United States

The alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the seamless flow of genomic information between RNA sequences and structures. In this study, we introduce OmniGenome, an RNA FM trained to align RNA sequences with respect to secondary structures through structure-contextualized modelling. This alignment enables free and bidirectional mappings between sequences and structures by utilizing a flexible RNA modelling paradigm that supports versatile input and output modalities, i.e., sequence and/or structure as input/output. We implement RNA design and zero-shot secondary structure prediction as case studies to evaluate the Seq2Str and Str2Seq mapping capabilities of OmniGenome. Results on the EternaV2 benchmark show that OmniGenome solved 74% of puzzles, whereas existing FMs solved only up to 3% of the puzzles due to the lack of sequence-structure alignment. We leverage four comprehensive in-silico genome modelling benchmarks to evaluate performance across a diverse set of downstream genome tasks, where the results show that OmniGenome achieves state-of-the-art performance on RNA and DNA benchmarks, even without any training on DNA genomes.

AAAI 2025

Bridging Sequence-Structure Alignment in RNA Foundation Models

bio inspired learning

poster

We are pleased to announce the Thirty-Ninth AAAI Conference on Artificial Intelligence (AAAI-25), which will be held in Philadelphia, Pennsylvania at the Pennsylvania Convention Center from February 25 to March 4, 2025.

The purpose of the AAAI conference series is to promote research in Artificial Intelligence (AI) and foster scientific exchange between researchers, practitioners, scientists, students, and engineers across the entirety of AI and its affiliated disciplines. AAAI-25 will feature technical paper presentations, special tracks, invited speakers, workshops, tutorials, poster sessions, senior member presentations, competitions, and exhibit programs, and a range of other activities to be announced.

### [Invited Speakers](https://aaai.org/conference/aaai/aaai-25/aaai-25-invited-speakers/)

Register [here](https://aaai.org/conference/aaai/aaai-25/registration/)

The purpose of the AAAI conference series is to promote research in Artificial Intelligence (AI) and foster scientific exchange between researchers, practitioners, scientists, students, and engineers across the entirety of AI and its affiliated disciplines. AAAI-25 will feature technical paper presentations, special tracks, invited speakers, workshops, tutorials, poster sessions, senior member presentations, competitions, and exhibit programs, and a range of other activities to be announced.



Contrastive Language-Image Pretraining (CLIP) has been widely used in vision tasks. Notably, CLIP has demonstrated promising performance in few-shot learning (FSL).
However, existing CLIP-based methods in training-free FSL ($\textit{i.e.,}$ without the requirement of additional training) mainly learn different modalities independently, leading to two essential issues: 1) severe anomalous match in image modality; 2) varying quality of generated text prompts.
To address these issues, we build a mutual guidance mechanism, that introduces an Image-Guided-Text (IGT) component to rectify varying quality of text prompts through image representations, and a Text-Guided-Image (TGI) component to mitigate the anomalous match of image modality through text representations.
By integrating IGT and TGI, we adopt a perspective of $\textbf{T}$ext-$\textbf{I}$mage $\textbf{M}$utual guidance $\textbf{O}$ptimization, proposing TIMO.
Extensive experiments show that TIMO significantly outperforms the state-of-the-art (SOTA) training-free method. Additionally, by exploring the extent of mutual guidance, we propose an enhanced variant, TIMO-S, which even surpasses the best training-required methods by 0.33$\%$ with approximately $\textbf{×100}$ less time cost.

Text and Image Are Mutually Beneficial: Enhancing Training-Free Few-Shot Classification with CLIP

In this work, we present an in-context policy adaptation (ICPAD) framework designed for long-horizon multi-task environments, exploring diffusion-based skill learning techniques in cross-domain settings. The framework enables rapid adaptation of skill-based reinforcement learning policies to diverse target domains, especially under stringent constraints on no model updates and only limited target domain data. Specifically, the framework employs a cross-domain skill diffusion scheme, where domain-agnostic prototype skills and a domain-grounded skill adapter are learned jointly and effectively from an offline dataset through cross-domain consistent  diffusion processes. The prototype skills act as primitives for common behavior representations of long-horizon policies, serving as a lingua franca to bridge different domains. Furthermore, to enhance the in-context adaptation performance, we develop a dynamic domain prompting scheme that guides the diffusion-based skill adapter toward better alignment with the target domain. Through experiments with robotic manipulation in Metaworld and autonomous driving in CARLA, we show that our ICPAD framework achieves superior policy adaptation performance under limited target domain data conditions for various cross-domain configurations including differences in environment dynamics, agent embodiment, and task horizon.

