Canada

Accurate identification of protein nucleic-acid-binding residues poses a significant challenge with important implications for various biological processes and drug design. Many typical computational methods for protein analysis rely on a single model that could ignore either the semantic context of the protein or the global 3D geometric information. Consequently, these approaches may result in incomplete or inaccurate protein analysis. To address the above issue, in this paper, we present CrossBind, a novel collaborative cross-modal approach for identifying binding residues by exploiting both protein geometric structure and its sequence prior knowledge extracted from a large-scale protein language model. Specifically, our multi-modal approach leverages a contrastive learning technique and atom-wise attention to capture the positional relationships between atoms and residues, thereby incorporating fine-grained local geometric knowledge, for better binding residue prediction. Extensive experimental results demonstrate that our approach outperforms the next best state-of-the-art methods, GraphSite and GraphBind, on DNA and RNA datasets by 10.8/17.3% in terms of the harmonic mean of precision and recall (F1-Score) and 11.9/24.8% in Matthews correlation coefficient (MCC), respectively.

AAAI 2024

CrossBind: Collaborative Cross-Modal Identification of Protein Nucleic-Acid-Binding Residues

cv: biometrics

gesture & pose

cv: multi-modal vision

face

## Welcome!
"I am excited to welcome you to this year’s edition of the Conference on Empirical Methods in Natural Language Processing! Importantly, it marks the 30th edition of EMNLP. With over 8,000 submissions, more than 3,000 accepted papers, and thousands of attendees, we have come a long way from that first
workshop, which had 14 accepted papers. As the field looks ahead, Suzhou is the fitting location for celebrating this milestone: rooted in a long literary tradition, yet modern and forward-looking, and home to a large share of the NLP community." 

*Message from the General Chair, Dirk Hovy*

EMNLP 2025

Celebrate 30 Years of EMNLP! 
EMNLP 2025 will be held in Suzhou, China from November 5th to November 9th, 2025.

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/)

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. 

Optimal control deals with optimization problems in which variables steer a
dynamical system, and its outcome contributes to the objective function. Two
classical approaches to solving these problems are Dynamic Programming
and the Pontryagin Maximum Principle. In both approaches, Hamiltonian
equations offer an interpretation of optimality through auxiliary variables
known as costates. However, Hamiltonian equations are rarely used due
to their reliance on forward-backward algorithms across the entire temporal
domain.  This paper introduces a novel neural-based approach to optimal
control. Neural networks are employed not only for implementing state
dynamics but also for estimating costate variables. The parameters of the
latter network are determined at each time step using a newly introduced
local policy referred to as the time-reversed generalized
Riccati equation. This policy is inspired by a result discussed in the
Linear Quadratic (LQ) problem, which we conjecture stabilizes state
dynamics. We support this conjecture by discussing experimental results from
a range of optimal control case studies.

Neural Time-Reversed Generalized Riccati Equation

Large Language Models (LLMs) have demonstrated impressive planning abilities due to their vast "world knowledge". Yet, obtaining plans that are both feasible (grounded in affordances) and cost-effective (in plan length), remains a challenge, despite recent progress. This contrasts with heuristic planning methods that employ domain knowledge (formalized in action models such as PDDL) and heuristic search to generate feasible, optimal plans. Inspired by this, we propose to combine the power of LLMs and heuristic planning by leveraging the world knowledge of LLMs and the principles of heuristic search. Our approach, SayCanPay, employs LLMs to generate actions (Say) guided by learnable domain knowledge, that evaluates actions' feasibility (Can) and long-term reward/payoff (Pay), and heuristic search to select the best sequence of actions. Our contributions are (1) a novel framing of the LLM planning problem in the context of heuristic planning, (2) integrating grounding and cost-effective elements into the generated plans, and (3) using heuristic search over actions. Our extensive evaluations show that our model surpasses other LLM planning approaches.

SayCanPay: Heuristic Planning with Large Language Models Using Learnable Domain Knowledge | VIDEO

In Time Series Classification (TSC), temporal pooling methods that consider sequential information have been proposed. However, we found that each temporal pooling has a distinct mechanism, and then can perform better or worse depending on time series data. We term this fixed pooling mechanism a single \textit{perspective} of temporal poolings. In this paper, we propose a novel temporal pooling method with diverse perspective learning: Selection over Multiple Temporal Poolings (SoM-TP). SoM-TP dynamically selects the optimal temporal pooling among multiple methods for each data by attention. The dynamic pooling selection is motivated by the ensemble concept of Multiple Choice Learning (MCL) which selects the best among multiple outputs. The pooling selection by SoM-TP's attention enables a non-iterative pooling ensemble within a single classifier. Additionally, we define a \textit{perspective loss} and Diverse Perspective Learning Network (DPLN). The loss works as a regularizer to reflect all the pooling perspectives from DPLN. Our perspective analysis using Layer-wise Relevance Propagation (LRP) reveals the limitation of a single perspective and ultimately demonstrates diverse perspective learning of SoM-TP. We also show that SoM-TP outperforms CNN models based on other temporal poolings and state-of-the-art models in TSC with extensive UCR/UEA repositories.

