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.

Towards a Physics Engine to Simulate Robotic Laser Surgery: Finite Element Modeling of Thermal Laser-Tissue Interactions

This paper presents a computational model, based on the Finite Element Method (FEM), that simulates the thermal response of laser-irradiated tissue. This model addresses a gap in the current ecosystem of surgical robot simulators, which generally lack support for lasers and other energy-based end effectors. In the proposed model, the thermal dynamics of the tissue are calculated as the solution to a heat conduction problem with appropriate boundary conditions. The FEM formulation allows the model to capture complex phenomena, such as convection, which is crucial for creating realistic simulations. The accuracy of the model was verified via benchtop laser-tissue interaction experiments using agar tissue phantoms and ex-vivo chicken muscle. The results revealed an average root-mean-square error (RMSE) of less than 2 degrees Celsius across most experimental conditions.

Physics Informed Distillation for Diffusion Models

Diffusion models have recently emerged as a potent tool in generative modeling. However, their inherent iterative nature often results in sluggish image generation due to the requirement for multiple model evaluations. Recent progress has unveiled the intrinsic link between diffusion models and Probability Flow Ordinary Differential Equations (ODEs), thus enabling us to conceptualize diffusion models as ODE systems. Simultaneously, Physics Informed Neural Networks (PINNs) have substantiated their effectiveness in solving intricate differential equations through implicit modeling of their solutions. Building upon these foundational insights, we introduce Physics Informed Distillation (PID), which employs a student model to represent the solution of the ODE system corresponding to the teacher diffusion model, akin to the principles employed in PINNs. Through experiments on CIFAR 10 and ImageNet 64x64, we observe that PID achieves performance comparable to recent distillation methods. Notably, it demonstrates predictable trends concerning method-specific hyperparameters and eliminates the need for synthetic dataset generation during the distillation process. Both of which contribute to its easy-to-use nature as a distillation approach for Diffusion Models. Our code and pre-trained checkpoint are publicly available at: https://github.com/pantheon5100/pid_diffusion.git.

"Benefit Game: Alien Seaweed Swarms" -- Real-time Gamification of Digital Seaweed Ecology

"Benefit Game: Alien Seaweed Swarms" combines artificial life art and interactive game with installation to explore the impact of human activity on fragile seaweed ecosystems. The project aims to promote ecological consciousness by creating a balance in digital seaweed ecologies. Inspired by the real species "Laminaria saccharina", the author employs Procedural Content Generation via Machine Learning technology to generate variations of virtual seaweeds and symbiotic fungi. The audience can explore the consequences of human activities through gameplay and observe the ecosystem's feedback on the benefits and risks of seaweed aquaculture. This Benefit Game offers dynamic and real-time responsive artificial seaweed ecosystems for an interactive experience that enhances ecological consciousness.

DEGAS: Detailed Expressions on Full-Body Gaussian Avatars

Although neural rendering has made significant advancements in creating lifelike, animatable full-body and head avatars, incorporating detailed expressions into full-body avatars remains largely unexplored. We present DEGAS, the first 3D Gaussian Splatting (3DGS)-based modeling method for full-body avatars with rich facial expressions. Trained on multiview videos of a given subject, our method learns a conditional variational autoencoder that takes both the body motion and facial expression as driving signals to generate Gaussian maps in the UV layout. To drive the facial expressions, instead of the commonly used 3D Morphable Models (3DMMs) in 3D head avatars, we propose to adopt the expression latent space trained solely on 2D portrait images, bridging the gap between 2D talking faces and 3D avatars. Leveraging the rendering capability of 3DGS and the rich expressiveness of the expression latent space, the learned avatars can be reenacted to reproduce photorealistic rendering images with subtle and accurate facial expressions. Experiments on an existing dataset and our newly proposed dataset of full-body talking avatars demonstrate the efficacy of our method. We also propose an audio-driven extension of our method with the help of 2D talking faces, opening new possibilities to interactive AI agents.

BI-MDRG: Bridging Image History in Multimodal Dialogue Response Generation

Multimodal Dialogue Response Generation (MDRG) is a recently proposed task where the model needs to generate responses in texts, images, or a blend of both based on the dialogue context. Due to the lack of a large-scale dataset specifically for this task and the benefits of leveraging powerful pre-trained models, previous work relies on the text modality as an intermediary step for both the image input and output of the model rather than adopting an end-to-end approach. However, this approach can overlook crucial information about the image, hindering 1) image-grounded text response and 2) consistency of objects in the image response. In this paper, we propose BI-MDRG that bridges the response generation path such that the image history information is utilized for enhanced relevance of text responses to the image content and the consistency of objects in sequential image responses. Through extensive experiments on the multimodal dialogue benchmark dataset, we show that BI-MDRG can effectively increase the quality of multimodal dialogue. Additionally, recognizing the gap in benchmark datasets for evaluating the image consistency in multimodal dialogue, we have created a curated set of 300 dialogues annotated to track object consistency across conversations.

