Daily Papers

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. The MCU framework leverages the concept of atom tasks as fundamental building blocks, enabling the generation of diverse or even arbitrary tasks. 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.

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 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.

Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs are mainly good at leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method that implicitly projects all original atoms into a few Neural Atoms, which abstracts the collective information of atomic groups within a molecule. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms' representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection with the traditional LRI calculation method, Ewald Summation. We conduct extensive experiments on three long-range graph benchmarks, covering both graph-level and link-level tasks on molecular graphs. We empirically justify that our method can be equipped with an arbitrary GNN and help to capture LRI.

Two-dimensional (2D) Nuclear Magnetic Resonance (NMR) spectroscopy, particularly Heteronuclear Single Quantum Coherence (HSQC) spectroscopy, plays a critical role in elucidating molecular structures, interactions, and electronic properties. However, accurately interpreting 2D NMR data remains labor-intensive and error-prone, requiring highly trained domain experts, especially for complex molecules. Machine Learning (ML) holds significant potential in 2D NMR analysis by learning molecular representations and recognizing complex patterns from data. However, progress has been limited by the lack of large-scale and high-quality annotated datasets. In this work, we introduce 2DNMRGym, the first annotated experimental dataset designed for ML-based molecular representation learning in 2D NMR. It includes over 22,000 HSQC spectra, along with the corresponding molecular graphs and SMILES strings. Uniquely, 2DNMRGym adopts a surrogate supervision setup: models are trained using algorithm-generated annotations derived from a previously validated method and evaluated on a held-out set of human-annotated gold-standard labels. This enables rigorous assessment of a model's ability to generalize from imperfect supervision to expert-level interpretation. We provide benchmark results using a series of 2D and 3D GNN and GNN transformer models, establishing a strong foundation for future work. 2DNMRGym supports scalable model training and introduces a chemically meaningful benchmark for evaluating atom-level molecular representations in NMR-guided structural tasks. Our data and code is open-source and available on Huggingface and Github.

The SoccerNet 2023 challenges were the third annual video understanding challenges organized by the SoccerNet team. For this third edition, the challenges were composed of seven vision-based tasks split into three main themes. The first theme, broadcast video understanding, is composed of three high-level tasks related to describing events occurring in the video broadcasts: (1) action spotting, focusing on retrieving all timestamps related to global actions in soccer, (2) ball action spotting, focusing on retrieving all timestamps related to the soccer ball change of state, and (3) dense video captioning, focusing on describing the broadcast with natural language and anchored timestamps. The second theme, field understanding, relates to the single task of (4) camera calibration, focusing on retrieving the intrinsic and extrinsic camera parameters from images. The third and last theme, player understanding, is composed of three low-level tasks related to extracting information about the players: (5) re-identification, focusing on retrieving the same players across multiple views, (6) multiple object tracking, focusing on tracking players and the ball through unedited video streams, and (7) jersey number recognition, focusing on recognizing the jersey number of players from tracklets. Compared to the previous editions of the SoccerNet challenges, tasks (2-3-7) are novel, including new annotations and data, task (4) was enhanced with more data and annotations, and task (6) now focuses on end-to-end approaches. More information on the tasks, challenges, and leaderboards are available on https://www.soccer-net.org. Baselines and development kits can be found on https://github.com/SoccerNet.

Language-guided human motion synthesis has been a challenging task due to the inherent complexity and diversity of human behaviors. Previous methods face limitations in generalization to novel actions, often resulting in unrealistic or incoherent motion sequences. In this paper, we propose ATOM (ATomic mOtion Modeling) to mitigate this problem, by decomposing actions into atomic actions, and employing a curriculum learning strategy to learn atomic action composition. First, we disentangle complex human motions into a set of atomic actions during learning, and then assemble novel actions using the learned atomic actions, which offers better adaptability to new actions. Moreover, we introduce a curriculum learning training strategy that leverages masked motion modeling with a gradual increase in the mask ratio, and thus facilitates atomic action assembly. This approach mitigates the overfitting problem commonly encountered in previous methods while enforcing the model to learn better motion representations. We demonstrate the effectiveness of ATOM through extensive experiments, including text-to-motion and action-to-motion synthesis tasks. We further illustrate its superiority in synthesizing plausible and coherent text-guided human motion sequences.

