unknown variable to infer lets us formulate the sampling process in the language of Bayesian probability. Our model uses a sequence of prediction and posterior update steps to narrow down the unknown sample from a broad initial belief. In addition to a rigorous theoretical analysis, we establish a connection between our model and diffusion models and show that it includes Bayesian Flow Networks (BFNs) as a special case. In our experiments, we demonstrate improved performance over both BFNs and Variational Diffusion Models, achieving competitive likelihood scores on CIFAR10 and ImageNet.