Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis; improving peptide and protein identification and quantification; characterizing protein-protein interactions and protein complexes; advancing spatial and perturbation proteomics; integrating multi-omics data; and ultimately enabling AI-empowered virtual cells.

Not-So-Optimal Transport Flows for 3D Point Cloud Generation

Learning generative models of 3D point clouds is one of the fundamental problems in 3D generative learning. One of the key properties of point clouds is their permutation invariance, i.e., changing the order of points in a point cloud does not change the shape they represent. In this paper, we analyze the recently proposed equivariant OT flows that learn permutation invariant generative models for point-based molecular data and we show that these models scale poorly on large point clouds. Also, we observe learning (equivariant) OT flows is generally challenging since straightening flow trajectories makes the learned flow model complex at the beginning of the trajectory. To remedy these, we propose not-so-optimal transport flow models that obtain an approximate OT by an offline OT precomputation, enabling an efficient construction of OT pairs for training. During training, we can additionally construct a hybrid coupling by combining our approximate OT and independent coupling to make the target flow models easier to learn. In an extensive empirical study, we show that our proposed model outperforms prior diffusion- and flow-based approaches on a wide range of unconditional generation and shape completion on the ShapeNet benchmark.

ChartInsighter: An Approach for Mitigating Hallucination in Time-series Chart Summary Generation with A Benchmark Dataset

Effective chart summary can significantly reduce the time and effort decision makers spend interpreting charts, enabling precise and efficient communication of data insights. Previous studies have faced challenges in generating accurate and semantically rich summaries of time-series data charts. In this paper, we identify summary elements and common hallucination types in the generation of time-series chart summaries, which serve as our guidelines for automatic generation. We introduce ChartInsighter, which automatically generates chart summaries of time-series data, effectively reducing hallucinations in chart summary generation. Specifically, we assign multiple agents to generate the initial chart summary and collaborate iteratively, during which they invoke external data analysis modules to extract insights and compile them into a coherent summary. Additionally, we implement a self-consistency test method to validate and correct our summary. We create a high-quality benchmark of charts and summaries, with hallucination types annotated on a sentence-by-sentence basis, facilitating the evaluation of the effectiveness of reducing hallucinations. Our evaluations using our benchmark show that our method surpasses state-of-the-art models, and that our summary hallucination rate is the lowest, which effectively reduces various hallucinations and improves summary quality. The benchmark is available at https://github.com/wangfen01/ChartInsighter.

BlobGEN-Vid: Compositional Text-to-Video Generation with Blob Video Representations

Existing video generation models struggle to follow complex text prompts and synthesize multiple objects, raising the need for additional grounding input for improved controllability. In this work, we propose to decompose videos into visual primitives - blob video representation, a general representation for controllable video generation. Based on blob conditions, we develop a blob-grounded video diffusion model named BlobGEN-Vid that allows users to control object motions and fine-grained object appearance. In particular, we introduce a masked 3D attention module that effectively improves regional consistency across frames. In addition, we introduce a learnable module to interpolate text embeddings so that users can control semantics in specific frames and obtain smooth object transitions. We show that our framework is model-agnostic and build BlobGEN-Vid based on both U-Net and DiT-based video diffusion models. Extensive experimental results show that BlobGEN-Vid achieves superior zero-shot video generation ability and state-of-the-art layout controllability on multiple benchmarks. When combined with an LLM for layout planning, our framework even outperforms proprietary text-to-video generators in terms of compositional accuracy.

Autonomous Alignment with Human Value on Altruism through Considerate Self-imagination and Theory of Mind

With the widespread application of Artificial Intelligence (AI) in human society, enabling AI to autonomously align with human values has become a pressing issue to ensure its sustainable development and benefit to humanity. One of the most important aspects of aligning with human values is the necessity for agents to autonomously make altruistic, safe, and ethical decisions, considering and caring for human well-being. Current AI extremely pursues absolute superiority in certain tasks, remaining indifferent to the surrounding environment and other agents, which has led to numerous safety risks. Altruistic behavior in human society originates from humans' capacity for empathizing others, known as Theory of Mind (ToM), combined with predictive imaginative interactions before taking action to produce thoughtful and altruistic behaviors. Inspired by this, we are committed to endow agents with considerate self-imagination and ToM capabilities, driving them through implicit intrinsic motivations to autonomously align with human altruistic values. By integrating ToM within the imaginative space, agents keep an eye on the well-being of other agents in real time, proactively anticipate potential risks to themselves and others, and make thoughtful altruistic decisions that balance negative effects on the environment. The ancient Chinese story of Sima Guang Smashes the Vat illustrates the moral behavior of the young Sima Guang smashed a vat to save a child who had accidentally fallen into it, which is an excellent reference scenario for this paper. We design an experimental scenario similar to Sima Guang Smashes the Vat and its variants with different complexities, which reflects the trade-offs and comprehensive considerations between self-goals, altruistic rescue, and avoiding negative side effects.

