United States

Missense mutations could affect the Liquid-Liquid Phase Separation (LLPS) propensity of proteins and lead to aberrant phase-separating behaviours, which are recently found to be associated with many diseases including Alzheimer&#39;s and cancer. However, the regulatory role of mutations in LLPS remains unclear due to challenges in accurately characterizing the LLPS ability of mutants, including the high similarity in features, lack of labeled data, and vast amounts of data involved. To bridge this gap and facilitate the discovery of therapeutic strategies, we propose the first machine learning-based guider for protein phase-separating behaviour alteration, PScalpel. PScalpel leverages both structural information and an auxiliary tasks-based graph contrastive learning framework to distinguish the mutants’ LLPS ability, and incorporates a genetic algorithms-based recommendation method to identify mutants with desired LLPS properties. Comprehensive computational and biological experiments validate the effectiveness of PScalpel as a versatile tool for guiding alterations in protein phase separation behavior.

AAAI 2025

PScalpel: A Machine Learning-based Guider for Protein Phase-Separating Behaviour Alteration

2021 Annual Conference of the North American Chapter of the Association for Computational Linguistics.

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NAACL 2021

Missense mutations could affect the Liquid-Liquid Phase Separation (LLPS) propensity of proteins and lead to aberrant phase-separating behaviours, which are recently found to be associated with many diseases including Alzheimer's and cancer. However, the regulatory role of mutations in LLPS remains unclear due to challenges in accurately characterizing the LLPS ability of mutants, including the high similarity in features, lack of labeled data, and vast amounts of data involved. To bridge this gap and facilitate the discovery of therapeutic strategies, we propose the first machine learning-based guider for protein phase-separating behaviour alteration, PScalpel. PScalpel leverages both structural information and an auxiliary tasks-based graph contrastive learning framework to distinguish the mutants’ LLPS ability, and incorporates a genetic algorithms-based recommendation method to identify mutants with desired LLPS properties. Comprehensive computational and biological experiments validate the effectiveness of PScalpel as a versatile tool for guiding alterations in protein phase separation behavior.

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/)<br><br><br>

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

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.



We propose iMoT, an innovative  Transformer-based inertial odometry method that retrieves cross-modal information from motion and rotation modalities for accurate positional estimation. Unlike prior work, during the encoding of the motion context, we introduce Progressive Series Decoupler at the beginning of each encoder layer to stand out critical motion events inherent in acceleration and angular velocity signals. 
To better aggregate cross-modal interactions, we present Adaptive Positional Encoding, which dynamically modifies positional embeddings for temporal discrepancies between different modalities.
During decoding, we introduce a small set of learnable query motion particles as priors to model motion uncertainties within velocity segments. Each query motion particle is intended to draw cross-modal features dedicated to a specific motion mode, all taken together allowing the model to refine its understanding of motion dynamics effectively. Lastly, we design a dynamic scoring mechanism to stabilize iMoT's optimization by considering all aligned motion particles at the final decoding step, ensuring robust and accurate velocity segment estimation. Extensive evaluations on various inertial datasets demonstrate that iMoT significantly outperforms state-of-the-art methods in delivering superior robustness and accuracy in trajectory reconstruction.

iMoT: Inertial Motion Transformer for Inertial Navigation

Vision-based 3D occupancy prediction has become a popular research task due to its versatility and affordability. Nowadays, conventional methods usually project the image-based vision features to 3D space and learn the geometric information through the attention mechanism, enabling the 3D semantic occupancy prediction. However, these works usually face two main challenges: 1) Limited geometric information. Due to the lack of geometric information in the image itself, it is challenging to directly predict 3D space information, especially in large-scale outdoor scenes. 2) Local restricted interaction. Due to the quadratic complexity of the attention mechanism, they often use modified local attention to fuse features, resulting in a restricted fusion. To address these problems, in this paper, we propose a language-assisted 3D semantic occupancy prediction network, named LOMA. In the proposed vision-language framework, we first introduce a VL-aware Scene Generator (VSG) module to generate the 3D language feature of the scene. By leveraging the vision-language model, this module provides implicit geometric knowledge and explicit semantic information from the language. Furthermore, we present a Tri-plane Fusion Mamba (TFM) block to efficiently fuse the 3D language feature and 3D vision feature. The proposed module not only fuses the two features with global modeling but also avoids too much computation costs. Experiments on the SemanticKITTI and SSCBench-KITTI360 datasets show that our algorithm achieves new state-of-the-art performances in both geometric and semantic completion tasks. Our code will be open soon.

