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Protein post-translational modification (PTM) site prediction is a fundamental task in bioinformatics. Several computational methods have been developed to predict PTM sites. However, existing methods ignore the structure information and merely utilize protein sequences. These methods consequently fail to correctly identify PTM sites that show low conservation at the sequence level. Furthermore, designing a more fine-grained structure representation learning method is urgently needed as PTM is a biological event that occurs at the atom scale. In this paper, we propose a PTM site prediction method by Coupling of Multi-Granularity structure and Multi-Scale sequence representation, PTM-CMGMS for brevity. Specifically, a multi-granularity structure-aware representation learning, including the atom, amino acid, and whole-protein granularity, is designed to learn neighborhood structure representations from AlphaFold predicted structures, followed by utilizing contrastive learning to optimize the structure representations. Additionally, the multi-scale sequence representation learning is used to extract context sequence information, and motif generated by aligning all context sequences of positive sites assists the prediction. Extensive experiments on three datasets show that PTM-CMGMS outperforms the state-of-the-art methods.

AAAI 2024

Improving PTM Site Prediction by Coupling of Multi-Granularity Structure and Multi-Scale Sequence Representation

post-translational modification (ptm)，multi-granularity structure ，multi-scale sequence representation

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.<br><br><br><br>

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

technical paper

Extensive utilization of deep reinforcement learning (DRL) policy networks in diverse continuous control tasks has raised questions regarding performance degradation in expansive state spaces where the input state norm is larger than that in the training environment. This paper aims to uncover the underlying factors contributing to such performance deterioration when dealing with expanded state spaces, using a novel analysis technique known as state division. In contrast to prior approaches that employ state division merely as a post-hoc explanatory tool, our methodology delves into the intrinsic characteristics of DRL policy networks. Specifically, we demonstrate that the expansion of state space induces the activation function $\tanh$ to exhibit saturability, resulting in the transformation of the state division boundary from nonlinear to linear. Our analysis centers on the paradigm of the double-integrator system, revealing that this gradual shift towards linearity imparts a control behavior reminiscent of bang-bang control. However, the inherent linearity of the division boundary prevents the attainment of an ideal bang-bang control, thereby introducing unavoidable overshooting. Our experimental investigations, employing diverse RL algorithms, establish that this performance phenomenon stems from inherent attributes of the DRL policy network, remaining consistent across various optimization algorithms.

Analyzing Generalization in Policy Networks: A Case Study with the Double-Integrator System | VIDEO

Multi-task learning (MTL) has gained significant popularity in recommender systems as it enables the simultaneous optimization of multiple objectives. 
A key challenge in MTL is negative transfer, but existing research explored negative transfer on all samples, overlooking the inherent complexities within them. 
To this end, we split the samples according to the relative amount of positive feedback among tasks.
Surprisingly, negative transfer still occurs in existing MTL methods on samples that receive comparable feedback across tasks. 
Existing methods commonly employ a shared-embedding paradigm, limiting capacity of modeling diverse user preferences on those samples. 
In this paper, we introduce a novel Shared and Task-specific EMbeddings (STEM) paradigm that aims to incorporate both shared and task-specific embeddings to effectively capture task-specific user preferences. Under this paradigm, we propose a simple model STEM-Net, which is equipped with a customized gating network with stop-gradient operations to facilitate the learning of these embeddings. Remarkably, STEM-Net demonstrates exceptional performance on comparable samples, surpassing the single-task model and achieves positive transfer. Comprehensive evaluation on three public MTL recommendation datasets demonstrates that STEM-Net outperforms state-of-the-art models by a substantial margin, providing evidence of its effectiveness and superiority. Our code is released at https://github.com/LiangcaiSu/STEM.