Towards Diverse Perspective Learning with Selection over Multiple Temporal Poolings

Traditional gradient descent (GD) has been fully investigated for convex or $L$-smoothness functions, and it is widely utilized in current neural network optimization. The classical descent lemma ensures that for a function with $L$-smoothness, the GD trajectory converges stably towards the minimum when the learning rate is below $2 / L$. This convergence is marked by a consistent reduction in the loss function throughout the iterations. However, recent experimental studies have demonstrated that even when the $L$-smoothness condition is not met, or if the learning rate is increased leading to oscillations in the loss function during iterations, the GD trajectory still exhibits convergence over the long run. This phenomenon is referred to as the unstable convergence regime of GD. In this paper, we present a theoretical perspective to offer a qualitative analysis of this phenomenon. The unstable convergence is in fact an inherent property of GD for general twice differentiable functions. Specifically, the forwardinvariance of GD is established, i.e., it ensures that any point within a local region will always remain within this region under GD iteration. Then, based on the forward-invariance, for the initialization outside an open set containing the local minimum, the loss function will oscillate at the first several iterations and then become monotonely decreasing after the GD trajectory jumped into the open set. This work theoretically clarifies the unstable convergence phenomenon of GD discussed in previous experimental works. The unstable convergence of GD mainly depends on the selection of the initialization, and it is actually inevitable due to the complex nature of loss function.

On the Unstable Convergence Regime of Gradient Descent

Query-focused summarization (QFS) aims to summarize the source document(s) with regard to a specific aspect of information given in a query. It plays an important role in presenting users with a concise answer summary from a set of query-relevant documents retrieved by the information retrieval system. Nonetheless, the QFS research has long been hampered by the lack of adequate datasets in terms of both quality and quantity. In this paper, we introduce a large-scale multi-document query-focused summarization dataset, called QuerySum, which contains 27,041 data samples covering diverse topics and its quality is guaranteed through human verification. Unlike some previous QFS datasets constructed directly from the question answering datasets, 74% queries in our dataset are the challenging non-factoid What-, Why-, and How- questions. More importantly, we also provide a set of similar queries together with the corresponding summaries pairs for each query as the retrieved context, presenting a new feature of QuerySum. We aim to encourage research efforts in query intention understanding in the context of QFS. Leveraging QuerySum's depth, we propose a model for query-aware multi-document summarization and set a new QFS benchmark.

QuerySum: A Multi-Document Query-Focused Summarization Dataset Augmented with Similar Query Clusters

As a new paradigm to erase data from a model and protect user privacy, machine unlearning has drawn significant attention. However, existing studies on machine unlearning mainly focus on its effectiveness and efficiency, neglecting the security challenges introduced by this technique. In this paper, we aim to bridge this gap and study the possibility of conducting malicious attacks leveraging machine unlearning. Specifically, we consider the backdoor attack via machine unlearning, where an attacker seeks to inject a backdoor in the unlearned model by submitting malicious unlearning requests, so that the prediction made by the unlearned model can be changed when a particular trigger presents. In our study, we propose two attack approaches. The first attack approach does not require the attacker to poison any training data of the model. The attacker can achieve the attack goal only by requesting to unlearn a small subset of his contributed training data. The second approach allows the attacker to poison a few training instances with a pre-defined trigger upfront, and then activate the attack via submitting a malicious unlearning request. Both attack approaches are proposed with the goal of maximizing the attack utility while ensuring attack stealthiness. The effectiveness of the proposed attacks is demonstrated with different machine unlearning algorithms as well as different models on different datasets.