In-Context Policy Adaptation via Cross-Domain Skill Diffusion

Large language models (LLMs) have achieved outstanding performance in natural language processing, but enormous model sizes and high computational costs limit their practical deployment. Structured pruning can effectively reduce the resource demands for deployment by removing redundant model parameters. However, the randomly selected calibration data and fixed single importance estimation metrics in existing structured pruning methods lead to degraded performance of pruned models. This study introduces AdaPruner, a sample-aware adaptive structured pruning framework for LLMs, aiming to optimize the calibration data and importance estimation metrics in the structured pruning process. Specifically, AdaPruner effectively removes redundant parameters from LLMs by constructing a structured pruning solution space and then employing Bayesian optimization to adaptively search for the optimal calibration data and importance estimation metrics. Experimental results show that the AdaPruner outperforms existing structured pruning methods on a family of LLMs with varying pruning ratios, demonstrating its applicability and robustness. Remarkably, at a 20% pruning ratio, the model pruned with AdaPruner maintains 97% of the performance of the unpruned model.

Sample-aware Adaptive Structured Pruning for Large Language Models

Autonomous driving is a challenging task that requires perceiving and understanding the surrounding environment for safe trajectory planning. While existing vision-based end-to-end models have achieved promising results, these methods are still facing the challenges of vision understanding, decision reasoning and scene generalization. To solve these issues, a generative planning with 3D-vision language pre-training model named GPVL is proposed for end-to-end autonomous driving. The proposed paradigm has two significant aspects. On one hand, a 3D-vision language pre-training module is designed to bridge the gap between visual perception and linguistic understanding in the bird's eye view. On the other hand, a cross-modal language model is introduced to generate reasonable planning with perception and navigation information in an auto-regressive manner. Experiments on the challenging nuScenes dataset demonstrate that the proposed scheme achieves excellent performances compared with state-of-the-art methods. Besides, the proposed GPVL presents strong generalization ability and real-time potential when handling high-level commands in various scenarios. It is believed that the effective, robust and efficient performance of GPVL is crucial for the practical application of future autonomous driving systems.

Generative Planning with 3D-Vision Language Pre-training for End-to-End Autonomous Driving

Obtaining high certainty in predictive models is crucial for making informed and trustworthy decisions in many scientific and engineering domains. 
However, extensive experimentation required for model accuracy can be both costly and time-consuming. 
This paper presents an adaptive sampling approach designed to reduce epistemic uncertainty in predictive models. 
Our primary contribution is the development of a metric that estimates potential epistemic uncertainty leveraging prediction interval-generation neural networks.
This estimation relies on the distance between the predicted upper and lower bounds and the observed data at the tested positions and their neighboring points. 
Our second contribution is the proposal of a batch sampling strategy based on Gaussian processes (GPs). 
A GP is used as a surrogate model of the networks trained at each iteration of the adaptive sampling process. 
Using this GP, we design an acquisition function that selects a combination of sampling locations to maximize the reduction of epistemic uncertainty across the domain.
We test our approach on three unidimensional synthetic problems and a multi-dimensional dataset based on an agricultural field for selecting experimental fertilizer rates.
The results demonstrate that our method consistently converges faster to minimum epistemic uncertainty levels compared to Normalizing Flows Ensembles, MC-Dropout, and simple GPs.

Adaptive Sampling to Reduce Epistemic Uncertainty Using Prediction Interval-Generation Neural Networks

In a surge of text-to-image (T2I) models and their customization methods that generate new images of a user-provided subject, current works focus on alleviating the costs incurred by a lengthy per-subject optimization. These zero-shot customization methods encode the image of a specified subject into a visual embedding which is then utilized alongside the textual embedding for diffusion guidance. The visual embedding incorporates intrinsic information about the subject, while the textual embedding provides a new context. However, the existing methods often 1) generate images with the same pose as an input image, and 2) exhibit deterioration in the subject's identity when facing a pose variation prompt. We first pin down the problem and show that redundant pose information in the visual embedding interferes with the pose indication in the textual embedding. Conversely, the textual embedding also harms the subject's identity which is tightly entangled with the pose in the visual embedding. As a remedy, we propose text-orthogonal visual embedding which effectively harmonizes with the given textual embedding. We also adopt the visual-only embedding and inject the subject's clear features utilizing a self-attention swap. Our method is both effective and robust, offering highly flexible zero-shot generation while effectively maintaining the subject's identity. The code will be publicly released.

