United States

Is there a foreign language describing protein sequences and structures simultaneously? Protein structures, represented by continuous 3D points, have long posed a challenge due to the contrasting modeling paradigms of discrete sequences. We introduce \textbf{FoldTokenizer} to represent protein sequence-structure as discrete symbols. This approach involves projecting residue types and structures into a discrete space, guided by a reconstruction loss for information preservation. We name the learned discrete symbols as \textbf{FoldToken}, and the sequence of FoldTokens serves as a new protein language, transforming the protein sequence-structure into a unified modality. We apply the created protein language on general backbone inpainting task, building the first GPT-style model (\textbf{FoldGPT}) for sequence-structure co-generation with promising results. Key to our success is the substantial enhancement of the vector quantization module, Soft Conditional Vector Quantization (\textbf{SoftCVQ}). Code will be released upon acceptance.

AAAI 2025

FoldToken: Learning Protein Language via Vector Quantization and Beyond

### Welcome!
The 62nd Annual Meeting of the Association for Computational Linguistics (ACL 2024) will take place in Bangkok, Thailand from August 11th to 16th, 2024. Our Virtual Poster Sessions will take place online Thursday, August 22, 2024.

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ACL 2024

The 62nd Annual Meeting of the Association for Computational Linguistics (ACL 2024) will take place in Bangkok, Thailand from August 11th to 16th, 2024. More information will be announced soon.

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.



In the age of data and AI, study or forecasting relations among entities have paramount importance. But most often we forget that real-world relations are directional, for example, buyer-seller, sender-receiver, etc. In this paper, we provide a comprehensive solution to the problem of forecasting directional relations, in a very challenging setting, where relations are higher order i.e., directed hyperedges in a hypergraph. This problem is, so far, not addressed in the literature. This challenge here is that the number of possible hyperedges is exponential in the number of nodes at each event time. In this paper we propose a sequential generative process that divides the forecasting into multiple stages, each conditioned upon all the previous, thereby reducing the search space involved in finding the type of hyperedge occurring. The first is a temporal point process-based node event forecasting module that identifies the subset of nodes involved in an event. The second is a candidate generation module that forecasts hyperedge sizes and adjacency vectors for the nodes observing events. The third module is a directed hyperedge predictor that identifies the truth by searching over the set of candidate hyperedges. To demonstrate the efficiency of our model, we curated five datasets and conducted an extensive empirical study to evaluate each of the downstream tasks. Our model gave 32\% and 41\%  performance gain compared to the state-of-the-art pairwise and hyperedge event forecasting models, respectively, for the event type prediction.

Neural Temporal Point Processes for Forecasting Directional Relations in Evolving Hypergraphs

Previous research on causal reasoning often overlooks the subtleties crucial to understanding causal reasoning.  To address this gap, our study introduces the concept of *causal epistemic consistency*, which focuses on the self-consistency of Large Language Models (LLMs) in differentiating intermediates with nuanced differences in causal reasoning. We propose a suite of novel metrics -- intensity ranking concordance, cross-group position agreement, and intra-group clustering -- to evaluate LLMs on this front. Through extensive empirical studies on 21 high-profile LLMs, including GPT-4, Claude3, and LLaMA3-70B, we have favoring evidence that current models struggle to maintain epistemic consistency in identifying the polarity and intensity of intermediates in causal reasoning. Additionally, we explore the potential of using internal token probabilities as an auxiliary tool to maintain causal epistemic consistency.  In summary, our study bridges a critical gap in AI research by investigating the self-consistency over fine-grained intermediates involved in causal reasoning.

Nuance Matters: Probing Epistemic Consistency in Causal Reasoning

We consider the conditional generation of 3D drug-like molecules with \textit{explicit control} over molecular properties 
such as drug-like properties (e.g., Quantitative Estimate of Druglikeness or Synthetic Accessibility score) and effectively binding to specific protein sites. 
To tackle this problem, we propose an E(3)-equivariant Wasserstein autoencoder and factorize the latent space of 
our generative model into two disentangled aspects: molecular properties and the remaining structural context of 3D molecules.
Our model ensures explicit control over these molecular attributes while maintaining equivariance of coordinate representation and invariance of data likelihood. 
Furthermore, we introduce a novel alignment-based coordinate loss to adapt equivariant networks for auto-regressive de-novo 3D molecule generation from scratch.
Extensive experiments validate our model's effectiveness on property-guided and context-guided molecule generation, both for de-novo 3D molecule design and structure-based drug discovery against protein targets.

Learning Disentangled Equivariant Representation for Explicitly Controllable 3D Molecule Generation

Can LLMs continually improve their previous outputs for better results? An affirmative answer would require LLMs to be better at discriminating among previously-generated alternatives, than generating initial responses. We explore the validity of this hypothesis in practice. We first introduce a unified framework that allows us to compare the generative and discriminative capability of any model on any task. Then, in our resulting experimental analysis of several LLMs, we do not observe the performance of those models on discrimination to be reliably better than generation. We hope these findings inform the growing literature on self-improvement AI systems.

SELF-[IN]CORRECT: LLMs Struggle with Discriminating Self-Generated Responses

We propose Intra and Inter Parser-Prompted Transformers (PPTformer) that explore useful features from visual foundation models for image restoration. Specifically, PPTformer contains two parts: an Image Restoration Network (IRNet) for restoring images from degraded observations and a Parser-Prompted Feature Generation Network (PPFGNet) for providing IRNet with reliable parser information to boost restoration. To enhance the integration of the parser within IRNet, we propose Intra Parser-Prompted Attention (IntraPPA) and Inter Parser-Prompted Attention (InterPPA) to implicitly and explicitly learn useful parser features to facilitate restoration. The IntraPPA re-considers cross attention between parser and restoration features, enabling implicit perception of the parser from a long-range and intra-layer perspective. Conversely, the InterPPA initially fuses restoration features with those of the parser, followed by formulating these fused features within an attention mechanism to explicitly perceive parser information. Further, we propose a parser-prompted feed-forward network to guide restoration within pixel-wise gating modulation. Experimental results show that PPTformer achieves state-of-the-art performance on image deraining, defocus deblurring, desnowing, and low-light enhancement.

