Peptides, short chains of amino acid residues, play a vital role in numerous biological processes by interacting with other target molecules, offering substantial potential in drug discovery. In this work, we present PepFlow, the first multi-modal deep generative model grounded in the flow-matching framework for the design of full-atom peptides that target specific protein receptors. Drawing inspiration from the crucial roles of residue backbone orientations and side-chain dynamics in protein-peptide interactions, we characterize the peptide structure using rigid backbone frames within the $\mathrm{SE}(3)$ manifold and side-chain angles on high-dimensional tori. Furthermore, we represent discrete residue types in the peptide sequence as categorical distributions on the probability simplex. By learning the joint distributions of each modality using derived flows and vector fields on corresponding manifolds, our method excels in the fine-grained design of full-atom peptides. Harnessing the multi-modal paradigm, our approach adeptly tackles various tasks such as fix-backbone sequence design and side-chain packing through partial sampling. Through meticulously crafted experiments, we demonstrate that PepFlow exhibits superior performance in comprehensive benchmarks, highlighting its significant potential in computational peptide design and analysis.

Designing 3D ligands within a target binding site is a fundamental task in drug discovery. Existing structured-based drug design methods treat all ligand atoms equally, which ignores different roles of atoms in the ligand for drug design and can be less efficient for exploring the large drug-like molecule space. In this paper, inspired by the convention in pharmaceutical practice, we decompose the ligand molecule into two parts, namely arms and scaffold, and propose a new diffusion model, DecompDiff, with decomposed priors over arms and scaffold. In order to facilitate the decomposed generation and improve the properties of the generated molecules, we incorporate both bond diffusion in the model and additional validity guidance in the sampling phase. Extensive experiments on CrossDocked2020 show that our approach achieves state-of-the-art performance in generating high-affinity molecules while maintaining proper molecular properties and conformational stability, with up to -8.39 Avg. Vina Dock score and 24.5 Success Rate. The code is provided at https://github.com/bytedance/DecompDiff

The ever-growing ecosystem of LLMs has posed a challenge in selecting the most appropriate pre-trained model to fine-tune amidst a sea of options. Given constrained resources, fine-tuning all models and making selections afterward is unrealistic. In this work, we formulate this resource-constrained selection task into predicting fine-tuning performance and illustrate its natural connection with scaling laws. Unlike pre-training, We find that the fine-tuning scaling curve includes not just the well-known "power phase" but also the previously unobserved "pre-power phase". We also explain why existing scaling laws fail to capture this phase transition phenomenon both theoretically and empirically. To address this, we introduce the concept of "pre-learned data size" into our rectified scaling law, which overcomes theoretical limitations and fits experimental results much better. By leveraging our law, we propose a novel LLM selection algorithm that selects the near-optimal model with hundreds of times less resource consumption, while other methods may provide negatively correlated selection.

Advances in high-throughput sequencing technology have led to significant progress in measuring gene expressions at the single-cell level. The amount of publicly available single-cell RNA-seq (scRNA-seq) data is already surpassing 50M records for humans with each record measuring 20,000 genes. This highlights the need for unsupervised representation learning to fully ingest these data, yet classical transformer architectures are prohibitive to train on such data in terms of both computation and memory. To address this challenge, we propose a novel asymmetric encoder-decoder transformer for scRNA-seq data, called xTrimoGene$^\alpha$ (or xTrimoGene for short), which leverages the sparse characteristic of the data to scale up the pre-training. This scalable design of xTrimoGene reduces FLOPs by one to two orders of magnitude compared to classical transformers while maintaining high accuracy, enabling us to train the largest transformer models over the largest scRNA-seq dataset today. Our experiments also show that the performance of xTrimoGene improves as we scale up the model sizes, and it also leads to SOTA performance over various downstream tasks, such as cell type annotation, perturb-seq effect prediction, and drug combination prediction. xTrimoGene model is now available for use as a service via the following link: https://api.biomap.com/xTrimoGene/apply.

To pursue the goal of creating an open-ended agent in Minecraft, an open-ended game environment with unlimited possibilities, this paper introduces a task-centric framework named MCU for Minecraft agent evaluation. Within the MCU framework, each task is measured with six distinct difficulty scores (time consumption, operational effort, planning complexity, intricacy, creativity, novelty). These scores offer a multi-dimensional assessment of a task from different angles, and thus can reveal an agent's capability on specific facets. The difficulty scores also serve as the feature of each task, which creates a meaningful task space and unveils the relationship between tasks. For efficient evaluation of Minecraft agents employing the MCU framework, we maintain a unified benchmark, namely SkillForge, which comprises representative tasks with diverse categories and difficulty distribution. We also provide convenient filters for users to select tasks to assess specific capabilities of agents. We show that MCU has the high expressivity to cover all tasks used in recent literature on Minecraft agent, and underscores the need for advancements in areas such as creativity, precise control, and out-of-distribution generalization under the goal of open-ended Minecraft agent development. In artificial intelligence (AI), an agent is a computer program or system that is designed to perceive its environment, make decisions and take actions to solve a specific task or set of tasks. On top of that, an open-ended agent is an agent that possesses the capabilities to solve arbitrary tasks that are feasible and can be solved by humans. The open-ended agent has crucial difference with task-specific agent or multi-task agent, which can only handle a limited spectrum of tasks.

