PepCompass: Navigating peptide embedding spaces using Riemannian Geometry

Antimicrobial peptide discovery is challenged by the astronomical size of peptide space and the relative scarcity of active peptides. Generative models provide continuous latent "maps" of peptide space, but conventionally ignore decoder-induced geometry and rely on flat Euclidean metrics, rendering exploration and optimization distorted and inefficient. Prior manifold-based remedies assume fixed intrinsic dimensionality, which critically fails in practice for peptide data. Here, we introduce PepCompass, a geometry-aware framework for peptide exploration and optimization. At its core, we define a Union of $\kappa$-Stable Riemannian Manifolds $\mathbb{M}^{\kappa}$, a family of decoder-induced manifolds that captures local geometry while ensuring computational stability. We propose two local exploration methods: Second-Order Riemannian Brownian Efficient Sampling, which provides a convergent second-order approximation to Riemannian Brownian motion, and Mutation Enumeration in Tangent Space, which reinterprets tangent directions as discrete amino-acid substitutions. Combining these yields Local Enumeration Bayesian Optimization (LE-BO), an efficient algorithm for local activity optimization. Finally, we introduce Potential-minimizing Geodesic Search (PoGS), which interpolates between prototype embeddings along property-enriched geodesics, biasing discovery toward seeds, i.e. peptides with favorable activity. In-vitro validation confirms the effectiveness of PepCompass: PoGS yields four novel seeds, and subsequent optimization with LE-BO discovers 25 highly active peptides with broad-spectrum activity, including against resistant bacterial strains. These results demonstrate that geometry-informed exploration provides a powerful new paradigm for antimicrobial peptide design.

From Supervision to Exploration: What Does Protein Language Model Learn During Reinforcement Learning?

Protein language models (PLMs) have advanced computational protein science through large-scale pretraining and scalable architectures. In parallel, reinforcement learning (RL) has broadened exploration and enabled precise multi-objective optimization in protein design. Yet whether RL can push PLMs beyond their pretraining priors to uncover latent sequence-structure-function rules remains unclear. We address this by pairing RL with PLMs across four domains: antimicrobial peptide design, kinase variant optimization, antibody engineering, and inverse folding. Using diverse RL algorithms and model classes, we ask if RL improves sampling efficiency and, more importantly, if it reveals capabilities not captured by supervised learning. Across benchmarks, RL consistently boosts success rates and sample efficiency. Performance follows a three-factor interaction: task headroom, reward fidelity, and policy capacity jointly determine gains. When rewards are accurate and informative, policies have sufficient capacity, and tasks leave room beyond supervised baselines, improvements scale; when rewards are noisy or capacity is constrained, gains saturate despite exploration. This view yields practical guidance for RL in protein design: prioritize reward modeling and calibration before scaling policy size, match algorithm and regularization strength to task difficulty, and allocate capacity where marginal gains are largest. Implementation is available at https://github.com/chq1155/RL-PLM.

A Dataset for Distilling Knowledge Priors from Literature for Therapeutic Design

AI-driven discovery can greatly reduce design time and enhance new therapeutics' effectiveness. Models using simulators explore broad design spaces but risk violating implicit constraints due to a lack of experimental priors. For example, in a new analysis we performed on a diverse set of models on the GuacaMol benchmark using supervised classifiers, over 60\% of molecules proposed had high probability of being mutagenic. In this work, we introduce \ourdataset, a dataset of priors for design problems extracted from literature describing compounds used in lab settings. It is constructed with LLM pipelines for discovering therapeutic entities in relevant paragraphs and summarizing information in concise fair-use facts. \ourdataset~ consists of 32.3 million pairs of natural language facts, and appropriate entity representations (i.e. SMILES or refseq IDs). To demonstrate the potential of the data, we train LLM, CLIP, and LLava architectures to reason jointly about text and design targets and evaluate on tasks from the Therapeutic Data Commons (TDC). \ourdataset~is highly effective for creating models with strong priors: in supervised prediction problems that use our data as pretraining, our best models with 15M learnable parameters outperform larger 2B TxGemma on both regression and classification TDC tasks, and perform comparably to 9B models on average. Models built with \ourdataset~can be used as constraints while optimizing for novel molecules in GuacaMol, resulting in proposals that are safer and nearly as effective. We release our dataset at \href{https://huggingface.co/datasets/medexanon/Medex}{huggingface.co/datasets/medexanon/Medex}, and will provide expanded versions as available literature grows.

