Singapore

The prediction of compound–protein interactions (CPIs) is crucial for drug discovery. Most existing CPI prediction models rely on protein sequence information as input. However, in early-stage drug development, particularly in phenotype-driven studies or compound-response analyses, proteins are often annotated only with functional labels, and their sequences remain undetermined. Consequently, current methods are inapplicable in such scenarios. Furthermore, our experiments find that even when large-scale perturbations were applied to protein sequences, the predictive performance of the existing models did not show a significant decline. It indicates that the high investment in sequencing may not bring corresponding returns. To address the above issues, we propose an inexpensive, protein-sequencing-free framework BioText-CPI, based on the Biomedical Textual description of protein for CPI prediction. Firstly, during the pre-training stage of the model, we use contrastive learning to align protein texts and sequence modalities. Subsequently, we add biological text descriptions of proteins to the existing public CPI dataset to construct a new CPI dataset. Finally, in the CPI prediction stage, the sequence and biomedical text descriptions of proteins can be used as the input for CPI prediction either separately or simultaneously to meet the application requirements of different scenarios. The experiments demonstrate that BioText-CPI achieves comparable effects to the traditional methods when only the biomedical description of protein is input. Moreover, when the two modalities of protein information are input simultaneously, BioText-CPI achieves state-of-the-art performance across multiple scenarios. The source code and data are accessible through the supplementary material.

AAAI 2026

Sequence-Free for Compound Protein Interaction Prediction

social network analysis & community

app: natural sciences

dmkm: applications

dmkm: graph mining

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.

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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. 

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We are pleased to announce the Fortieth AAAI Conference on Artificial Intelligence (AAAI-26), which will be held in Singapore EXPO from January 20 to January 27, 2026.

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-26 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.

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We are pleased to announce the Fortieth AAAI Conference on Artificial Intelligence (AAAI-26), which will be held in Singapore EXPO from January 20 to January 27, 2026.

While Large Reasoning Models (LRMs) exhibit remarkable capabilities in complex tasks, they often suffer from excessive redundancy in their chain-of-thought reasoning. This significantly reduces inference efficiency and increases computational costs. We identify that LRM redundancy is not uniformly homogeneous but can be taxonomized according to whether it is destructive to the final answer: destructive redundancy (e.g., logical drift, hallucination amplification) versus non-destructive redundancy (e.g., repetition, over-elaboration). Moreover, LRM's redundant and concise responses exhibit a significant distinction in their hidden layer representation spaces.
Based on these insights, we propose CATS (Category-Aware Token-level Steering), a training-free and lightweight method to reduce the redundancy phenomenon. CATS decomposes redundancy into six semantically interpretable characteristic dimensions. By flexibly weighting and combining the differential vectors corresponding to these dimensions, CATS synthesizes a composite intervention vector, enabling zero-parameter intervention in the hidden layers. Experiments across three LRM models and five mathematical reasoning datasets demonstrate that CATS reduces reasoning length by an average of 25% while maintaining or even slightly improving task accuracy. CATS offers a pluggable, training-free, and lightweight solution, making it particularly beneficial for users in low-resource environments.

CATS: Category-Aware Token-level Steering for Training-Free Redundancy Reduction in Large Reasoning Models

We study the common generalization of Markov decision processes (MDPs) with sets of transition probabilities, known as robust MDPs (RMDPs). A standard goal in RMDPs is to compute a policy that maximizes the expected return under an adversarial choice of the transition probabilities. If the uncertainty in the probabilities is independent between the states, known as s-rectangularity, such optimal robust policies can be computed efficiently using robust value iteration. However, there might still be multiple optimal robust policies, which, while equivalent with respect to the worst-case, reflect different expected returns under non-adversarial choices of the transition probabilities. Hence, we propose a refined policy selection criterion for RMDPs, drawing inspiration from the notions of dominance and best-effort in game theory. Instead of seeking a policy that only maximizes the worst-case expected return, we additionally require the policy to achieve a maximal expected return under different (i.e., not fully adversarial) transition probabilities. We call such a policy an optimal robust best-effort (ORBE) policy. We prove that ORBE policies always exist, characterize their structure, and present an algorithm to compute them with a small overhead over standard robust value iteration. ORBE policies offer a principled tie-breaker among optimal robust policies. Numerical experiments show the feasibility of our approach.

Best-Effort Policies for Robust Markov Decision Processes

In recent years, Cross-Modal Retrieval (CMR) has made significant progress in the field of multi-modal analysis. However, since it is time-consuming and labor-intensive to collect large-scale and well-annotated data, the annotation of multi-modal data inevitably contains some noise. This will degrade the retrieval performance of the model. To tackle the problem, numerous robust CMR methods have been developed, including robust learning paradigms, label calibration strategies, and instance selection mechanisms. Unfortunately, they often fail to simultaneously satisfy model performance ceilings, calibration reliability, and data utilization rate. To overcome the limitations, we propose a novel robust cross-modal learning framework, namely Neighbor-aware Instance Refining with Noisy Labels (NIRNL). Specifically, we first propose Cross-modal Margin Preserving (CMP) to adjust the relative distance between positive and negative pairs, thereby enhancing the discrimination between sample pairs. Then, we propose Neighbor-aware Instance Refining (NIR) to identify pure subset, hard subset, and noisy subset through cross-modal neighborhood consensus. Afterward, we construct different tailored optimization strategies for this fine-grained partitioning, thereby maximizing the utilization of all available data while mitigating error propagation. Extensive experiments on three benchmark datasets demonstrate that NIRNL achieves state-of-the-art performance, exhibiting remarkable robustness, especially under high noise rates.

