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Abstract Understanding biomolecular interactions is fundamental to advancing fields like drug discovery and protein design. In this paper, we introduce Boltz-1, an open-source deep learning model incorporating innovations in model architecture, speed optimization, and data processing achieving AlphaFold3-level accuracy in predicting the 3D structures of biomolecular complexes. Boltz-1 demonstrates a performance on-par with state-of-the-art commercial models on a range of diverse benchmarks, setting a new benchmark for commercially accessible tools in structural biology. By releasing the training and inference code, model weights, datasets, and benchmarks under the MIT open license, we aim to foster global collaboration, accelerate discoveries, and provide a robust platform for advancing biomolecular modeling. 

Abstract Sequence-specific RNA-binding proteins (RBPs) play central roles in splicing decisions. Here, we describe a modular splicing architecture that leverages in vitro-derived RNA affinity models for 79 human RBPs and the annotated human genome to produce improved models of RBP binding and activity. Binding and activity are modeled by separate Motif and Aggregator components that can be mixed and matched, enforcing sparsity to improve interpretability. Training a new Adjusted Motif (AM) architecture on the splicing task not only yields better splicing predictions but also improves prediction of RBP-binding sites in vivo and of splicing activity, assessed using independent data. 

We present a novel method for symbolic regression (SR), the task of searching for compact programmatic hypotheses that best explain a dataset. The problem is commonly solved using genetic algorithms; we show that we can enhance such methods by inducing a library of abstract textual concepts. Our algorithm, called LaSR, uses zero-shot queries to a large language model (LLM) to discover and evolve concepts occurring in known high-performing hypotheses. We discover new hypotheses using a mix of standard evolutionary steps and LLM-guided steps (obtained through zero-shot LLM queries) conditioned on discovered concepts. Once discovered, hypotheses are used in a new round of concept abstraction and evolution. We validate LaSR on the Feynman equations, a popular SR benchmark, as well as a set of synthetic tasks. On these benchmarks, LaSR substantially outperforms a variety of state-of-the-art SR approaches based on deep learning and evolutionary algorithms. Moreover, we show that LASR can be used to discover a new and powerful scaling law for LLMs. 

Robots are often built from standardized assemblies, (e.g. arms, legs, or fingers), but each robot must be trained from scratch to control all the actuators of all the parts together. In this paper we demonstrate a new approach that takes a single robot and its controller as input and produces a set of modular controllers for each of these assemblies such that when a new robot is built from the same parts, its control can be quickly learned by reusing the modular controllers. We achieve this with a framework called MeMo which learns (Me)aningful, (Mo)dular controllers. Specifically, we propose a novel modularity objective to learn an appropriate division of labor among the modules. We demonstrate that this objective can be optimized simultaneously with standard behavior cloning loss via noise injection. We benchmark our framework in locomotion and grasping environments on simple to complex robot morphology transfer. We also show that the modules help in task transfer. On both structure and task transfer, MeMo achieves improved training efficiency to graph neural network and Transformer baselines. 

Low-Rank Adaptation (LoRA) has recently gained attention for fine-tuning foundation models by incorporating trainable low-rank matrices, thereby reducing the number of trainable parameters. While LoRA offers numerous advantages, its applicability for real-time serving to a diverse and global user base is constrained by its incapability to handle multiple task-specific adapters efficiently. This imposes a performance bottleneck in scenarios requiring personalized, task-specific adaptations for each incoming request. To mitigate this constraint, we introduce Fast LoRA (FLoRA), a framework in which each input example in a minibatch can be associated with its unique low-rank adaptation weights, allowing for efficient batching of heterogeneous requests. We empirically demonstrate that FLoRA retains the performance merits of LoRA, showcasing competitive results on the MultiPL-E code generation benchmark spanning over 8 languages and a multilingual speech recognition task across 6 languages. 

We introduce a new family of physics-inspired generative models termed PFGM++ that unifies diffusion models and Poisson Flow Generative Models (PFGM). These models realize generative trajectories for N dimensional data by embedding paths in N+D dimensional space while still controlling the progression with a simple scalar norm of the D additional variables. The new models reduce to PFGM when D=1 and to diffusion models when D→∞. The flexibility of choosing D allows us to trade off robustness against rigidity as increasing D results in more concentrated coupling between the data and the additional variable norms. We dispense with the biased large batch field targets used in PFGM and instead provide an unbiased perturbation-based objective similar to diffusion models. To explore different choices of D, we provide a direct alignment method for transferring well-tuned hyperparameters from diffusion models (D→∞) to any finite D values. Our experiments show that models with finite D can be superior to previous state-of-the-art diffusion models on CIFAR-10/FFHQ 64×64 datasets/LSUN Churches 256×256, with median Ds. In class-conditional setting, D=2048 yields current state-of-the-art FID of 1.74 on CIFAR-10 without additional training. Furthermore, we demonstrate that models with smaller D exhibit improved robustness against modeling errors. Code is available at https://github.com/Newbeeer/pfgmpp 

The relational data model was designed to facilitate large-scale data management and analytics. We consider the problem of how to differentiate computations expressed relationally. We show experimentally that a relational engine running an auto-differentiated relational algorithm can easily scale to very large datasets, and is competitive with state-of-the-art, special-purpose systems for large-scale distributed machine learning. 

Many data extraction tasks of practical relevance require not only syntactic pattern matching but also semantic reasoning about the content of the underlying text. While regular expressions are very well suited for tasks that require only syntactic pattern matching, they fall short for data extraction tasks that involve both a syntactic and semantic component. To address this issue, we introduce semantic regexes, a generalization of regular expressions that facilitates combined syntactic and semantic reasoning about textual data. We also propose a novel learning algorithm that can synthesize semantic regexes from a small number of positive and negative examples. Our proposed learning algorithm uses a combination of neural sketch generation and compositional type-directed synthesis for fast and effective generalization from a small number of examples. We have implemented these ideas in a new tool called Smore and evaluated it on representative data extraction tasks involving several textual datasets. Our evaluation shows that semantic regexes can better support complex data extraction tasks than standard regular expressions and that our learning algorithm significantly outperforms existing tools, including state-of-the-art neural networks and program synthesis tools. 

Programmers and researchers are increasingly developing surrogates of programs, models of a subset of the observable behavior of a given program, to solve a variety of software development challenges. Programmers train surrogates from measurements of the behavior of a program on a dataset of input examples. A key challenge of surrogate construction is determining what training data to use to train a surrogate of a given program. We present a methodology for sampling datasets to train neural-network-based surrogates of programs. We first characterize the proportion of data to sample from each region of a program's input space (corresponding to different execution paths of the program) based on the complexity of learning a surrogate of the corresponding execution path. We next provide a program analysis to determine the complexity of different paths in a program. We evaluate these results on a range of real-world programs, demonstrating that complexity-guided sampling results in empirical improvements in accuracy.