Towards Understanding Dual BN In Hybrid Adversarial Training

There is a growing concern about applying batch normalization (BN) in adversarial training (AT), especially when the model is trained on both adversarial samples and clean samples (termed Hybrid-AT). With the assumption that adversarial and clean samples are from two different domains, a common practice in prior works is to adopt Dual BN, where BN and BN are used for adversarial and clean branches, respectively. A popular belief for motivating Dual BN is that estimating normalization statistics of this mixture distribution is challenging and thus disentangling it for normalization achieves stronger robustness. In contrast to this belief, we reveal that disentangling statistics plays a less role than disentangling affine parameters in model training. This finding aligns with prior work (Rebuffi et al., 2023), and we build upon their research for further investigations. We demonstrate that the domain gap between adversarial and clean samples is not very large, which is counter-intuitive considering the significant influence of adversarial perturbation on the model accuracy. We further propose a two-task hypothesis which serves as the empirical foundation and a unified framework for Hybrid-AT improvement. We also investigate Dual BN in test-time and reveal that affine parameters characterize the robustness during inference. Overall, our work sheds new light on understanding the mechanism of Dual BN in Hybrid-AT and its underlying justification.

BreakGPT: A Large Language Model with Multi-stage Structure for Financial Breakout Detection

Trading range breakout (TRB) is a key method in the technical analysis of financial trading, widely employed by traders in financial markets such as stocks, futures, and foreign exchange. However, distinguishing between true and false breakout and providing the correct rationale cause significant challenges to investors. Recently, large language models have achieved success in various downstream applications, but their effectiveness in the domain of financial breakout detection has been subpar. The reason is that the unique data and specific knowledge are required in breakout detection. To address these issues, we introduce BreakGPT, the first large language model for financial breakout detection. Furthermore, we have developed a novel framework for large language models, namely multi-stage structure, effectively reducing mistakes in downstream applications. Experimental results indicate that compared to GPT-3.5, BreakGPT improves the accuracy of answers and rational by 44%, with the multi-stage structure contributing 17.6% to the improvement. Additionally, it outperforms ChatGPT-4 by 42.07%. Our Code is publicly available: https://github.com/Neviim96/BreakGPT

Human Aesthetic Preference-Based Large Text-to-Image Model Personalization: Kandinsky Generation as an Example

With the advancement of neural generative capabilities, the art community has actively embraced GenAI (generative artificial intelligence) for creating painterly content. Large text-to-image models can quickly generate aesthetically pleasing outcomes. However, the process can be non-deterministic and often involves tedious trial-and-error, as users struggle with formulating effective prompts to achieve their desired results. This paper introduces a prompting-free generative approach that empowers users to automatically generate personalized painterly content that incorporates their aesthetic preferences in a customized artistic style. This approach involves utilizing ``semantic injection'' to customize an artist model in a specific artistic style, and further leveraging a genetic algorithm to optimize the prompt generation process through real-time iterative human feedback. By solely relying on the user's aesthetic evaluation and preference for the artist model-generated images, this approach creates the user a personalized model that encompasses their aesthetic preferences and the customized artistic style.

The Contemporary Art of Image Search: Iterative User Intent Expansion via Vision-Language Model

Image search is an essential and user-friendly method to explore vast galleries of digital images. However, existing image search methods heavily rely on proximity measurements like tag matching or image similarity, requiring precise user inputs for satisfactory results. To meet the growing demand for a contemporary image search engine that enables accurate comprehension of users' search intentions, we introduce an innovative user intent expansion framework. Our framework leverages visual-language models to parse and compose multi-modal user inputs to provide more accurate and satisfying results. It comprises two-stage processes: 1) a parsing stage that incorporates a language parsing module with large language models to enhance the comprehension of textual inputs, along with a visual parsing module that integrates an interactive segmentation module to swiftly identify detailed visual elements within images; and 2) a logic composition stage that combines multiple user search intents into a unified logic expression for more sophisticated operations in complex searching scenarios. Moreover, the intent expansion framework enables users to perform flexible contextualized interactions with the search results to further specify or adjust their detailed search intents iteratively. We implemented the framework into an image search system for NFT (non-fungible token) search and conducted a user study to evaluate its usability and novel properties. The results indicate that the proposed framework significantly improves users' image search experience. Particularly the parsing and contextualized interactions prove useful in allowing users to express their search intents more accurately and engage in a more enjoyable iterative search experience.