Jason Yang

Jarrid Rector-Brooks, Théophile Lambert, Marta Skreta et al.

Evolution is an extraordinary engine for enzymatic diversity, yet the chemistry it has explored remains a narrow slice of what DNA can encode. Deep generative models can design new proteins that bind ligands, but none have created enzymes without pre-specifying catalytic residues. We introduce DISCO (DIffusion for Sequence-structure CO-design), a multimodal model that co-designs protein sequence and 3D structure around arbitrary biomolecules, as well as inference-time scaling methods that optimize objectives across both modalities. Conditioned solely on reactive intermediates, DISCO designs diverse heme enzymes with novel active-site geometries. These enzymes catalyze new-to-nature carbene-transfer reactions, including alkene cyclopropanation, spirocyclopropanation, B-H, and C(sp$^3$)-H insertions, with high activities exceeding those of engineered enzymes. Random mutagenesis of a selected design further confirmed that enzyme activity can be improved through directed evolution. By providing a scalable route to evolvable enzymes, DISCO broadens the potential scope of genetically encodable transformations. Code is available at https://github.com/DISCO-design/DISCO.

Philipp Baumann, Olivier Goldschmidt, Dorit S. Hochbaum et al.

The anticlustering problem is to partition a set of objects into K equal-sized anticlusters such that the sum of distances within anticlusters is maximized. The anticlustering problem is NP-hard. We focus on anticlustering in Euclidean spaces, where the input data is tabular and each object is represented as a D-dimensional feature vector. Distances are measured as squared Euclidean distances between the respective vectors. Applications of Euclidean anticlustering include social studies, particularly in psychology, K-fold cross-validation in which each fold should be a good representative of the entire dataset, the creation of mini-batches for gradient descent in neural network training, and balanced K-cut partitioning. In particular, machine-learning applications involve million-scale datasets and very large values of K, making scalable anticlustering algorithms essential. Existing algorithms are either exact methods that can solve only small instances or heuristic methods, among which the most scalable is the exchange-based heuristic fast_anticlustering. We propose a new algorithm, the Assignment-Based Anticlustering algorithm (ABA), which scales to very large instances. A computational study shows that ABA outperforms fast_anticlustering in both solution quality and running time. Moreover, ABA scales to instances with millions of objects and hundreds of thousands of anticlusters within short running times, beyond what fast_anticlustering can handle. As a balanced K-cut partitioning method for tabular data, ABA is superior to the well-known METIS method in both solution quality and running time. The code of the ABA algorithm is available on GitHub.

Alex Ding, Tarun Rapaka, Willy Rodriguez et al.

Topic modeling is a branch of Natural Language Processing (NLP) that aims to organize large collections of texts into coherent groups according to word co-occurrence patterns, with Latent Dirichlet Allocation (LDA) remaining one of the most widely used and interpretable probabilistic approaches. Recent advances in NLP, particularly transformer-based language models, offer improved document representations. It is also known that the size of the model (in terms of number of parameters) has a significant impact in the performance of the language models on different pre-defined tasks. In this study, we systematically examine the effect of model size on topic quality by analyzing the performances of seven transformer-based language models (from small models such as MiniLM to large ones such as LLaMA-2) in a BERTopic pipeline on a variety of corpora. Topic quality is evaluated using coherence and divergence metrics following R{ö}der et al. (2015). Our results indicate that model size, ranging from 22 million to 13 billion parameters, has a negligible impact on the quality of the topic, suggesting that smaller models can achieve comparable performance to larger models.

Jason Yang, Ariane Mora, Shengchao Liu et al.

Enzymes are important proteins that catalyze chemical reactions. In recent years, machine learning methods have emerged to predict enzyme function from sequence; however, there are no standardized benchmarks to evaluate these methods. We introduce CARE, a benchmark and dataset suite for the Classification And Retrieval of Enzymes (CARE). CARE centers on two tasks: (1) classification of a protein sequence by its enzyme commission (EC) number and (2) retrieval of an EC number given a chemical reaction. For each task, we design train-test splits to evaluate different kinds of out-of-distribution generalization that are relevant to real use cases. For the classification task, we provide baselines for state-of-the-art methods. Because the retrieval task has not been previously formalized, we propose a method called Contrastive Reaction-EnzymE Pretraining (CREEP) as one of the first baselines for this task and compare it to the recent method, CLIPZyme. CARE is available at https://github.com/jsunn-y/CARE/.

Jason Yang, Wenda Chu, Daniel Khalil et al.

Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent advances in steering protein generative models (e.g., diffusion models and language models) with labeled data offer a promising approach. However, most previous studies have optimized surrogate rewards and/or utilized large amounts of labeled data for steering, making it unclear how well existing methods perform and compare to each other in real-world optimization campaigns where fitness is measured through low-throughput wet-lab assays. In this study, we explore fitness optimization using small amounts (hundreds) of labeled sequence-fitness pairs and comprehensively evaluate strategies such as classifier guidance and posterior sampling for guiding generation from different discrete diffusion models of protein sequences. We also demonstrate how guidance can be integrated into adaptive sequence selection akin to Thompson sampling in Bayesian optimization, showing that plug-and-play guidance strategies offer advantages over alternatives such as reinforcement learning with protein language models. Overall, we provide practical insights into how to effectively steer modern generative models for next-generation protein fitness optimization.