Compound-Protein Interaction (CPI) prediction aims to predict the pattern and strength of compound-protein interactions for rational drug discovery. Existing deep learning-based methods utilize only the single modality of protein sequences or structures and lack the co-modeling of the joint distribution of the two modalities, which may lead to significant performance drops in complex real-world scenarios due to various factors, e.g., modality missing and domain shifting. More importantly, these methods only model protein sequences and structures at a single fixed scale, neglecting more fine-grained multi-scale information, such as those embedded in key protein fragments. In this paper, we propose a novel multi-scale Protein Sequence-structure Contrasting framework for CPI prediction (PSC-CPI), which captures the dependencies between protein sequences and structures through both intra-modality and cross-modality contrasting. We further apply length-variable protein augmentation to allow contrasting to be performed at different scales, from the amino acid level to the sequence level. Finally, in order to more fairly evaluate the model generalizability, we split the test data into four settings based on whether compounds and proteins have been observed during the training stage. Extensive experiments have shown that PSC-CPI generalizes well in all four settings, particularly in the more challenging ``Unseen-Both" setting, where neither compounds nor proteins have been observed during training. Furthermore, even when encountering a situation of modality missing, i.e., inference with only single-modality protein data, PSC-CPI still exhibits comparable or even better performance than previous approaches.

PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction

Protein structure-based property prediction has emerged as a promising approach for various biological tasks, such as protein function prediction and sub-cellular location estimation. The existing methods highly rely on experimental protein structure data and fail in scenarios where these data are unavailable. Predicted protein structures from AI tools (e.g., AlphaFold2) were utilized as alternatives. However, we observed that current practices, which simply employ accurately predicted structures during inference, suffer from notable degradation in prediction accuracy. While similar phenomena have been extensively studied in general fields (e.g., Computer Vision) as model robustness, their impact on protein property prediction remains unexplored. In this paper, we first investigate the reason behind the performance decrease when utilizing predicted structures, attributing it to the structure embedding bias from the perspective of structure representation learning. To study this problem, we identify a Protein 3D Graph Structure Learning Problem for Robust Protein Property Prediction (PGSL-RP3), collect benchmark datasets, and present a protein Structure embedding Alignment Optimization framework (SAO) to mitigate the problem of structure embedding bias between the predicted and experimental protein structures. Extensive experiments have shown that our framework is model-agnostic and effective in improving the property prediction of both predicted structures and experimental structures.

Protein 3D Graph Structure Learning for Robust Structure-Based Protein Property Prediction

Recent years have witnessed the great success of Graph Neural Networks (GNNs) in handling graph-related tasks. However, MLPs remain the primary workhorse for practical industrial applications due to their desirable inference efficiency and scalability. To reduce their gaps, one can directly distill knowledge from a well-designed teacher GNN to a student MLP, which is termed as GNN-to-MLP distillation. However, the process of distillation usually entails a loss of information, and ``which knowledge patterns of GNNs are more likely to be left and distilled into MLPs?" becomes an important question. In this paper, we first factorize the knowledge learned by GNNs into low- and high-frequency components in the spectral domain and then derive their correspondence in the spatial domain. Furthermore, we identified a potential information drowning problem for existing GNN-to-MLP distillation, i.e., the high-frequency knowledge of the pre-trained GNNs may be overwhelmed by the low-frequency knowledge during distillation; we have described in detail what it represents, how it arises, what impact it has, and how to deal with it. In this paper, we propose an efficient Full-Frequency GNN-to-MLP (FF-G2M) distillation framework, which extracts both low-frequency and high-frequency knowledge from GNNs and injects it into MLPs. Extensive experiments show that FF-G2M improves over the vanilla MLPs by 12.6% and outperforms its corresponding teacher GNNs by 2.6% averaged over six graph datasets and three common GNN architectures.

