VLM-R$^3$: Region Recognition, Reasoning, and Refinement for Enhanced Multimodal Chain-of-Thought

Recently, reasoning-based MLLMs have achieved a degree of success in generating long-form textual reasoning chains. However, they still struggle with complex tasks that necessitate dynamic and iterative focusing on and revisiting of visual regions to achieve precise grounding of textual reasoning in visual evidence. We introduce \textbf{VLM-R$^3$} (\textbf{V}isual \textbf{L}anguage \textbf{M}odel with \textbf{R}egion \textbf{R}ecognition and \textbf{R}easoning), a framework that equips an MLLM with the ability to (i) decide \emph{when} additional visual evidence is needed, (ii) determine \emph{where} to ground within the image, and (iii) seamlessly weave the relevant sub-image content back into an interleaved chain-of-thought. The core of our method is \textbf{Region-Conditioned Reinforcement Policy Optimization (R-GRPO)}, a training paradigm that rewards the model for selecting informative regions, formulating appropriate transformations (e.g.\ crop, zoom), and integrating the resulting visual context into subsequent reasoning steps. To bootstrap this policy, we compile a modest but carefully curated Visuo-Lingual Interleaved Rationale (VLIR) corpus that provides step-level supervision on region selection and textual justification. Extensive experiments on MathVista, ScienceQA, and other benchmarks show that VLM-R$^3$ sets a new state of the art in zero-shot and few-shot settings, with the largest gains appearing on questions demanding subtle spatial reasoning or fine-grained visual cue extraction.

Chatting with Papers: A Hybrid Approach Using LLMs and Knowledge Graphs

This demo paper reports on a new workflow \textit{GhostWriter} that combines the use of Large Language Models and Knowledge Graphs (semantic artifacts) to support navigation through collections. Situated in the research area of Retrieval Augmented Generation, this specific workflow details the creation of local and adaptable chatbots. Based on the tool-suite \textit{EverythingData} at the backend, \textit{GhostWriter} provides an interface that enables querying and ``chatting'' with a collection. Applied iteratively, the workflow supports the information needs of researchers when interacting with a collection of papers, whether it be to gain an overview, to learn more about a specific concept and its context, and helps the researcher ultimately to refine their research question in a controlled way. We demonstrate the workflow for a collection of articles from the \textit{method data analysis} journal published by GESIS -- Leibniz-Institute for the Social Sciences. We also point to further application areas.

Quantifying the Noise of Structural Perturbations on Graph Adversarial Attacks

Graph neural networks have been widely utilized to solve graph-related tasks because of their strong learning power in utilizing the local information of neighbors. However, recent studies on graph adversarial attacks have proven that current graph neural networks are not robust against malicious attacks. Yet much of the existing work has focused on the optimization objective based on attack performance to obtain (near) optimal perturbations, but paid less attention to the strength quantification of each perturbation such as the injection of a particular node/link, which makes the choice of perturbations a black-box model that lacks interpretability. In this work, we propose the concept of noise to quantify the attack strength of each adversarial link. Furthermore, we propose three attack strategies based on the defined noise and classification margins in terms of single and multiple steps optimization. Extensive experiments conducted on benchmark datasets against three representative graph neural networks demonstrate the effectiveness of the proposed attack strategies. Particularly, we also investigate the preferred patterns of effective adversarial perturbations by analyzing the corresponding properties of the selected perturbation nodes.

Mitigating the Structural Bias in Graph Adversarial Defenses

In recent years, graph neural networks (GNNs) have shown great potential in addressing various graph structure-related downstream tasks. However, recent studies have found that current GNNs are susceptible to malicious adversarial attacks. Given the inevitable presence of adversarial attacks in the real world, a variety of defense methods have been proposed to counter these attacks and enhance the robustness of GNNs. Despite the commendable performance of these defense methods, we have observed that they tend to exhibit a structural bias in terms of their defense capability on nodes with low degree (i.e., tail nodes), which is similar to the structural bias of traditional GNNs on nodes with low degree in the clean graph. Therefore, in this work, we propose a defense strategy by including hetero-homo augmented graph construction, $k$NN augmented graph construction, and multi-view node-wise attention modules to mitigate the structural bias of GNNs against adversarial attacks. Notably, the hetero-homo augmented graph consists of removing heterophilic links (i.e., links connecting nodes with dissimilar features) globally and adding homophilic links (i.e., links connecting nodes with similar features) for nodes with low degree. To further enhance the defense capability, an attention mechanism is adopted to adaptively combine the representations from the above two kinds of graph views. We conduct extensive experiments to demonstrate the defense and debiasing effect of the proposed strategy on benchmark datasets.

Enhancing the Scalability and Applicability of Kohn-Sham Hamiltonians for Molecular Systems

Density Functional Theory (DFT) is a pivotal method within quantum chemistry and materials science, with its core involving the construction and solution of the Kohn-Sham Hamiltonian. Despite its importance, the application of DFT is frequently limited by the substantial computational resources required to construct the Kohn-Sham Hamiltonian. In response to these limitations, current research has employed deep-learning models to efficiently predict molecular and solid Hamiltonians, with roto-translational symmetries encoded in their neural networks. However, the scalability of prior models may be problematic when applied to large molecules, resulting in non-physical predictions of ground-state properties. In this study, we generate a substantially larger training set (PubChemQH) than used previously and use it to create a scalable model for DFT calculations with physical accuracy. For our model, we introduce a loss function derived from physical principles, which we call Wavefunction Alignment Loss (WALoss). WALoss involves performing a basis change on the predicted Hamiltonian to align it with the observed one; thus, the resulting differences can serve as a surrogate for orbital energy differences, allowing models to make better predictions for molecular orbitals and total energies than previously possible. WALoss also substantially accelerates self-consistent-field (SCF) DFT calculations. Here, we show it achieves a reduction in total energy prediction error by a factor of 1347 and an SCF calculation speed-up by a factor of 18%. These substantial improvements set new benchmarks for achieving accurate and applicable predictions in larger molecular systems.

