Classifying the Stoichiometry of Virus-like Particles with Interpretable Machine Learning

Virus-like particles (VLPs) are valuable for vaccine development due to their immune-triggering properties. Understanding their stoichiometry, the number of protein subunits to form a VLP, is critical for vaccine optimisation. However, current experimental methods to determine stoichiometry are time-consuming and require highly purified proteins. To efficiently classify stoichiometry classes in proteins, we curate a new dataset and propose an interpretable, data-driven pipeline leveraging linear machine learning models. We also explore the impact of feature encoding on model performance and interpretability, as well as methods to identify key protein sequence features influencing classification. The evaluation of our pipeline demonstrates that it can classify stoichiometry while revealing protein features that possibly influence VLP assembly. The data and code used in this work are publicly available at https://github.com/Shef-AIRE/StoicIML.

Theoretical Benefit and Limitation of Diffusion Language Model

Diffusion language models have emerged as a promising approach for text generation. One would naturally expect this method to be an efficient replacement for autoregressive models since multiple tokens can be sampled in parallel during each diffusion step. However, its efficiency-accuracy trade-off is not yet well understood. In this paper, we present a rigorous theoretical analysis of a widely used type of diffusion language model, the Masked Diffusion Model (MDM), and find that its effectiveness heavily depends on the target evaluation metric. Under mild conditions, we prove that when using perplexity as the metric, MDMs can achieve near-optimal perplexity in sampling steps regardless of sequence length, demonstrating that efficiency can be achieved without sacrificing performance. However, when using the sequence error rate--which is important for understanding the "correctness" of a sequence, such as a reasoning chain--we show that the required sampling steps must scale linearly with sequence length to obtain "correct" sequences, thereby eliminating MDM's efficiency advantage over autoregressive models. Our analysis establishes the first theoretical foundation for understanding the benefits and limitations of MDMs. All theoretical findings are supported by empirical studies.

GENERator: A Long-Context Generative Genomic Foundation Model

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

Human Decision-making is Susceptible to AI-driven Manipulation

Artificial Intelligence (AI) systems are increasingly intertwined with daily life, assisting users in executing various tasks and providing guidance on decision-making. This integration introduces risks of AI-driven manipulation, where such systems may exploit users' cognitive biases and emotional vulnerabilities to steer them toward harmful outcomes. Through a randomized controlled trial with 233 participants, we examined human susceptibility to such manipulation in financial (e.g., purchases) and emotional (e.g., conflict resolution) decision-making contexts. Participants interacted with one of three AI agents: a neutral agent (NA) optimizing for user benefit without explicit influence, a manipulative agent (MA) designed to covertly influence beliefs and behaviors, or a strategy-enhanced manipulative agent (SEMA) employing explicit psychological tactics to reach its hidden objectives. By analyzing participants' decision patterns and shifts in their preference ratings post-interaction, we found significant susceptibility to AI-driven manipulation. Particularly, across both decision-making domains, participants interacting with the manipulative agents shifted toward harmful options at substantially higher rates (financial, MA: 62.3%, SEMA: 59.6%; emotional, MA: 42.3%, SEMA: 41.5%) compared to the NA group (financial, 35.8%; emotional, 12.8%). Notably, our findings reveal that even subtle manipulative objectives (MA) can be as effective as employing explicit psychological strategies (SEMA) in swaying human decision-making. By revealing the potential for covert AI influence, this study highlights a critical vulnerability in human-AI interactions, emphasizing the need for ethical safeguards and regulatory frameworks to ensure responsible deployment of AI technologies and protect human autonomy.

Car-GS: Addressing Reflective and Transparent Surface Challenges in 3D Car Reconstruction

3D car modeling is crucial for applications in autonomous driving systems, virtual and augmented reality, and gaming. However, due to the distinctive properties of cars, such as highly reflective and transparent surface materials, existing methods often struggle to achieve accurate 3D car reconstruction.To address these limitations, we propose Car-GS, a novel approach designed to mitigate the effects of specular highlights and the coupling of RGB and geometry in 3D geometric and shading reconstruction (3DGS). Our method incorporates three key innovations: First, we introduce view-dependent Gaussian primitives to effectively model surface reflections. Second, we identify the limitations of using a shared opacity parameter for both image rendering and geometric attributes when modeling transparent objects. To overcome this, we assign a learnable geometry-specific opacity to each 2D Gaussian primitive, dedicated solely to rendering depth and normals. Third, we observe that reconstruction errors are most prominent when the camera view is nearly orthogonal to glass surfaces. To address this issue, we develop a quality-aware supervision module that adaptively leverages normal priors from a pre-trained large-scale normal model.Experimental results demonstrate that Car-GS achieves precise reconstruction of car surfaces and significantly outperforms prior methods. The project page is available at https://lcc815.github.io/Car-GS.