Extracting Low-/High- Frequency Knowledge from Graph Neural Networks and Injecting it into MLPs: An Effective GNN-to-MLP Distillation Framework

Although contextualized embeddings generated from large-scale pre-trained models perform well in many tasks, traditional static embeddings (e.g., Skip-gram, Word2Vec) still play an important role in low-resource and lightweight settings due to their low computational cost, ease of deployment, and stability. In this paper, we aim to improve word embeddings by 1) incorporating more contextual information from existing pre-trained models into the Skip-gram framework, which we call Context-to-Vec; 2) proposing a post-processing retrofitting method for static embeddings independent of training by employing priori synonym knowledge and weighted vector distribution. Through extrinsic and intrinsic tasks, our methods are well proven to outperform the baselines by a large margin.

Using Context-to-Vector with Graph Retrofitting to Improve Word Embeddings

Main track - Applications

technical paper

We are pleased to announce the Thirty-Eighth AAAI Conference on Artificial Intelligence (AAAI-24), which will be held in Vancouver, British Columbia at the Vancouver Convention Centre – West Building from 20-27 February, 2024.

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-24 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 expect for AAAI-24 to be an in-person conference – one author of all accepted papers will be expected to present work in person unless there are exceptional circumstances that prevent this.

In order to access the AAAI-24 event page you need to register [here](https://aaai.org/aaai-conference/registration/)

AAAI 2024

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. 

Main Track - Machine Learning

ML: Graph-based Machine Learning 5

poster

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-23 is the Thirty-Seventh AAAI Conference on Artificial Intelligence. The theme of this conference is to create collaborative bridges within and beyond AI. Like previous AAAI conferences, AAAI-23 will feature technical paper presentations, special tracks, invited speakers, workshops, tutorials, poster sessions, senior member presentations, competitions, and exhibit programs, and two new activities: a Bridge Program and a Lab Program. Many of these activities are tailored to the theme of bridges and all are selected according to the highest standards, with additional programs for students and young researchers. 
AAAI is providing you with a conference planner, which you can use to help organize your itinerary of activities. This includes talks to attend in person, talks to attend remotely, breaks with colleagues and your site seeing activities. To access this conference planner, please go to [https://aaai-2023.takemobi.io](https://aaai-2023.takemobi.io).

In order to access this site, you need to register. If you haven't already, please register [here](https://aaai.org/Conferences/AAAI-23/registration/).


AAAI 2023

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.

Posters: Machine Learning for NLP

# Welcome everyone to ACL 2022!

The 60th Annual Meeting of the Association for Computational Linguistics is taking place May 22-27, 2022 as a hybrid event, in Dublin and online. We are happy to welcome all of you to this anniversary edition with an almost 50-50 in-person and virtual participation. 
The main conference program features oral presentations, in-person and virtual posters and demo sessions, a plenary session for our best paper presentations and awards, three amazing keynote events and two new initiatives of invited talks: Spotlight Talks for Young Rising Stars (STIRS) and The Next Big Idea Talks. Posters (including Findings of ACL 2022) and demos are grouped by areas for both the in-person and the virtual sessions. For the virtual component, the talks will be on Zoom and the posters and the demos will be in GatherTown. The Student Research Workshop will have an oral session and a poster session as part of Poster Session 1. The program also features eight Tutorials and 28 Workshops. 

 
We wish you a wonderful conference! 
[**The ACL 2022 Organizing Committee**](https://www.2022.aclweb.org/organisers)
 
[**Conference Handbook**](https://drive.google.com/file/d/1_BUCMfhMVrjG9E2e71aHdHeE28KSje0l/view?usp=sharing) 
[**Mini Handbook**](https://drive.google.com/file/d/1qlBKl0wzmlVF1oCeMQl3BahLd9nLP5Ce/view?usp=sharing) 
[**Posters and Demo guides**](https://drive.google.com/file/d/1UucMAoCNncIOaH1rMMDa0owuG9qgvJTG/view?usp=sharing)

ACL 2022

The Association for Computational Linguistics (ACL) is the premier international scientific and professional society for people working on computational problems involving human language, a field often referred to as either computational linguistics or natural language processing (NLP). 

Yufei Huang

4

45

SHORT BIO

Presentations

PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction

Protein 3D Graph Structure Learning for Robust Structure-Based Protein Property Prediction

Extracting Low-/High- Frequency Knowledge from Graph Neural Networks and Injecting it into MLPs: An Effective GNN-to-MLP Distillation Framework

Using Context-to-Vector with Graph Retrofitting to Improve Word Embeddings

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