Predicting and generating antibiotics against future pathogens with ApexOracle

Antimicrobial resistance (AMR) is escalating and outpacing current antibiotic development. Thus, discovering antibiotics effective against emerging pathogens is becoming increasingly critical. However, existing approaches cannot rapidly identify effective molecules against novel pathogens or emerging drug-resistant strains. Here, we introduce ApexOracle, an artificial intelligence (AI) model that both predicts the antibacterial potency of existing compounds and designs de novo molecules active against strains it has never encountered. Departing from models that rely solely on molecular features, ApexOracle incorporates pathogen-specific context through the integration of molecular features captured via a foundational discrete diffusion language model and a dual-embedding framework that combines genomic- and literature-derived strain representations. Across diverse bacterial species and chemical modalities, ApexOracle consistently outperformed state-of-the-art approaches in activity prediction and demonstrated reliable transferability to novel pathogens with little or no antimicrobial data. Its unified representation-generation architecture further enables the in silico creation of "new-to-nature" molecules with high predicted efficacy against priority threats. By pairing rapid activity prediction with targeted molecular generation, ApexOracle offers a scalable strategy for countering AMR and preparing for future infectious-disease outbreaks.

Large Scale Multi-Task Bayesian Optimization with Large Language Models

In multi-task Bayesian optimization, the goal is to leverage experience from optimizing existing tasks to improve the efficiency of optimizing new ones. While approaches using multi-task Gaussian processes or deep kernel transfer exist, the performance improvement is marginal when scaling to more than a moderate number of tasks. We introduce a novel approach leveraging large language models (LLMs) to learn from, and improve upon, previous optimization trajectories, scaling to approximately 2000 distinct tasks. Specifically, we propose an iterative framework in which an LLM is fine-tuned using the high quality solutions produced by BayesOpt to generate improved initializations that accelerate convergence for future optimization tasks based on previous search trajectories. We evaluate our method on two distinct domains: database query optimization and antimicrobial peptide design. Results demonstrate that our approach creates a positive feedback loop, where the LLM's generated initializations gradually improve, leading to better optimization performance. As this feedback loop continues, we find that the LLM is eventually able to generate solutions to new tasks in just a few shots that are better than the solutions produced by "from scratch" by Bayesian optimization while simultaneously requiring significantly fewer oracle calls.

Covering Multiple Objectives with a Small Set of Solutions Using Bayesian Optimization

In multi-objective black-box optimization, the goal is typically to find solutions that optimize a set of T black-box objective functions, $f_1$, ..., $f_T$, simultaneously. Traditional approaches often seek a single Pareto-optimal set that balances trade-offs among all objectives. In this work, we introduce a novel problem setting that departs from this paradigm: finding a smaller set of K solutions, where K < T, that collectively "covers" the T objectives. A set of solutions is defined as "covering" if, for each objective $f_1$, ..., $f_T$, there is at least one good solution. A motivating example for this problem setting occurs in drug design. For example, we may have T pathogens and aim to identify a set of K < T antibiotics such that at least one antibiotic can be used to treat each pathogen. To address this problem, we propose Multi-Objective Coverage Bayesian Optimization (MOCOBO), a principled algorithm designed to efficiently find a covering set. We validate our approach through extensive experiments on challenging high-dimensional tasks, including applications in peptide and molecular design. Experiments demonstrate MOCOBO's ability to find high-performing covering sets of solutions. Additionally, we show that the small sets of K < T solutions found by MOCOBO can match or nearly match the performance of T individually optimized solutions for the same objectives. Our results highlight MOCOBO's potential to tackle complex multi-objective problems in domains where finding at least one high-performing solution for each objective is critical.