Neighbor-aware Instance Refining with Noisy Labels for Cross-Modal Retrieval

Current unsupervised time series clustering methods often struggle to fully exploit the inherent characteristics of time series data and commonly adopt a two-stage training strategy that separates feature learning from the clustering process. To address these limitations, this paper proposes a novel deep clustering framework, \textbf{T}ime-\textbf{F}requency augmented \textbf{M}ulti-level \textbf{C}ontrastive \textbf{C}lustering (TFMCC). TFMCC employs a multi-scale time-frequency augmentation strategy, where each training iteration stochastically selects time and frequency scales to generate diverse augmented views, enhancing the model’s ability to learn robust and generalizable representations. In addition, a multi-level contrastive learning mechanism is introduced to jointly capture temporal dependencies, inter-sample similarities, and cluster structures. By jointly optimizing these components, TFMCC enables the learning of temporally-aware and clustering-friendly representations. Experimental results on 40 benchmark datasets demonstrate that TFMCC outperforms six existing methods in clustering accuracy.

Time-Frequency Augmented Multi-level Contrastive Clustering for Time Series

Ensuring alignment with human values is essential for modern large language models (LLMs), especially amid growing concerns around AI safety and social impact. Yet achieving such alignment remains challenging due to the limited, noisy, and often conflicting nature of human feedback from diverse annotators. Most existing approaches, such as Direct Preference Optimization (DPO), assume consistent and conflict-free supervision, overlooking the ambiguity, inconsistency, and value trade-offs inherent in real-world preferences—often leading to reduced robustness and exclusion of minority views.
To address this, we propose **FGD-Align**, a novel pluralistic alignment framework grounded in Fuzzy Group Decision-Making theory. Our approach rigorously models and aggregates human preferences while retaining the complexity of real-world value trade-offs. Unlike traditional methods that rely on coarse-grained preference pairs, FGD-Align introduces fuzzy preference modeling via triangular fuzzy numbers to capture nuanced, multi-criteria human judgments. We further develop a new training objective, Probabilistic Fuzzy DPO, which incorporates fuzzy preference strength as adaptive loss weights and gradient filters, enhancing robustness to ambiguity and inconsistency in feedback. 
Comprehensive experiments demonstrate that FGD-Align consistently outperforms both DPO variants and advanced preference aggregation methods in terms of preference accuracy and robustness to ambiguity. It achieves superior alignment stability and better preserves minority preferences, all with minimal computational overhead.
Our work bridges the gap between algorithmic tractability and the nuanced landscape of human values, enabling more scalable, inclusive, and socially-aware AI alignment.

FGD-Align: Pluralistic Alignment for Large Language Models via Fuzzy Group Decision-Making

The rapid advancement of Large Vision Language Models (LVLMs) has demonstrated excellent abilities in various visual tasks. Building upon these developments, the \textit{thinking with images} paradigm has emerged, enabling models to dynamically edit and re-encode visual information at each reasoning step, mirroring human visual processing. However, this paradigm also introduces significant challenges as diverse errors may occur during reasoning processes. This naturally necessitates Process Reward Models (PRMs) as an essential pattern for distinguishing positive and negative reasoning steps, yet existing benchmarks for PRMs are predominantly text-centric and lack comprehensive assessment of PRMs' capabilities under this paradigm,~\ourbench. To address these gaps, this work introduces the first comprehensive benchmark specifically designed for evaluating PRMs under \textit{thinking with images} paradigm. Our main contributions are as follows: (1) Through extensive analysis of reasoning trajectories under \textit{thinking with images} paradigm and guided search experiments with PRMs, we define 7 fine-grained error types and demonstrate both the necessity for specialized PRMs and the potential for improvement. (2) We construct and curate a comprehensive benchmark comprising 1,134 manually annotated high-quality thinking with images reasoning trajectories spanning 4 categories and 16 subcategories for fine-grained evaluation of PRMs. (3) Our comprehensive experimental analysis reveals that current LVLMs fall short as effective PRMs, exhibiting limited capabilities in visual reasoning process evaluation with significant performance disparities across error types, consistent positive evaluation bias, and notable sensitivity to reasoning step positions. These findings demonstrate the effectiveness of our benchmark and establish crucial foundations for advancing PRMs in LVLMs.