TPAoI: Ensuring Fresh Service Status at the Network Edge in Compute-First Networking

In compute-first networking, maintaining fresh and accurate status information at the network edge is crucial for effective access to remote services. This process typically involves three phases: Status updating, user accessing, and user requesting. However, current studies on status effectiveness, such as Age of Information at Query (QAoI), do not comprehensively cover all these phases. Therefore, this paper introduces a novel metric, TPAoI, aimed at optimizing update decisions by measuring the freshness of service status. The stochastic nature of edge environments, characterized by unpredictable communication delays in updating, requesting, and user access times, poses a significant challenge when modeling. To address this, we model the problem as a Markov Decision Process (MDP) and employ a Dueling Double Deep Q-Network (D3QN) algorithm for optimization. Extensive experiments demonstrate that the proposed TPAoI metric effectively minimizes AoI, ensuring timely and reliable service updates in dynamic edge environments. Results indicate that TPAoI reduces AoI by an average of 47\% compared to QAoI metrics and decreases update frequency by an average of 48\% relative to conventional AoI metrics, showing significant improvement.

Coherent3D: Coherent 3D Portrait Video Reconstruction via Triplane Fusion

Recent breakthroughs in single-image 3D portrait reconstruction have enabled telepresence systems to stream 3D portrait videos from a single camera in real-time, democratizing telepresence. However, per-frame 3D reconstruction exhibits temporal inconsistency and forgets the user's appearance. On the other hand, self-reenactment methods can render coherent 3D portraits by driving a 3D avatar built from a single reference image, but fail to faithfully preserve the user's per-frame appearance (e.g., instantaneous facial expression and lighting). As a result, none of these two frameworks is an ideal solution for democratized 3D telepresence. In this work, we address this dilemma and propose a novel solution that maintains both coherent identity and dynamic per-frame appearance to enable the best possible realism. To this end, we propose a new fusion-based method that takes the best of both worlds by fusing a canonical 3D prior from a reference view with dynamic appearance from per-frame input views, producing temporally stable 3D videos with faithful reconstruction of the user's per-frame appearance. Trained only using synthetic data produced by an expression-conditioned 3D GAN, our encoder-based method achieves both state-of-the-art 3D reconstruction and temporal consistency on in-studio and in-the-wild datasets. https://research.nvidia.com/labs/amri/projects/coherent3d

Fine-Tuning Pre-trained Large Time Series Models for Prediction of Wind Turbine SCADA Data

The remarkable achievements of large models in the fields of natural language processing (NLP) and computer vision (CV) have sparked interest in their application to time series forecasting within industrial contexts. This paper explores the application of a pre-trained large time series model, Timer, which was initially trained on a wide range of time series data from multiple domains, in the prediction of Supervisory Control and Data Acquisition (SCADA) data collected from wind turbines. The model was fine-tuned on SCADA datasets sourced from two wind farms, which exhibited differing characteristics, and its accuracy was subsequently evaluated. Additionally, the impact of data volume was studied to evaluate the few-shot ability of the Timer. Finally, an application study on one-turbine fine-tuning for whole-plant prediction was implemented where both few-shot and cross-turbine generalization capacity is required. The results reveal that the pre-trained large model does not consistently outperform other baseline models in terms of prediction accuracy whenever the data is abundant or not, but demonstrates superior performance in the application study. This result underscores the distinctive advantages of the pre-trained large time series model in facilitating swift deployment.

Learning Object Properties Using Robot Proprioception via Differentiable Robot-Object Interaction

Differentiable simulation has become a powerful tool for system identification. While prior work has focused on identifying robot properties using robot-specific data or object properties using object-specific data, our approach calibrates object properties by using information from the robot, without relying on data from the object itself. Specifically, we utilize robot joint encoder information, which is commonly available in standard robotic systems. Our key observation is that by analyzing the robot's reactions to manipulated objects, we can infer properties of those objects, such as inertia and softness. Leveraging this insight, we develop differentiable simulations of robot-object interactions to inversely identify the properties of the manipulated objects. Our approach relies solely on proprioception -- the robot's internal sensing capabilities -- and does not require external measurement tools or vision-based tracking systems. This general method is applicable to any articulated robot and requires only joint position information. We demonstrate the effectiveness of our method on a low-cost robotic platform, achieving accurate mass and elastic modulus estimations of manipulated objects with just a few seconds of computation on a laptop.

PDSR: A Privacy-Preserving Diversified Service Recommendation Method on Distributed Data

The last decade has witnessed a tremendous growth of service computing, while efficient service recommendation methods are desired to recommend high-quality services to users. It is well known that collaborative filtering is one of the most popular methods for service recommendation based on QoS, and many existing proposals focus on improving recommendation accuracy, i.e., recommending high-quality redundant services. Nevertheless, users may have different requirements on QoS, and hence diversified recommendation has been attracting increasing attention in recent years to fulfill users' diverse demands and to explore potential services. Unfortunately, the recommendation performances relies on a large volume of data (e.g., QoS data), whereas the data may be distributed across multiple platforms. Therefore, to enable data sharing across the different platforms for diversified service recommendation, we propose a Privacy-preserving Diversified Service Recommendation (PDSR) method. Specifically, we innovate in leveraging the Locality-Sensitive Hashing (LSH) mechanism such that privacy-preserved data sharing across different platforms is enabled to construct a service similarity graph. Based on the similarity graph, we propose a novel accuracy-diversity metric and design a $2$-approximation algorithm to select $K$ services to recommend by maximizing the accuracy-diversity measure. Extensive experiments on real datasets are conducted to verify the efficacy of our PDSR method.