Singapore

The modeling of genomic sequences presents unique challenges due to their long length and structural complexity. Traditional sequence models struggle to capture long-range dependencies and biological features inherent in DNA. In this work, we propose TrinityDNA, a novel DNA foundational model designed to address these challenges. The model integrates biologically informed components, including Groove Fusion for capturing DNA&#39;s structural features and Gated Reverse Complement (GRC) to handle the inherent symmetry of DNA sequences. Additionally, we introduce a multi-scale attention mechanism that allows the model to attend to varying levels of sequence dependencies, and an evolutionary training strategy that progressively adapts the model to both prokaryotic and eukaryotic genomes. TrinityDNA provides a more accurate and efficient approach to genomic sequence modeling, offering significant improvements in gene function prediction, regulatory mechanism discovery, and other genomics applications. Our model bridges the gap between machine learning techniques and biological insights, paving the way for more effective analysis of genomic data. Additionally, we introduced a new DNA long-sequence CDS annotation benchmark to make evaluations more comprehensive and oriented toward practical applications.

AAAI 2026

TrinityDNA: A Bio-Inspired Foundational Model for Efficient Long-Sequence DNA Modeling

dna foundation model

long sequence

nlp: (large) language models

ml: bio-inspired learning

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The modeling of genomic sequences presents unique challenges due to their long length and structural complexity. Traditional sequence models struggle to capture long-range dependencies and biological features inherent in DNA. In this work, we propose TrinityDNA, a novel DNA foundational model designed to address these challenges. The model integrates biologically informed components, including Groove Fusion for capturing DNA's structural features and Gated Reverse Complement (GRC) to handle the inherent symmetry of DNA sequences. Additionally, we introduce a multi-scale attention mechanism that allows the model to attend to varying levels of sequence dependencies, and an evolutionary training strategy that progressively adapts the model to both prokaryotic and eukaryotic genomes. TrinityDNA provides a more accurate and efficient approach to genomic sequence modeling, offering significant improvements in gene function prediction, regulatory mechanism discovery, and other genomics applications. Our model bridges the gap between machine learning techniques and biological insights, paving the way for more effective analysis of genomic data. Additionally, we introduced a new DNA long-sequence CDS annotation benchmark to make evaluations more comprehensive and oriented toward practical applications.

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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.

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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.

Understanding complex human activities demands the ability to decompose motion into fine-grained, semantic-aligned sub-actions. This motion grounding process is crucial for behavior analysis, embodied AI and virtual reality.
Yet, most existing methods rely on dense supervision with predefined action classes, which are infeasible in open-vocabulary, real-world settings. In this paper, we propose ZOMG, a zero-shot, open-vocabulary framework that segments motion sequences into semantically meaningful sub-actions without requiring any annotations or fine-tuning. Technically, ZOMG integrates (1) language semantic partition, which leverages large language models to decompose instructions into ordered sub-action units, and (2) soft masking optimization, which learns instance-specific temporal masks to focus on frames critical to sub-actions, while maintaining intra-segment continuity and enforcing inter-segment separation, all without altering the pretrained encoder.
Experiments on three motion-language datasets demonstrate state-of-the-art effectiveness and efficiency of motion grounding performance, outperforming prior methods by +8.7\% mAP on HumanML3D benchmark. Meanwhile, significant improvements also exist in downstream retrieval, establishing a new paradigm for annotation-free motion understanding.

Zero-Shot Open-Vocabulary Human Motion Grounding with Test-Time Training

While leveraging pseudo-labels has become a common paradigm in untargeted gray-box graph poisoning attacks, it suffers from two critical limitations: the use of brittle hard pseudo-labels that overlook uncertainty and can amplify surrogate model errors, and static guidance that progressively becomes stale as the graph is perturbed. To resolve these issues, we propose MetaDist, a novel framework that reframes the attack as an adversarial self-knowledge distillation process. Here, a ''teacher'' model provides continuously refined soft pseudo-labels to a ''student'' model, with the attack objective being to maximize the divergence between them. MetaDist makes two synergistic innovations. It employs the Reverse KL (RKL) divergence as a more strategic attack loss that efficiently converts uncertain nodes into robust, high-confidence errors. Concurrently, it introduces the Online Adaptive Teacher (OAT) mechanism, which adapts the teacher via student feedback to ensure the guidance signal remains relevant. Extensive experiments demonstrate that MetaDist consistently and significantly outperforms strong baselines across multiple datasets, proving its effectiveness and transferability even against advanced graph defenses.