LOMA: Language-assisted Semantic Occupancy Network via Triplane Mamba

Video object detection has made significant progress in recent years thanks to convolutional neural networks (CNNs) and vision transformers (ViTs). CNNs excel at capturing local features but struggle to model global representations. Conversely, ViTs can capture long-range global features but face challenges in representing local feature details. Off-the-shelf video object detection methods solely rely on CNNs or ViTs to conduct feature aggregation, which hampers their capability to simultaneously leverage global and local information, thereby resulting in limited detection performance. In this paper, we propose a Transformer-GraphFormer Blender Network (TGBFormer) for video object detection, with three key technical improvements to fully exploit the advantages of transformers and graph convolutional networks while compensating for their limitations. First, we develop a spatial-temporal transformer module to aggregate global contextual information, constituting global representations with long-range feature dependencies. Second, we introduce a spatial-temporal GraphFormer module that utilizes local spatial and temporal relationships to aggregate features, generating new local representations that are complementary to the transformer outputs. Third, we design a global-local feature blender module to adaptively couple transformer-based global representations and GraphFormer-based local representations. Extensive experiments demonstrate that our TGBFormer establishes new state-of-the-art results on the ImageNet VID dataset. Particularly, our TGBFormer achieves 86.5% mAP while running at around 41.0 FPS on a single Tesla A100 GPU. The code will be available at Github.

TGBFormer: Transformer-GraphFormer Blender Network for Video Object Detection

The problem of forecasting spatiotemporal events such as crime and accident, is crucial to public safety and city management. Besides accuracy, interpretability is also a key requirement for spatiotemporal forecasting models to justify the decisions.  %Merely presenting predicted scores fails to convince the public and does not contribute to future urban planning. Interpretation of the spatiotemporal forecasting mechanism is, however, challenging due to the complexity of multi-source spatiotemporal features, the non-intuitive nature of spatiotemporal patterns for non-expert users, and the presence of spatial heterogeneity in the data.
Currently, no existing deep learning model intrinsically interprets the complex predictive process learned from multi-source spatiotemporal features. To bridge the gap, we propose GeoPro-Net, an intrinsically interpretable spatiotemporal model for spatiotemporal event forecasting problems. GeoPro-Net introduces a novel Geo-concept convolution operation, which employs statistical tests to extract predictive patterns in the input as "Geo-concepts'', and condenses the "Geo-concept-encoded'' input through interpretable channel fusion and geographic-based pooling. In addition, GeoPro-Net learns different sets of prototypes of concepts inherently, and projects them to real-world cases for interpretation. Comprehensive experiments and case studies on four real-world datasets demonstrate that GeoPro-Net provides better interpretability while still achieving competitive prediction performance compared with state-of-the-art baselines.

GeoPro-Net: Learning Interpretable Spatiotemporal Prediction Models Through Statistically-Guided Geo-Prototyping

The Multi-modal Large Language Models (MLLMs) with extensive world knowledge have revitalized autonomous driving, particularly in reasoning tasks within perceivable regions. 
However, when faced with perception-limited areas (dynamic or static occlusion regions), MLLMs struggle to effectively integrate perception ability with world knowledge for reasoning. 
These perception-limited regions can conceal crucial safety information, especially for vulnerable road users.
In this paper, we propose a framework, which aims to improve autonomous driving performance under perception-limited conditions by enhancing the integration of perception capabilities and world knowledge.
Specifically, we propose a plug-and-play instruction-guided interaction module that bridges modality gaps and significantly reduces the input sequence length, allowing it to adapt effectively to multi-view video inputs.
Combined with our three-stage multi-task training strategy, this module substantially enhances perception ability.
Furthermore, to better integrate world knowledge with driving-related tasks, we have collected and refined a large-scale multi-modal dataset that includes 2 million natural language QA pairs, 1.7 million grounding task data. 
To evaluate the model’s utilization of world knowledge, we introduce an object-level risk assessment dataset comprising 200K QA pairs, where the questions necessitate multi-step reasoning leveraging world knowledge for resolution. 
Extensive experiments validate the effectiveness of our proposed method.

World Knowledge-Enhanced Reasoning Using Instruction-Guided Interactor in Autonomous Driving

Infrared-visible object detection (IVOD) seeks to harness the complementary information in infrared and visible images, thereby enhancing the performance of detectors in complex environments. However, existing methods often neglect the frequency characteristics of complementary information, such as the abundant high-frequency details in visible images and the valuable low-frequency thermal information in infrared images, thus constraining detection performance. To solve this problem, we introduce a novel Frequency-Driven Feature Decomposition Network for IVOD, called FD2-Net, which effectively captures the unique frequency representations of complementary information across multimodal visual spaces. Speciﬁcally, we propose a feature decomposition encoder, wherein the high-frequency unit (HFU) utilizes discrete cosine transform to capture representative high-frequency features, while the low-frequency unit (LFU) employs dynamic receptive ﬁelds to model the multi-scale context of diverse objects. Next, we adopt a parameter-free complementary strengths strategy to enhance multimodal features through seamless inter-frequency recoupling. Furthermore, we innovatively design a multimodal reconstruction mechanism that recovers image details lost during feature extraction, further leveraging the complementary information from infrared and visible images to enhance overall representational capacity. Extensive experiments demonstrate that FD2-Net outperforms state-of-the-art (SoTA) models across various IVOD benchmarks, i.e. LLVIP (96.2% mAP), FLIR (82.9% mAP), and M3FD (83.5% mAP).