Diffusion models have revolutionized text-to-image generation with its exceptional quality and creativity. However, its multi-step sampling process is known to be slow, often requiring tens of inference steps to obtain satisfactory results. Previous attempts to improve its sampling speed and reduce computational costs through distillation have been unsuccessful in achieving a functional one-step model. In this paper, we explore a recent method called Rectified Flow, which, thus far, has only been applied to small datasets. The core of Rectified Flow lies in its \emph{reflow} procedure, which straightens the trajectories of probability flows, refines the coupling between noises and images, and facilitates the distillation process with student models. We propose a novel text-conditioned pipeline to turn Stable Diffusion (SD) into an ultra-fast one-step model, in which we find reflow plays a critical role in improving the assignment between noise and images. Leveraging our new pipeline, we create, to the best of our knowledge, the first one-step diffusion-based text-to-image generator with SD-level image quality, achieving an FID (Frechet Inception Distance) of $23.3$ on MS COCO 2017-5k, surpassing the previous state-of-the-art technique, progressive distillation, by a significant margin ($37.2$ $\rightarrow$ $23.3$ in FID). By utilizing an expanded network with 1.7B parameters, we further improve the FID to $22.4$. We call our one-step models \emph{InstaFlow}. On MS COCO 2014-30k, InstaFlow yields an FID of $13.1$ in just $0.09$ second, the best in $\leq 0.1$ second regime, outperforming the recent StyleGAN-T ($13.9$ in $0.1$ second). Notably, the training of InstaFlow only costs 199 A100 GPU days. Project page:~\url{https://github.com/gnobitab/InstaFlow}.

Deep generative models have recently achieved superior performance in 3D molecule generation. Most of them first generate atoms and then add chemical bonds based on the generated atoms in a post-processing manner. However, there might be no corresponding bond solution for the temporally generated atoms as their locations are generated without considering potential bonds. We define this problem as the atom-bond inconsistency problem and claim it is the main reason for current approaches to generating unrealistic 3D molecules. To overcome this problem, we propose a new diffusion model called MolDiff which can generate atoms and bonds simultaneously while still maintaining their consistency by explicitly modeling the dependence between their relationships. We evaluated the generation ability of our proposed model and the quality of the generated molecules using criteria related to both geometry and chemical properties. The empirical studies showed that our model outperforms previous approaches, achieving a three-fold improvement in success rate and generating molecules with significantly better quality.

Message Passing Neural Networks (MPNNs) are a widely used class of Graph Neural Networks (GNNs). However, knowing one model is more powerful than another gives little insight about what functions they can or cannot express. It is still unclear whether these models are able to approximate specific functions such as counting certain graph substructures, which is essential for applications in biology, chemistry and social network analysis. Motivated by this, we propose to study the counting power of Subgraph MPNNs, a recent and popular class of powerful GNN models that extract rooted subgraphs for each node, assign the root node a unique identifier and encode the root node's representation within its rooted subgraph. Specifically, we prove that Subgraph MPNNs fail to count more-than-4-cycles at node level, implying that node representations cannot correctly encode the surrounding substructures like ring systems with more than four atoms. To the best of our knowledge, it is the first linear-time GNN model that can count 6-cycles with theoretical guarantees. We validate its counting power in cycle counting tasks and demonstrate its competitive performance in molecular prediction benchmarks. Relational and structured data are usually represented by graphs. Representation learning over graphs with Graph Neural Networks (GNNs) has achieved remarkable results in drug discovery, computational chemistry, combinatorial optimization and social network analysis [40, 41, 42, 43, 44, 45, 46]. Among various GNNs, Message Passing Neural Network (MPNN) is one of the most commonly used GNNs [47, 48, 49]. However, the representational power of MPNNs is shown to be limited by the Weisfeiler-Lehman (WL) test [4, 5], a classical algorithm for graph isomorphism test. MPNNs cannot recognize even some simple substructures like cycles [19]. It leads to increasing attention on studying the representational power of different GNNs and designing more powerful GNN models.

Rich data and powerful machine learning models allow us to design drugs for a specific protein target \textit{in silico}. Recently, the inclusion of 3D structures during targeted drug design shows superior performance to other target-free models as the atomic interaction in the 3D space is explicitly modeled. However, current 3D target-aware models either rely on the voxelized atom densities or the autoregressive sampling process, which are not equivariant to rotation or easily violate geometric constraints resulting in unrealistic structures. In this work, we develop a 3D equivariant diffusion model to solve the above challenges. To achieve target-aware molecule design, our method learns a joint generative process of both continuous atom coordinates and categorical atom types with a SE(3)-equivariant network. Moreover, we show that our model can serve as an unsupervised feature extractor to estimate the binding affinity under proper parameterization, which provides an effective way for drug screening. To evaluate our model, we propose a comprehensive framework to evaluate the quality of sampled molecules from different dimensions. Empirical studies show our model could generate molecules with more realistic 3D structures and better affinities towards the protein targets, and improve binding affinity ranking and prediction without retraining.

Machine learning (ML) has demonstrated the state-of-the-art performance in a variety of applications, such as computer vision (1, 2), medicine (3), finance (4), autonomous engineering design (5), and scientific computing (6, 7), but performing ML tasks on hardware systems requires substantial energy and computational resources. The fundamental quantum mechanics limit leads to a bottleneck of reducing the energy consumption and simultaneously increasing the integration density of electronic circuits to catch up with the increasing scale of modern large-scale ML models (8,9). Optical architectures are emerging as promising high-throughput and energy-efficient ML hardware accelerators by leveraging the parallelism and low static energy consumption of a fundamentally different particle, photon, for computing (10, 11). Among optical systems, free-space diffractive optical neural networks (DONNs) that are able to host millions of computing neurons and form deep neural network architectures can optically perform ML tasks through the spatial light modulation and optical diffraction of coherent light in multiple diffractive layers (12-30). Prior demonstrations have shown the capability of DONNs systems to recognize input images directly in optical domain.