Surrogate as Teacher: Distillation-Guided Graph Poisoning Attack

The capacity for social reasoning, particularly Theory of Mind (ToM), is a foundational prerequisite for aligning Large Language Models (LLMs) with human values. However, current evaluations are predominantly confined to simplistic, short-text scenarios, obscuring their true capabilities and potential failure modes in complex, long-range social dynamics. To address this deficit, we introduce MovieGraph-ToM, a large-scale benchmark for evaluating long-range ToM and social cognition within extended, multimodal narratives. We employ a "scaffold-and-probe" methodology: we construct a ground-truth Social-Causal Graph offline, which maps the narrative's latent mental states and causal chains. During evaluation, the model is denied access to this graph and must reason directly from raw multimodal inputs. This decoupling forces genuine inference over superficial pattern matching. Reasoning is probed via a hierarchical questioning framework designed to differentiate spontaneous understanding from logical robustness. Our empirical results reveal systematic vulnerabilities in even state-of-the-art models. We identify a critical "multiple-choice pitfall," where accuracy plummets against well-crafted distractors, and a stark "generative-discriminative divide," where models fail to construct coherent explanations for answers they correctly identify. These findings highlight a latent risk, as models that feign comprehension could lead to unpredictable and misaligned behaviors. MovieGraph-ToM thus offers a rigorous platform for assessing and advancing the robust social intelligence required for safely aligned AI systems.

MovieGraph-ToM: Evaluating Long-Range Theory of Mind in Large Language Models via Implicit Social-Causal Graphs

We propose Multi-Agent Reflective Policy Optimization (MARPO) to alleviate the issue of sample inefficiency in multi-agent reinforcement learning. MARPO introduces the reflection mechanism into multi-agent settings, effectively leveraging subsequent trajectories to improve sample efficiency. We theoretically derive an asymmetric clipping mechanism that dynamically adjusts the clipping range based on the KL divergence to overcome the limitations of fixed clipping boundaries and improve the stability of the training process. We evaluate MARPO on the StarCraft II Multi-Agent Challenge (SMAC) benchmark, including both standard SMAC tasks and the more challenging SMAC-Hard variants, with results demonstrating its superior performance.The code is provided in the supplementary material.

MARPO: A Reflective Policy Optimization for Multi-Agent Reinforcement Learning

Large language models (LLMs) have demonstrated their instruction-following capabilities and achieved powerful performance on various tasks. Inspired by their success, recent works in the molecular domain have led to the development of large molecular language models (LMLMs) that integrate 1D molecular strings or 2D molecular graphs into the language models. However, existing LMLMs often suffer from hallucination and limited robustness, largely due to inadequate integration of diverse molecular modalities such as 1D sequences, 2D molecular graphs, and 3D conformations. To address these limitations, we propose CoLLaMo, a large language model-based molecular assistant equipped with a multi-level molecular modality-collaborative projector. The relation-aware modality-collaborative attention mechanism in the projector facilitates fine-grained and relation-guided information exchange between atoms by incorporating 2D structural and 3D spatial relations. Furthermore, we present a molecule-centric new automatic measurement, including a hallucination assessment metric and GPT-based caption quality evaluation to address the limitations of token-based generic evaluation metrics (i.e., BLEU) widely used in assessing molecular comprehension of LMLMs. Our extensive experiments demonstrate that our CoLLaMo enhances the molecular modality generalization capabilities of LMLMs, achieving the best performance on multiple tasks, including molecule captioning, computed property QA, descriptive property QA, motif counting, and IUPAC name prediction.

Improving Large Molecular Language Model via Relation-aware Multimodal Collaboration

In recent years, neural image compression methods have achieved impressive performance in image compression tasks, most of which are based on variational auto-encoder with hyper-prior and autoregressive Gaussian entropy model. We first demonstrate that the way these end-to-end approaches handle quantization during training leads to a mismatch between the gradients direction of entropy model parameters (i.e., mean and standard deviation) and the direction they should be optimized towards during inference, making neural network difficult to learn accurate estimates of entropy model parameters. To address this issue, we then propose a two-step improvement: in the first step, use straight-through estimator to align the forward propagation during training with inference, thereby correcting the gradients of standard deviation parameters; in the second step, utilize gradients transfer that we propose and MSE-guided gradients to manually compensate for the gradients of mean parameters lost due to straight-through estimator. Finally, we also propose to freeze the auto-encoder and hyper auto-encoder in pre-trained models provided by existing works, and fine-tune only the modules that predict the entropy model parameters, enabling efficient validation of proposed improvements. Experimental results show that our improvements bring appreciable performance gains to state-of-the-art neural image compression models in recent years. Meanwhile, our improvements require no modification to the structure of pre-trained models and only lightweight fine-tuning, which shows strong plug-and-play capability and practical utility.