Antibody design is an essential yet challenging task in various domains like therapeutics and biology. There are two major defects in current learning-based methods: 1) tackling only a certain subtask of the whole antibody design pipeline, making them suboptimal or resource-intensive. 2) omitting either the framework regions or side chains, thus incapable of capturing the full-atom geometry. To address these pitfalls, we propose dynamic Multi-channel Equivariant grAph Network (dyMEAN), an end-to-end full-atom model for E(3)-equivariant antibody design given the epitope and the incomplete sequence of the antibody. Specifically, we first explore structural initialization as a knowledgeable guess of the antibody structure and then propose shadow paratope to bridge the epitope-antibody connections. Both 1D sequences and 3D structures are updated via an adaptive multi-channel equivariant encoder that is able to process protein residues of variable sizes when considering full atoms. Finally, the updated antibody is docked to the epitope via the alignment of the shadow paratope. Experiments on epitope-binding CDR-H3 design, complex structure prediction, and affinity optimization demonstrate the superiority of our end-to-end framework and full-atom modeling.

Recently, text-to-motion models have opened new possibilities for creating realistic human motion with greater efficiency and flexibility. However, aligning motion generation with event-level textual descriptions presents unique challenges due to the complex relationship between textual prompts and desired motion outcomes. To address this, we introduce AToM, a framework that enhances the alignment between generated motion and text prompts by leveraging reward from GPT-4Vision. AToM comprises three main stages: Firstly, we construct a dataset MotionPrefer that pairs three types of event-level textual prompts with generated motions, which cover the integrity, temporal relationship and frequency of motion. Secondly, we design a paradigm that utilizes GPT-4Vision for detailed motion annotation, including visual data formatting, task-specific instructions and scoring rules for each sub-task. Finally, we fine-tune an existing text-to-motion model using reinforcement learning guided by this paradigm. Experimental results demonstrate that AToM significantly improves the event-level alignment quality of text-to-motion generation.

Identifying the chemical structure from a graphical representation, or image, of a molecule is a challenging pattern recognition task that would greatly benefit drug development. Yet, existing methods for chemical structure recognition do not typically generalize well, and show diminished effectiveness when confronted with domains where data is sparse, or costly to generate, such as hand-drawn molecule images. To address this limitation, we propose a new chemical structure recognition tool that delivers state-of-the-art performance and can adapt to new domains with a limited number of data samples and supervision. Unlike previous approaches, our method provides atom-level localization, and can therefore segment the image into the different atoms and bonds. Our model is the first model to perform OCSR with atom-level entity detection with only SMILES supervision. Through rigorous and extensive benchmarking, we demonstrate the preeminence of our chemical structure recognition approach in terms of data efficiency, accuracy, and atom-level entity prediction.

Inverse protein folding -- the task of predicting a protein sequence from its backbone atom coordinates -- has surfaced as an important problem in the "top down", de novo design of proteins. Contemporary approaches have cast this problem as a conditional generative modelling problem, where a large generative model over protein sequences is conditioned on the backbone. While these generative models very rapidly produce promising sequences, independent draws from generative models may fail to produce sequences that reliably fold to the correct backbone. Furthermore, it is challenging to adapt pure generative approaches to other settings, e.g., when constraints exist. In this paper, we cast the problem of improving generated inverse folds as an optimization problem that we solve using recent advances in "deep" or "latent space" Bayesian optimization. Our approach consistently produces protein sequences with greatly reduced structural error to the target backbone structure as measured by TM score and RMSD while using fewer computational resources. Additionally, we demonstrate other advantages of an optimization-based approach to the problem, such as the ability to handle constraints.

Generating the periodic structure of stable materials is a long-standing challenge for the material design community. This task is difficult because stable materials only exist in a low-dimensional subspace of all possible periodic arrangements of atoms: 1) the coordinates must lie in the local energy minimum defined by quantum mechanics, and 2) global stability also requires the structure to follow the complex, yet specific bonding preferences between different atom types. Existing methods fail to incorporate these factors and often lack proper invariances. We propose a Crystal Diffusion Variational Autoencoder (CDVAE) that captures the physical inductive bias of material stability. By learning from the data distribution of stable materials, the decoder generates materials in a diffusion process that moves atomic coordinates towards a lower energy state and updates atom types to satisfy bonding preferences between neighbors. Our model also explicitly encodes interactions across periodic boundaries and respects permutation, translation, rotation, and periodic invariances. We significantly outperform past methods in three tasks: 1) reconstructing the input structure, 2) generating valid, diverse, and realistic materials, and 3) generating materials that optimize a specific property. We also provide several standard datasets and evaluation metrics for the broader machine learning community.