Automatic Annotation Augmentation Boosts Translation between Molecules and Natural Language

Recent advancements in AI for biological research focus on integrating molecular data with natural language to accelerate drug discovery. However, the scarcity of high-quality annotations limits progress in this area. This paper introduces LA$^3$, a Language-based Automatic Annotation Augmentation framework that leverages large language models to augment existing datasets, thereby improving AI training. We demonstrate the effectiveness of LA$^3$ by creating an enhanced dataset, LaChEBI-20, where we systematically rewrite the annotations of molecules from an established dataset. These rewritten annotations preserve essential molecular information while providing more varied sentence structures and vocabulary. Using LaChEBI-20, we train LaMolT5 based on a benchmark architecture to learn the mapping between molecular representations and augmented annotations. Experimental results on text-based *de novo* molecule generation and molecule captioning demonstrate that LaMolT5 outperforms state-of-the-art models. Notably, incorporating LA$^3$ leads to improvements of up to 301% over the benchmark architecture. Furthermore, we validate the effectiveness of LA$^3$ notable applications in *image*, *text* and *graph* tasks, affirming its versatility and utility.

SFC-GAN: A Generative Adversarial Network for Brain Functional and Structural Connectome Translation

Modern brain imaging technologies have enabled the detailed reconstruction of human brain connectomes, capturing structural connectivity (SC) from diffusion MRI and functional connectivity (FC) from functional MRI. Understanding the intricate relationships between SC and FC is vital for gaining deeper insights into the brain's functional and organizational mechanisms. However, obtaining both SC and FC modalities simultaneously remains challenging, hindering comprehensive analyses. Existing deep generative models typically focus on synthesizing a single modality or unidirectional translation between FC and SC, thereby missing the potential benefits of bi-directional translation, especially in scenarios where only one connectome is available. Therefore, we propose Structural-Functional Connectivity GAN (SFC-GAN), a novel framework for bidirectional translation between SC and FC. This approach leverages the CycleGAN architecture, incorporating convolutional layers to effectively capture the spatial structures of brain connectomes. To preserve the topological integrity of these connectomes, we employ a structure-preserving loss that guides the model in capturing both global and local connectome patterns while maintaining symmetry. Our framework demonstrates superior performance in translating between SC and FC, outperforming baseline models in similarity and graph property evaluations compared to ground truth data, each translated modality can be effectively utilized for downstream classification.

Generalizable Origin Identification for Text-Guided Image-to-Image Diffusion Models

Text-guided image-to-image diffusion models excel in translating images based on textual prompts, allowing for precise and creative visual modifications. However, such a powerful technique can be misused for spreading misinformation, infringing on copyrights, and evading content tracing. This motivates us to introduce the task of origin IDentification for text-guided Image-to-image Diffusion models (ID$^2$), aiming to retrieve the original image of a given translated query. A straightforward solution to ID$^2$ involves training a specialized deep embedding model to extract and compare features from both query and reference images. However, due to visual discrepancy across generations produced by different diffusion models, this similarity-based approach fails when training on images from one model and testing on those from another, limiting its effectiveness in real-world applications. To solve this challenge of the proposed ID$^2$ task, we contribute the first dataset and a theoretically guaranteed method, both emphasizing generalizability. The curated dataset, OriPID, contains abundant Origins and guided Prompts, which can be used to train and test potential IDentification models across various diffusion models. In the method section, we first prove the existence of a linear transformation that minimizes the distance between the pre-trained Variational Autoencoder (VAE) embeddings of generated samples and their origins. Subsequently, it is demonstrated that such a simple linear transformation can be generalized across different diffusion models. Experimental results show that the proposed method achieves satisfying generalization performance, significantly surpassing similarity-based methods ($+31.6\%$ mAP), even those with generalization designs.

Unified Graph Networks (UGN): A Deep Neural Framework for Solving Graph Problems

Deep neural networks have enabled researchers to create powerful generalized frameworks, such as transformers, that can be used to solve well-studied problems in various application domains, such as text and image. However, such generalized frameworks are not available for solving graph problems. Graph structures are ubiquitous in many applications around us and many graph problems have been widely studied over years. In recent times, there has been a surge in deep neural network based approaches to solve graph problems, with growing availability of graph structured datasets across diverse domains. Nevertheless, existing methods are mostly tailored to solve a specific task and lack the capability to create a generalized model leading to solutions for different downstream tasks. In this work, we propose a novel, resource-efficient framework named \emph{U}nified \emph{G}raph \emph{N}etwork (UGN) by leveraging the feature extraction capability of graph convolutional neural networks (GCN) and 2-dimensional convolutional neural networks (Conv2D). UGN unifies various graph learning tasks, such as link prediction, node classification, community detection, graph-to-graph translation, knowledge graph completion, and more, within a cohesive framework, while exercising minimal task-specific extensions (e.g., formation of supernodes for coarsening massive networks to increase scalability, use of \textit{mean target connectivity matrix} (MTCM) representation for achieving scalability in graph translation task, etc.) to enhance the generalization capability of graph learning and analysis. We test the novel UGN framework for six uncorrelated graph problems, using twelve different datasets. Experimental results show that UGN outperforms the state-of-the-art baselines by a significant margin on ten datasets, while producing comparable results on the remaining dataset.