What, Whether and How? Unveiling Process Reward Models for Thinking with Images Reasoning

With the development of diffusion models, enhancing spatial controllability in text-to-image generation has become a vital challenge. As a representative task for addressing this challenge, layout-to-image generation aims to generate images that are spatially consistent with the given layout condition. Existing layout-to-image methods typically introduce the layout condition by integrating adapter modules into the base generative model. However, the generated images often exhibit low visual quality and stylistic inconsistency with the base model, indicating a loss of pretrained knowledge. To alleviate this issue, we construct the Layout Synthesis (LaySyn) dataset, which leverages images synthesized by the base model itself to mitigate the distribution shift from the pretraining data. Moreover, we propose the Layout Control (Laytrol) Network, in which parameters are inherited from MM-DiT to preserve the pretrained knowledge of the base model. To effectively activate the copied parameters and avoid disturbance from unstable control conditions, we adopt a dedicated initialization scheme for Laytrol. In this scheme, the layout encoder is initialized as a pure text encoder to ensure that its output tokens remain within the data domain of MM-DiT. Meanwhile, the outputs of the layout control network are initialized to zero. In addition, we apply Object-level Rotary Position Embedding to the layout tokens to provide coarse positional information. Qualitative and quantitative experiments demonstrate the effectiveness of our method.

Laytrol: Preserving Pretrained Knowledge in Layout Control for Multimodal Diffusion Transformers

Federated Learning (FL) faces significant challenges arising from both data and system heterogeneity. While Clustered Federated Learning (CFL) mitigates data heterogeneity by grouping clients with similar data distributions, it remains vulnerable to system heterogeneity, which can slow convergence due to performance disparities among clients. Moreover, data drift may degrade clustering accuracy and training efficiency over time. In this work, we propose a Model Structure-aware Clustered Federated Learning (MSCFL) framework that simultaneously addresses the issues of data heterogeneity, system heterogeneity, and data drift. MSCFL incorporates model pruning (MP) into the CFL framework to enhance training efficiency under system heterogeneity. To enable this integration, we address the key challenge of performing effective clustering based on heterogeneous, pruned local models with varying structures. To this end, we design a model structure-based similarity computation algorithm to integrate CFL with MP. To effectively address data drift, we propose a dynamic cluster migration strategy that efficiently monitors model structures via Hamming Distance and triggers re-clustering only when necessary. Extensive experimental results show that MSCFL improves the accuracy and convergence speed of cluster models, outperforming traditional CFL in various settings. Additional results and our codes are available in supplementary materials.

MSCFL: Model Structure-Aware Clustered Federated Learning for System Heterogeneity and Data Drift

High‑quality Question–Answer (QA) datasets are foundational for reliable Large Language Model (LLM) evaluation, yet even expert‑crafted datasets exhibit persistent gaps in domain coverage, misaligned difficulty distributions, and factual inconsistencies. The recent surge in generative model-powered datasets has compounded these quality challenges. In this work, we introduce RefineLab, the first LLM‑driven framework that automatically refines raw QA textual data into high-quality datasets under a controllable token‑budget constraint. RefineLab takes a set of target quality attributes as refinement objectives and performs selective edits within a predefined token budget to ensure practicality and efficiency. In essence, RefineLab addresses a constrained optimization problem: improving the quality of QA samples as much as possible while respecting resource limitations. With a set of available refinement operations, RefineLab takes as input the original dataset, a specified set of target quality dimensions, and a token budget, and determines which refinement operations should be applied to each QA sample. This process is guided by an assignment module that selects optimal refinement strategies to maximize overall dataset quality while adhering to the budget constraint. Experiments demonstrate that RefineLab consistently narrows divergence from expert datasets across coverage, difficulty alignment, factual fidelity, and distractor quality. RefineLab pioneers a scalable, customizable path to reproducible dataset design, with broad implications for LLM evaluation.

Better Datasets Start from RefineLab: Automatic Optimization for High-Quality Dataset Refinement

Reinforcement Learning with Verifiable Rewards (RLVR) significantly enhances the reasoning capability of Large Language Models (LLMs). Current RLVR approaches typically conduct training across all generated tokens, but neglect to explore which tokens (e.g., prefix tokens) actually contribute to reasoning. This uniform training strategy spends substantial effort on optimizing low-return tokens, which in turn impedes the potential improvement from high-return tokens and reduces overall training effectiveness. To address this issue, we propose a novel RLVR approach called Progressive Prefix-token Policy Optimization (PPPO), which highlights the significance of the prefix segment of generated outputs. Specifically, inspired by the well-established human thinking theory of Path Dependence, where early-stage thoughts substantially constrain subsequent thinking trajectory, we identify an analogous phenomenon in LLM reasoning termed Beginning Lock-in Effect (BLE). PPPO leverages this finding by focusing its optimization objective on the prefix reasoning process of LLMs. This targeted optimization strategy can positively influence subsequent reasoning processes, and ultimately improve final results. To improve the learning effectiveness of LLMs on how to start reasoning with high quality, PPPO introduces two training strategies: (a) Progressive Prefix Retention, which shapes a progressive learning process by increasing the proportion of retained prefix tokens during training; (b) Continuation Accumulated Reward, which mitigates reward bias by sampling multiple continuations for one prefix token sequence, and accumulating their scores as the reward signal. Extensive experimental results on various reasoning tasks (e.g., math, physics, chemistry, and biology) demonstrate that our proposed PPPO outperforms representative RLVR methods, with the accuracy improvements of 18.02% on only 26.17% training tokens.

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