Correcting Quantization-Induced Gradient Mismatch in Neural Image Compression

Multi-trait Essay Scoring (MES) aims to evaluate the quality of essays across multiple traits (e.g., Language, Content, and Organization). The task can be summarized into three crucial steps: essay content encoding, trait feature learning, and multi-trait scoring. However, previous methods fall short in these steps due to neglecting essential scoring-oriented knowledge, leading to suboptimal performance. To track these issues, we propose a novel multi-trait scoring framework with multi-knowledge enhancement. Specifically, linguistic knowledge is used to model syntactic structural relations between words, highlighting structurally-informed essay encoding. We learn trait knowledge by capturing the knowledge dependencies between traits to enhance trait-specific features. Further, score-aware ordinal knowledge is integrated to promote ordinal alignment in trait-specific features associated with score rankings, improving scoring performance. Extensive experiments show that our proposed method achieves significant performance.

Multi-knowledge Enhanced Graph Neural Network for Multi-trait Essay Scoring

Time series forecasting faces a fundamental challenge: the uneven distribution of predictive importance in time series data, where some specific time points and feature combinations carry disproportionately predictive power. As a result, uniform processing methods that treat all data alike inevitably fall short of optimal performance. To address this problem, we propose FeTS, a feature-aware framework that comprehensively learns temporal features through two key components: (i) Adaptive Feature Extraction (AdaFE), which dynamically discovers the most important features within each temporal patch and extracts them on the fly, yielding sharper and more focused local representations; and (ii) Dual-Scale Feed-Forward Network (DSFFN), which strategically integrates fine-grained local features with global long-term dependencies to achieve richer dual-scale representation learning. Extensive experiments on eight benchmark datasets demonstrate that FeTS achieves state-of-the-art performance in time series forecasting tasks, offering a novel solution to the challenge of uneven predictive importance in forecasting.

FeTS: A Feature-Aware Framework for Time Series Forecasting

Source-free unsupervised domain adaptation (SF-UDA), which relies only on a pre-trained source model and unlabeled target data, has gained significant attention. Pseudo-labeling, valued for its simplicity and effectiveness, is a key approach in SF-UDA. However, existing methods neglect the consistency priors of anatomical features across samples, leading them fail to revise of high-confidence noise in structurally inconsistent regions, ultimately manifesting as significant discrepancies in pseudo-labeled samples especially in limited source data scenarios. Motivated by this insight, we propose a novel Geometric Correspondence Constrained (GCC) pseudo-labeling framework. GCC first stratifies pseudo-labeled samples into high/low-quality subsets. It then refines low-quality samples by leveraging the anatomical features inherent in high-quality samples while injecting Gaussian perturbation to perturb high-confidence noise towards the decision boundaries. This process effectively mitigates high-confidence noise disruptive effect and preserves critical prior anatomical knowledge, making it particularly powerful for scenarios with limited source data. Experiments on cross-domain fundus image datasets demonstrate that our method achieves state-of-the-art performance.

Geometric Correspondence Constrained Pseudo-Label Alignment for Source-Free Domain Adaptive Fundus Image Segmentation

In many practical reinforcement learning tasks, feedback is only provided at the end of a long horizon, leading to sparse and delayed rewards. Existing reward redistribution methods typically assume that per-step rewards are independent, thus overlooking interdependencies among state–action pairs. In this paper, we propose a Gaussian Process-based Likelihood Reward Redistribution (GP-LRR) framework that addresses this issue by modeling the reward function as a sample from a Gaussian Process (GP), which explicitly captures dependencies between state–action pairs through the kernel function. By maximizing the likelihood of the observed episodic return via a leave-one-out strategy that leverages the entire trajectory, our framework inherently introduces uncertainty regularization. Moreover, we show that the conventional mean squared error (MSE)-based reward redistribution arises as a special case of our GP-LRR framework when using a degenerate kernel without observation noise. When integrated with an off-policy algorithm such as Soft Actor-Critic, GP-LRR yields dense and informative reward signals, resulting in superior sample efficiency and policy performance on several MuJoCo benchmarks.

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