Molecule-dynamic-based Aging Clock and Aging Roadmap Forecast with Sundial

Addressing the unavoidable bias inherent in supervised aging clocks, we introduce Sundial, a novel framework that models molecular dynamics through a diffusion field, capturing both the population-level aging process and the individual-level relative aging order. Sundial enables unbiasedestimation of biological age and the forecast of aging roadmap. Fasteraging individuals from Sundial exhibit a higher disease risk compared to those identified from supervised aging clocks. This framework opens new avenues for exploring key topics, including age- and sex-specific aging dynamics and faster yet healthy aging paths.

ProtCLIP: Function-Informed Protein Multi-Modal Learning

Multi-modality pre-training paradigm that aligns protein sequences and biological descriptions has learned general protein representations and achieved promising performance in various downstream applications. However, these works were still unable to replicate the extraordinary success of language-supervised visual foundation models due to the ineffective usage of aligned protein-text paired data and the lack of an effective function-informed pre-training paradigm. To address these issues, this paper curates a large-scale protein-text paired dataset called ProtAnno with a property-driven sampling strategy, and introduces a novel function-informed protein pre-training paradigm. Specifically, the sampling strategy determines selecting probability based on the sample confidence and property coverage, balancing the data quality and data quantity in face of large-scale noisy data. Furthermore, motivated by significance of the protein specific functional mechanism, the proposed paradigm explicitly model protein static and dynamic functional segments by two segment-wise pre-training objectives, injecting fine-grained information in a function-informed manner. Leveraging all these innovations, we develop ProtCLIP, a multi-modality foundation model that comprehensively represents function-aware protein embeddings. On 22 different protein benchmarks within 5 types, including protein functionality classification, mutation effect prediction, cross-modal transformation, semantic similarity inference and protein-protein interaction prediction, our ProtCLIP consistently achieves SOTA performance, with remarkable improvements of 75% on average in five cross-modal transformation benchmarks, 59.9% in GO-CC and 39.7% in GO-BP protein function prediction. The experimental results verify the extraordinary potential of ProtCLIP serving as the protein multi-modality foundation model.

Physical Informed Driving World Model

Autonomous driving requires robust perception models trained on high-quality, large-scale multi-view driving videos for tasks like 3D object detection, segmentation and trajectory prediction. While world models provide a cost-effective solution for generating realistic driving videos, challenges remain in ensuring these videos adhere to fundamental physical principles, such as relative and absolute motion, spatial relationship like occlusion and spatial consistency, and temporal consistency. To address these, we propose DrivePhysica, an innovative model designed to generate realistic multi-view driving videos that accurately adhere to essential physical principles through three key advancements: (1) a Coordinate System Aligner module that integrates relative and absolute motion features to enhance motion interpretation, (2) an Instance Flow Guidance module that ensures precise temporal consistency via efficient 3D flow extraction, and (3) a Box Coordinate Guidance module that improves spatial relationship understanding and accurately resolves occlusion hierarchies. Grounded in physical principles, we achieve state-of-the-art performance in driving video generation quality (3.96 FID and 38.06 FVD on the Nuscenes dataset) and downstream perception tasks. Our project homepage: https://metadrivescape.github.io/papers_project/DrivePhysica/page.html

Benchmarking Large Vision-Language Models via Directed Scene Graph for Comprehensive Image Captioning

Generating detailed captions comprehending text-rich visual content in images has received growing attention for Large Vision-Language Models (LVLMs). However, few studies have developed benchmarks specifically tailored for detailed captions to measure their accuracy and comprehensiveness. In this paper, we introduce a detailed caption benchmark, termed as CompreCap, to evaluate the visual context from a directed scene graph view. Concretely, we first manually segment the image into semantically meaningful regions (i.e., semantic segmentation mask) according to common-object vocabulary, while also distinguishing attributes of objects within all those regions. Then directional relation labels of these objects are annotated to compose a directed scene graph that can well encode rich compositional information of the image. Based on our directed scene graph, we develop a pipeline to assess the generated detailed captions from LVLMs on multiple levels, including the object-level coverage, the accuracy of attribute descriptions, the score of key relationships, etc. Experimental results on the CompreCap dataset confirm that our evaluation method aligns closely with human evaluation scores across LVLMs.

Pysical Informed Driving World Model

Autonomous driving requires robust perception models trained on high-quality, large-scale multi-view driving videos for tasks like 3D object detection, segmentation and trajectory prediction. While world models provide a cost-effective solution for generating realistic driving videos, challenges remain in ensuring these videos adhere to fundamental physical principles, such as relative and absolute motion, spatial relationship like occlusion and spatial consistency, and temporal consistency. To address these, we propose DrivePhysica, an innovative model designed to generate realistic multi-view driving videos that accurately adhere to essential physical principles through three key advancements: (1) a Coordinate System Aligner module that integrates relative and absolute motion features to enhance motion interpretation, (2) an Instance Flow Guidance module that ensures precise temporal consistency via efficient 3D flow extraction, and (3) a Box Coordinate Guidance module that improves spatial relationship understanding and accurately resolves occlusion hierarchies. Grounded in physical principles, we achieve state-of-the-art performance in driving video generation quality (3.96 FID and 38.06 FVD on the Nuscenes dataset) and downstream perception tasks. Our project homepage: https://metadrivescape.github.io/papers_project/DrivePhysica/page.html