FD2-Net: Frequency-Driven Feature Decomposition Network for Infrared-Visible Object Detection

Point cloud upsampling aims to generate dense and uniformly distributed point sets from sparse point clouds. Existing point cloud upsampling methods typically approach the task as an interpolation problem. They achieve upsampling by performing local interpolation between point clouds or in the feature space, then regressing the interpolated points to appropriate positions. By contrast, our proposed method treats point cloud upsampling as a global shape completion problem. Specifically, our method first divides the point cloud into multiple patches. Then a masking operation is applied to remove some patches, leaving visible point cloud patches. Finally, our custom-designed neural network iterative completes the missing sections of the point cloud through the visible parts. During testing, by selecting different mask sequences, we can restore various complete patches. A sufficiently dense upsampled point cloud can be obtained by merging all the completed patches. We demonstrate the superior performance of our method through both quantitative and qualitative experiments, showing overall superiority against both existing self-supervised and supervised methods.

SPU-IMR: Self-supervised Arbitrary-scale Point Cloud Upsampling via Iterative Mask-recovery Network

This paper investigates the connection between neural networks and sufficient dimension reduction (SDR), demonstrating that neural networks inherently perform SDR in regression tasks under appropriate rank regularizations. Specifically, the weights in the first layer span the central mean subspace. We establish the statistical consistency of the neural network-based estimator for the central mean subspace, underscoring the suitability of neural networks in addressing SDR-related challenges. Numerical experiments further validate our theoretical findings, and highlight the underlying capability of neural networks to facilitate SDR compared to the existing methods. Additionally, we discuss an extension to unravel the central subspace, broadening the scope of our investigation.

Neural Networks Perform Sufficient Dimension Reduction

Implicit Neural Representation (INR) has shown great potential in constructing the complex nature signal as a continuous implicit function. However, the representation results are incomplete since different components of the signal correspond to different frequencies and neural network inherently tends to low-frequency convergence. In this paper, we propose the adaptive Wavelet-Positional Encoding (WPE) to precisely represent content under different frequency distributions for coordinate-based implicit representations. The High-Frequency Perception (HFP) method is first proposed to query locations of high-frequency components from input signals, which can be indicated as local centers of WPE. Then, motivated by wavelet series regression, we present to embed these queried low-dimensional coordinate inputs into wavelet-frequency space by WPE to represent fine details of target signals. Experiments demonstrate that the proposed method can be integrated into various INR methods without modifying training frameworks while significantly improving their performance in 1D signal fitting, 2D image regression, and even 3D scene representation.

Adaptive Wavelet-Positional Encoding for High-Frequency Information Learning in Implicit Neural Representation

Recent years have witnessed the rise of Neural-enhanced Video Streaming (NeVS), which integrates neural restoration models into video codecs for higher compression-restoration performance. Despite its benefit, existing work has not well explored the full potential of NeVS paradigm, due to: (1) post-streaming restoration by decoder while lacking the proactive collaboration of encoder, (2) end-to-end optimization based on conventional rate-distortion theory, which has been verified that low distortion is not always a synonym for high perceptual quality, and (3) coupled design for domain-specific tasks that cannot generalize to various video codecs. Observing these limitations, our objective is not to incrementally present an improved restoration model. Instead, we focus on the encoder-decoder synergy, i.e., the codec, which is non-trivial since it inherently strikes the rate-distortion-perception trade-off of NeVS. Aiming at this target, we propose the Diffusion-enhanced Neural Codec (DeNC), a plug-and-play module for current NeVS paradigm, to significantly reduce the required bitrates while preserving high perceptual quality of restored videos. Our key design is twofold. First, DeNC improves the encoder's compression efficiency by simultaneously reducing the resolution and color bit-depth of frame referencing. Second, DeNC empowers the decoder with perception-oriented restoration capability by making its diffusion-based restoration process aware of the encoder's compression conditions. Real-world evaluations show that DeNC improves compression ratios with nearly an order of magnitude and achieves much higher restoration quality (e.g., 93+ VMAF and 23% higher MOS) over the latest baselines.

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