Backdoor Attacks via Machine Unlearning

We propose expanding the shared Transformer module to produce and initialize Transformers of varying depths, enabling adaptation to diverse resource constraints. Drawing an analogy to genetic expansibility, we term such module as learngene. To identify the expansion mechanism, we delve into the relationship between the layer's position and its corresponding weight value, and find that linear function appropriately approximates this relationship. Building on this insight, we present Transformer as Linear Expansion of learnGene (TLEG), a novel approach for flexibly producing and initializing Transformers of diverse depths. Specifically, to learn learngene, we firstly construct an auxiliary Transformer linearly expanded from learngene, after which we train it through employing soft distillation. Subsequently, we can produce and initialize Transformers of varying depths via linearly expanding the well-trained learngene, thereby supporting diverse downstream scenarios. Extensive experiments on ImageNet-1K demonstrate that TLEG achieves comparable or better performance in contrast to many individual models trained from scratch, while reducing around 2× training cost. When transferring to several downstream classification datasets, TLEG surpasses existing initialization methods by a large margin (e.g., +6.87% on iNat 2019 and +7.66% on CIFAR-100). Under the situation where we need to produce models of varying depths adapting for different resource constraints, TLEG achieves comparable results while reducing around 19× parameters stored to initialize these models and around 5× pre-training costs, in contrast to the pre-training and fine-tuning approach. When transferring a fixed set of parameters to initialize different models, TLEG presents better flexibility and competitive performance while reducing around 2.9× parameters stored to initialize, compared to the pre-training approach.

Transformer as Linear Expansion of Learngene

Graph representation learning (GRL) methods, such as graph neural networks and graph transformer models, have been successfully used to analyze graph-structured data, mainly focusing on node classification and link prediction tasks. However, the existing studies mostly only consider local connectivity while ignoring long-range connectivity and the roles of nodes. In this paper, we propose Unified Graph Transformer Networks (UGT) that effectively integrate local and global structural information into fixed-length vector representations. First, UGT learns local structure by identifying the local sub-structures and aggregating features of the k-hop neighborhoods of each node. Second, we construct virtual edges, bridging distant nodes with structural similarity to capture the long-range dependencies. Third, UGT learns unified representations through self-attention, encoding structural distance and p-step transition probability between node pairs. Furthermore, we propose a self-supervised learning task that effectively learns transition probability to fuse local and global structural features, which could then be transferred to other downstream tasks. Experimental results on real-world benchmark datasets over various downstream tasks showed that UGT significantly outperformed baselines that consist of state-of-the-art models. In addition, UGT reaches the third-order Weisfeiler-Lehman power to distinguish non-isomorphic graph pairs.

Transitivity-Preserving Graph Representation Learning for Bridging Local Connectivity and Role-Based Similarity

Domain model acquisition has been identified as a bottleneck in the application of planning technology, especially within narrative planning. Learning action models from narrative texts in an automated way is essential to overcome this barrier, but challenging because of the inherent complexities of such texts. We present an evaluation of planning domain models derived from narrative texts using our fully automated, unsupervised system, NaRuto. Our system combines structured event extraction, predictions of commonsense event relations, and textual contradictions and similarities. Evaluation results show that NaRuto generates domain models of significantly better quality than existing fully automated methods, and even sometimes on par with those created by semi-automated methods, with human assistance.

NaRuto: Automatically Acquiring Planning Models from Narrative Texts

Recently, dense retrieval (DR) models, which represent queries and documents with fixed-width vectors and retrieve relevant ones via nearest neighbor search, have drawn increasing attention from the IR community. 
However, previous studies have shown that the effectiveness of DR critically relies on sufficient training signals, which leads to severe performance degradation when applied in out-of-domain scenarios, where large-scale training data are usually unavailable.
To solve this problem, existing studies adopt a data-augmentation-plus-joint-training paradigm to construct weak/pseudo supervisions on the target domain and combine them with the large-scale human annotated data on the source domain to train the DR models. However, they don't explicitly distinguish the data and the supervision signals in the training process and simply assume that the DR models are mighty enough to capture and memorize different domain knowledge and relevance matching patterns without guidance, which, as shown in this paper, is not true.
Based on this observation, we propose a Robust Multi-Supervision Combining strategy (RMSC) that
decouples the domain and supervision signals by explicitly telling the DR models how the domain data and supervision signals are combined in the training data with specially designed soft tokens. 
With the extra soft tokens to store the domain-specific and supervision-specific knowledge, RMSC allows the DR models 
to conduct retrieval based on human-like relevance matching patterns and target-specific language distribution on the target domain without human annotations.
Extensive experiments on zero-shot DR benchmarks show that RMSC significantly improves the ranking performance on the target domain compared to strong DR baselines and domain adaptation methods, while being stable during training and can be combined with query generation or second-stage pre-training.

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