Harmonizing Visual and Textual Embeddings for Zero-Shot Text-to-Image Customization

Deep learning has significantly advanced time series forecasting through its powerful capacity to capture sequence relationships.
However, training these models with the Mean Square Error (MSE) loss often results in over-smooth predictions, making it challenging to handle the complexity and learn high-entropy features from time series data with high variability and unpredictability.
In this work, we introduce a novel approach by tokenizing time series values to train forecasting models via cross-entropy loss, while considering the continuous nature of time series data. Specifically, we propose a Hierarchical Classification Auxiliary Network, HCAN, a general model-agnostic component that can be integrated with any forecasting model. HCAN is based on a Hierarchy-Aware Attention module that integrates multi-granularity high-entropy features at different hierarchy levels. At each level, we assign a class label for timesteps to train an Uncertainty-Aware Classifier. This classifier mitigates the over-confidence in softmax loss via evidence theory. We also implement a Hierarchical Consistency Loss to maintain prediction consistency across hierarchy levels. Extensive experiments integrating HCAN with state-of-the-art forecasting models demonstrate substantial improvements over baselines on several real-world datasets. Code is available at: https://anonymous.4open.science/r/HCAN-4F7C.

Hierarchical Classification Auxiliary Network for Time Series Forecasting

Recently, diffusion-based video generation models have achieved significant success. However, existing models often suffer from issues like weak consistency and declining image quality over time. To overcome these challenges, inspired by aesthetic principles, we propose a non-invasive plug-in called Uniform Frame Organizer (UFO), which is compatible with any diffusion-based video generation model. The UFO comprises a series of adaptive adapters with adjustable intensities, which can significantly enhance the consistency between the foreground and background of videos and improve image quality without altering the original model parameters when integrated. The training for UFO is simple, efficient, requires minimal resources, and supports stylized training. Its modular design allows for the combination of multiple UFOs, enabling the customization of personalized video generation models. Furthermore, the UFO also supports direct transferability across different models of the same specification without the need for specific retraining. The experimental results indicate that UFO effectively enhances video generation quality and demonstrates its superiority in public video generation benchmarks. The code will soon be publicly available.

UFO: Enhancing Diffusion-Based Video Generation with a Uniform Frame Organizer

Recent advances in diffusion-based generative models have demonstrated superior performance in subject-driven image generation. Identity(ID) preserving image generation, as a subtask of subject-image generation, aims to generate customized images for specific human identity and has broad application potential. However, this task remains challenging due to the requirement for high ID fidelity and precise detail preservation. Additionally, generating high-quality context alongside the human ID presents another challenge, as existing methods struggle to achieve both high ID fidelity and satisfactory context simultaneously. To address the issues of insufficient ID fidelity, we introduced a simple yet effective test-time fine-tuning approach. Specifically, we propose an attribute-driven training method that establishes global-level and local-level tasks to learn the global face feature and fine-grained attribute features, respectively. Furthermore, we introduce a novel ID-context decoupling framework that decouples image context generation from human ID generation, ensuring the quality of contextual content as well as facilitating the learning ID information. Through extensive experiments, we demonstrated the effectiveness of the proposed method and showcase its capabilities across various applications.

FaceA-Net: Facial Attribute-driven ID Preserving Image Generation Network

Incomplete multi-view multi-label classification aims to accurately predict labels for each sample in the face of some missing views. Moreover, it also encounters problems brought by redundant views. In this paper, we make the first attempt to take advantage of diffusion models to address the missing view problem and design a strategy to identify and remove redundant views. Specifically, we train a diffusion model conditioned on the pseudo-labels to recover information of missing views. The learned diffusion model can carry data distribution knowledge in training split to the data. Regarding redundant identification strategy, it is designed by considering both the additional information of views and the classification difficulty level of samples. We conduct extensive experiments on five datasets, and the proposed method achieves favorable performance against several state-of-the-art methods on the multi-view multi-label classification task.

Bridging Sequence-Structure Alignment in RNA Foundation Models

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Text and Image Are Mutually Beneficial: Enhancing Training-Free Few-Shot Classification with CLIP

Bridging Sequence-Structure Alignment in RNA Foundation Models

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Text and Image Are Mutually Beneficial: Enhancing Training-Free Few-Shot Classification with CLIP

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