Intra and Inter Parser-Prompted Transformers for Effective Image Restoration

Partial label learning (PLL) addresses situations where each training example is associated with a set of candidate labels, among which only one corresponds to the true class label. As the candidate labels often come from crowdsourced workers, their generation is inherently dependent on the features of the instance. Existing PLL methods primarily aim to resolve these ambiguous labels to enhance classification accuracy, overlooking the opportunity to use this feature dependency for causal representation learning. This focus on accuracy can make PLL systems vulnerable to stylistic variations and shifts in domain. In this paper, we explore the learning of causal representations within an instance-dependent PLL framework, introducing a new approach that uncovers identifiable latent representations. By separating content from style in the identified causal representation, we introduce CausalPLL+, an algorithm for instance-dependent PLL based on causal representation. Our algorithm performs exceptionally well in terms of both classification accuracy and generalization robustness. Qualitative and quantitative experiments on instance-dependent PLL benchmarks and domain generalization tasks verify the effectiveness of our approach.

Partial Label Causal Representation Learning for Instance-Dependent Supervision and Domain Generalization

In recent years, multi-view multi-label learning (MVML) has gained popularity due to its close resemblance to real-world scenarios. However, the challenge of selecting informative features to ensure both performance and efficiency remains a significant question in MVML. Existing methods often extract information separately from the consistency part and the complementary part, which may result in noise due to unclear segmentation. In this paper, we propose a unified model constructed from the perspective of global-view reconstruction. Additionally, while feature selection methods can discern the importance of features, they typically overlook the uncertainty of samples, which is prevalent in realistic scenarios. To address this, we incorporate the perception of sample uncertainty during the reconstruction process to enhance trustworthiness. Thus, the global-view is reconstructed through the graph structure between samples, sample confidence, and the view relationship. The accurate mapping is established between the reconstructed view and the label matrix. Experimental results demonstrate the superior performance of our method on multi-view datasets.

Uncertainty-Aware Global-View Reconstruction for Multi-View Multi-Label Feature Selection

The goal of image change captioning is to capture the content differences between two images and describe them in natural language. The key is how to learn stable content changes from noise such as viewpoint and image structure. However, current work mostly focuses on identifying changes, and the influence of global noise leads to unstable recognition of global features. In order to tackle this problem, we propose a Self-supervised Global-Part Alignment (SSGPA) network and revisit the image change captioning task by enhancing the construction process of overall image global features, enabling the model to integrate global changes such as viewpoint into local changes, and to detect and describe changes in the image through alignment.  Concretely, we first design a Global-Part Transport Alignment mechanism to enhance global features and learn stable content changes through a self-supervised method of optimal transport. Further, we design a Change Fusion Adapter with pre-trained vision-language model to enhance the similar parts features of paired images, thereby enhancing global features, and expanding content changes. Extensive experiments show our method achieves the state-of-the-art results on four datasets.

Revisiting Change Captioning from Self-supervised Global-Part Alignment

Emerging advancements in Large Language Models (LLMs) show significant potential for enhancing recommendations. However, prompt-based methods often struggle to find ideal prompts without task-specific feedback, while fine-tuning-based methods are hindered by high computational demands and dependence on open-source backbones. To address these challenges, we propose a Reflective Reinforcement Large Language Model (Re2LLM) for session-based recommendation, which refines LLMs to generate and utilize specialized knowledge effectively and efficiently. Specifically, we first devise the Reflective Exploration Module to extract and present knowledge in a form that LLMs can easily process. This module enables LLMs to reflect on their recommendation mistakes and construct a hint knowledge base to rectify them effectively. Next, we design the Reinforcement Utilization Module to train a lightweight retrieval agent that elicits correct LLM reasoning. This module recognizes hints as signals to facilitate LLM recommendations and learns to select appropriate hints from the constructed knowledge base using task-specific feedback efficiently. Lastly, we conduct experiments on real-world datasets and demonstrate the superiority of our Re2LLM over state-of-the-art methods.

Re2LLM: Reflective Reinforcement Large Language Model for Session-based Recommendation

The out-of-distribution (OOD) detection on graph-structured data is crucial for deploying graph neural networks securely in open-world scenarios. However, existing methods have overlooked the prevalent scenario of multi-label classification in real-world applications. In this work, we investigate the unexplored issue of OOD detection within multi-label node classification tasks. We propose ML-GOOD, a simple yet sufficient approach that utilizes an energy function to gauge the OOD score for each label. We further develop a strategy for amalgamating multiple label energies, allowing for the comprehensive utilization of label information to tackle the primary challenges encountered in multi-label scenarios. Extensive experimentation conducted on seven diverse sets of real-world multi-label graph datasets, encompassing cross-domain scenarios. The results show that the AUROC of ML-GOOD is improved by 5.26% in intra-domain and 6.54% in cross-domain compared to the previous methods. These empirical validations not only affirm the robustness of our methodology but also illuminate new avenues for further exploration within this burgeoning field of research. The codes are available at https://anonymous.4open.science/r/ML-GOOD-E6CB/.

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Neural Temporal Point Processes for Forecasting Directional Relations in Evolving Hypergraphs

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