STEM: Unleashing the Power of Embeddings for Multi-Task Recommendation

Research interests in the robustness of deep neural networks  against domain shifts have been rapidly increasing in recent years. Most existing works, however, focus on improving the accuracy of the model, not the calibration performance which is another important requirement for trustworthy AI systems. Temperature scaling (TS), an accuracy-preserving post-hoc calibration method, has been proven to be effective in in-domain settings, but not in out-of-domain (OOD) due to the difficulty in obtaining a validation set for the unseen domain beforehand. In this paper, we propose consistency-guided temperature scaling (CTS), a new temperature scaling strategy that can significantly enhance the OOD calibration performance by providing mutual supervision among data samples in the source domains. Motivated by our observation that over-confidence stemming from inconsistent sample predictions  is the main obstacle to OOD calibration, we propose to guide the scaling process by taking consistencies into account in terms of two different aspects - style and content - which are the key components that can well-represent data samples in multi-domain settings. Experimental results demonstrate that our proposed strategy outperforms existing works, achieving superior OOD calibration performance on various datasets. This can be accomplished by employing only the source domains without compromising accuracy, making our scheme directly applicable to various trustworthy AI systems.

Consistency-Guided Temperature Scaling Using Style and Content Information for Out-of-Domain Calibration | VIDEO

Named entity recognition (NER) aims to identify and classify specific entities mentioned in textual sentences. Most existing superior NER models employ the standard fully supervised paradigm, which requires a large amount of annotated data during training. In order to maintain performance with insufficient annotation resources (i.e., low resources), in-context learning (ICL) has drawn a lot of attention, due to its plug-and-play nature compared to other methods (e.g., meta-learning and prompt learning). In this manner, how to retrieve high-correlated demonstrations for target sentences serves as the key to emerging ICL ability. For the NER task, the correlation implies the consistency of both ontology (i.e., generalized entity type) and context (i.e., sentence semantic), which is ignored by previous NER demonstration retrieval techniques. To address this issue, we propose ConsistNER, a novel three-stage framework that incorporates ontological and contextual information for low-resource NER. Firstly, ConsistNER employs large language models (LLMs) to pre-recognize potential entities in a zero-shot manner. Secondly, ConsistNER retrieves the sentence-specific demonstrations for each target sentence based on the two following considerations: (1) Regarding ontological consistency, demonstrations are filtered into a candidate set based on ontology distribution. (2) Regarding contextual consistency, an entity-aware self-attention mechanism is introduced to focus more on the potential entities and semantic-correlated tokens. Finally, ConsistNER feeds the retrieved demonstrations for all target sentences into LLMs for prediction. We conduct experiments on four widely-adopted NER datasets, including both general and specific domains. Experimental results show that ConsistNER achieves a 6.01%-26.37% and 3.07%-21.18% improvement over the state-of-the-art baselines on Micro-F1 scores under 1- and 5-shot settings, respectively.

ConsistNER: Towards Instructive NER Demonstrations for LLMs with the Consistency of Ontology and Context

Attributed graph clustering is an unsupervised task that partitions nodes into different groups. Self-supervised learning (SSL) shows great potential in handling this task, and some recent studies simultaneously learn multiple SSL tasks to further boost performance. Currently, different SSL tasks are assigned the same set of weights for all graph nodes. However, we observe that some graph nodes whose neighbors are in different groups require significantly different emphases on SSL tasks. In this paper, we propose to dynamically learn the weights of SSL tasks for different nodes and fuse the embeddings learned from different SSL tasks to boost performance. We design an innovative graph clustering approach, namely Dynamically Fusing Self-Supervised Learning (DyFSS). Specifically, DyFSS fuses features extracted from diverse SSL tasks using distinct weights derived from a gating network. To effectively learn the gating network, we design a dual-level self-supervised strategy that incorporates pseudo labels and the graph structure. Extensive experiments on five datasets show that DyFSS outperforms the state-of-the-art multi-task SSL methods by up to 8.66% on the accuracy metric. The code of DyFSS is available at: https://github.com/q086/DyFSS.

Every Node Is Different: Dynamically Fusing Self-Supervised Tasks for Attributed Graph Clustering

The ability to generalise from a small number of examples is a fundamental challenge in machine learning. To tackle this challenge, we introduce an inductive logic programming (ILP) approach that combines negation and predicate invention. 
Combining these two features allows an ILP system to generalise better by learning rules with universally quantified body-only variables. We implement our idea in NOPI, which can learn normal logic programs with predicate invention, including Datalog programs with stratified negation. Our experimental results on multiple domains show that our approach can improve predictive accuracies and learning times.