Multi-Teacher Knowledge Distillation with Reinforcement Learning for Visual Recognition

Multi-teacher Knowledge Distillation (KD) transfers diverse knowledge from a teacher pool to a student network. The core problem of multi-teacher KD is how to balance distillation strengths among various teachers. Most existing methods often develop weighting strategies from an individual perspective of teacher performance or teacher-student gaps, lacking comprehensive information for guidance. This paper proposes Multi-Teacher Knowledge Distillation with Reinforcement Learning (MTKD-RL) to optimize multi-teacher weights. In this framework, we construct both teacher performance and teacher-student gaps as state information to an agent. The agent outputs the teacher weight and can be updated by the return reward from the student. MTKD-RL reinforces the interaction between the student and teacher using an agent in an RL-based decision mechanism, achieving better matching capability with more meaningful weights. Experimental results on visual recognition tasks, including image classification, object detection, and semantic segmentation tasks, demonstrate that MTKD-RL achieves state-of-the-art performance compared to the existing multi-teacher KD works.

Uncertainty Aware Human-machine Collaboration in Camouflaged Object Detection

Camouflaged Object Detection (COD), the task of identifying objects concealed within their environments, has seen rapid growth due to its wide range of practical applications. A key step toward developing trustworthy COD systems is the estimation and effective utilization of uncertainty. In this work, we propose a human-machine collaboration framework for classifying the presence of camouflaged objects, leveraging the complementary strengths of computer vision (CV) models and noninvasive brain-computer interfaces (BCIs). Our approach introduces a multiview backbone to estimate uncertainty in CV model predictions, utilizes this uncertainty during training to improve efficiency, and defers low-confidence cases to human evaluation via RSVP-based BCIs during testing for more reliable decision-making. We evaluated the framework in the CAMO dataset, achieving state-of-the-art results with an average improvement of 4.56\% in balanced accuracy (BA) and 3.66\% in the F1 score compared to existing methods. For the best-performing participants, the improvements reached 7.6\% in BA and 6.66\% in the F1 score. Analysis of the training process revealed a strong correlation between our confidence measures and precision, while an ablation study confirmed the effectiveness of the proposed training policy and the human-machine collaboration strategy. In general, this work reduces human cognitive load, improves system reliability, and provides a strong foundation for advancements in real-world COD applications and human-computer interaction. Our code and data are available at: https://github.com/ziyuey/Uncertainty-aware-human-machine-collaboration-in-camouflaged-object-identification.

NatureLM: Deciphering the Language of Nature for Scientific Discovery

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

Efficient and Scalable Density Functional Theory Hamiltonian Prediction through Adaptive Sparsity

Hamiltonian matrix prediction is pivotal in computational chemistry, serving as the foundation for determining a wide range of molecular properties. While SE(3) equivariant graph neural networks have achieved remarkable success in this domain, their substantial computational cost-driven by high-order tensor product (TP) operations-restricts their scalability to large molecular systems with extensive basis sets. To address this challenge, we introduce SPHNet, an efficient and scalable equivariant network that incorporates adaptive sparsity into Hamiltonian prediction. SPHNet employs two innovative sparse gates to selectively constrain non-critical interaction combinations, significantly reducing tensor product computations while maintaining accuracy. To optimize the sparse representation, we develop a Three-phase Sparsity Scheduler, ensuring stable convergence and achieving high performance at sparsity rates of up to 70 percent. Extensive evaluations on QH9 and PubchemQH datasets demonstrate that SPHNet achieves state-of-the-art accuracy while providing up to a 7x speedup over existing models. Beyond Hamiltonian prediction, the proposed sparsification techniques also hold significant potential for improving the efficiency and scalability of other SE(3) equivariant networks, further broadening their applicability and impact.

\underline{E2}Former: A Linear-time \underline{E}fficient and \underline{E}quivariant Trans\underline{former} for Scalable Molecular Modeling

Equivariant Graph Neural Networks (EGNNs) have demonstrated significant success in modeling microscale systems, including those in chemistry, biology and materials science. However, EGNNs face substantial computational challenges due to the high cost of constructing edge features via spherical tensor products, making them impractical for large-scale systems. To address this limitation, we introduce E2Former, an equivariant and efficient transformer architecture that incorporates the Wigner $6j$ convolution (Wigner $6j$ Conv). By shifting the computational burden from edges to nodes, the Wigner $6j$ Conv reduces the complexity from $O(|\mathcal{E}|)$ to $ O(| \mathcal{V}|)$ while preserving both the model's expressive power and rotational equivariance. We show that this approach achieves a 7x-30x speedup compared to conventional $\mathrm{SO}(3)$ convolutions. Furthermore, our empirical results demonstrate that the derived E2Former mitigates the computational challenges of existing approaches without compromising the ability to capture detailed geometric information. This development could suggest a promising direction for scalable and efficient molecular modeling.