Generalisation through Negation and Predicate Invention

Deep learning-based models have made great progress in image tampering localization, which aims to distinguish between manipulated and authentic regions. However, these models suffer from inefficient training. This is because they use ground-truth mask labels mainly through the cross-entropy loss, which prioritizes per-pixel precision but disregards the spatial location and shape details of manipulated regions. To address this problem, we propose a Mask-Guided Query-based Transformer Framework (MGQFormer), which uses ground-truth masks to guide the learnable query token (LQT) in identifying the forged regions. Specifically, we extract feature embeddings of ground-truth masks as the guiding query token (GQT) and feed GQT and LQT into MGQFormer to estimate fake regions, respectively. Then we make MGQFormer learn the position and shape information in ground-truth mask labels by proposing a mask-guided loss to reduce the feature distance between GQT and LQT.  We also observe that such mask-guided training strategy has a significant impact on the convergence speed of MGQFormer training. Extensive experiments on multiple benchmarks show that our method significantly improves over state-of-the-art methods.

MGQFormer: Mask-Guided Query-Based Transformer for Image Manipulation Localization | VIDEO

Multivariate Time-Series (MTS) data is crucial in various application fields. With its sequential and multi-source (multiple sensors) properties, MTS data inherently exhibits Spatial-Temporal (ST) dependencies, involving temporal correlations between timestamps and spatial correlations between sensors in each timestamp. To effectively leverage this information, Graph Neural Network-based methods (GNNs) have been widely adopted. However, existing approaches separately capture spatial dependency and temporal dependency and fail to capture the correlations between Different sEnsors at Different Timestamps (DEDT). Overlooking such correlations hinders the comprehensive modelling of ST dependencies within MTS data, thus restricting existing GNNs from learning effective representations. To address this limitation, we propose a novel method called Fully-Connected Spatial-Temporal Graph Neural Network (FC-STGNN), including two key components namely FC graph construction and FC graph convolution. For graph construction, we design a decay graph to connect sensors across all timestamps based on their temporal distances, enabling us to fully model the ST dependencies by considering the correlations between DEDT. Further, we devise FC graph convolution with a moving-pooling GNN layer to effectively capture the ST dependencies for learning effective representations. Extensive experiments show the effectiveness of FC-STGNN on multiple MTS datasets compared to SOTA methods. The code is available at https://github.com/Frank-Wang-oss/FCSTGNN.

Fully-Connected Spatial-Temporal Graph for Multivariate Time-Series Data

In the dynamic and rapidly evolving world of social media, detecting anomalous users has become a crucial task to address malicious activities such as misinformation and cyberbullying. As the increasing number of anomalous users improves the ability to mimic normal users and evade detection, existing methods only focusing on bot detection are ineffective in terms of capturing subtle distinctions between users. To address these challenges, we proposed SeGA, preference-aware self-contrastive learning for anomalous user detection, which leverages heterogeneous entities and their relations in the Twittersphere to detect anomalous users with different malicious strategies. SeGA utilizes the knowledge of large language models to summarize user preferences via posts. In addition, integrating user preferences with prompts as pseudo-labels for preference-aware self-contrastive learning enables the model to learn multifaceted aspects for describing the behaviors of users. Extensive experiments on the proposed TwBNT benchmark demonstrate that SeGA significantly outperforms the state-of-the-art methods (+3.5% ∼ 27.6%) and empirically validate the effectiveness of the model design and pre-training strategies. Our code and data are publicly available at https://github.com/ying0409/SeGA.

SeGA: Preference-Aware Self-Contrastive Learning with Prompts for Anomalous User Detection on Twitter

Reasoning the 3D structure of a non-rigid dynamic scene from a single moving camera is an under-constrained problem. Inspired by the remarkable progress of neural radiance fields (NeRFs) in photo-realistic novel view synthesis of static scenes, extensions have been proposed for dynamic settings. These methods heavily rely on neural priors in order to regularize the problem. In this work, we take a step back and reinvestigate how current implementations may entail deleterious effects, including limited expressiveness, entanglement of light and density fields, and sub-optimal motion localization. To this end, we propose a framework that factorizes time and space by formulating a scene as a composition of bandlimited, high-dimensional signals. We demonstrate compelling results across complex dynamic scenes that involve changes in lighting, texture and long-range dynamics.

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