Enhancing Financial VQA in Vision Language Models using Intermediate Structured Representations

Chart interpretation is crucial for visual data analysis, but accurately extracting information from charts poses significant challenges for automated models. This study investigates the fine-tuning of DEPLOT, a modality conversion module that translates the image of a plot or chart to a linearized table, on a custom dataset of 50,000 bar charts. The dataset comprises simple, stacked, and grouped bar charts, targeting the unique structural features of these visualizations. The finetuned DEPLOT model is evaluated against its base version using a test set of 1,000 images and two metrics: Relative Mapping Similarity (RMS), which measures categorical mapping accuracy, and Relative Number Set Similarity (RNSS), which evaluates numerical interpretation accuracy. To further explore the reasoning capabilities of large language models (LLMs), we curate an additional set of 100 bar chart images paired with question answer sets. Our findings demonstrate that providing a structured intermediate table alongside the image significantly enhances LLM reasoning performance compared to direct image queries.

OceanChat: The Effect of Virtual Conversational AI Agents on Sustainable Attitude and Behavior Change

Marine ecosystems face unprecedented threats from climate change and plastic pollution, yet traditional environmental education often struggles to translate awareness into sustained behavioral change. This paper presents OceanChat, an interactive system leveraging large language models to create conversational AI agents represented as animated marine creatures -- specifically a beluga whale, a jellyfish, and a seahorse -- designed to promote environmental behavior (PEB) and foster awareness through personalized dialogue. Through a between-subjects experiment (N=900), we compared three conditions: (1) Static Scientific Information, providing conventional environmental education through text and images; (2) Static Character Narrative, featuring first-person storytelling from 3D-rendered marine creatures; and (3) Conversational Character Narrative, enabling real-time dialogue with AI-powered marine characters. Our analysis revealed that the Conversational Character Narrative condition significantly increased behavioral intentions and sustainable choice preferences compared to static approaches. The beluga whale character demonstrated consistently stronger emotional engagement across multiple measures, including perceived anthropomorphism and empathy. However, impacts on deeper measures like climate policy support and psychological distance were limited, highlighting the complexity of shifting entrenched beliefs. Our work extends research on sustainability interfaces facilitating PEB and offers design principles for creating emotionally resonant, context-aware AI characters. By balancing anthropomorphism with species authenticity, OceanChat demonstrates how interactive narratives can bridge the gap between environmental knowledge and real-world behavior change.

A Data-Efficient Pan-Tumor Foundation Model for Oncology CT Interpretation

Artificial intelligence-assisted imaging analysis has made substantial strides in tumor diagnosis and management. Here we present PASTA, a pan-tumor CT foundation model that achieves state-of-the-art performance on 45 of 46 representative oncology tasks -- including lesion segmentation, tumor detection in plain CT, tumor staging, survival prediction, structured report generation, and cross-modality transfer learning, significantly outperforming the second-best models on 35 tasks. This remarkable advancement is driven by our development of PASTA-Gen, an innovative synthetic tumor generation framework that produces a comprehensive dataset of 30,000 CT scans with pixel-level annotated lesions and paired structured reports, encompassing malignancies across ten organs and five benign lesion types. By leveraging this rich, high-quality synthetic data, we overcome a longstanding bottleneck in the development of CT foundation models -- specifically, the scarcity of publicly available, high-quality annotated datasets due to privacy constraints and the substantial labor required for scaling precise data annotation. Encouragingly, PASTA demonstrates exceptional data efficiency with promising practical value, markedly improving performance on various tasks with only a small amount of real-world data. The open release of both the synthetic dataset and PASTA foundation model effectively addresses the challenge of data scarcity, thereby advancing oncological research and clinical translation.

Merging Feed-Forward Sublayers for Compressed Transformers

With the rise and ubiquity of larger deep learning models, the need for high-quality compression techniques is growing in order to deploy these models widely. The sheer parameter count of these models makes it difficult to fit them into the memory constraints of different hardware. In this work, we present a novel approach to model compression by merging similar parameter groups within a model, rather than pruning away less important parameters. Specifically, we select, align, and merge separate feed-forward sublayers in Transformer models, and test our method on language modeling, image classification, and machine translation. With our method, we demonstrate performance comparable to the original models while combining more than a third of model feed-forward sublayers, and demonstrate improved performance over a strong layer-pruning baseline. For instance, we can remove over 21% of total parameters from a Vision Transformer, while maintaining 99% of its original performance. Additionally, we observe that some groups of feed-forward sublayers exhibit high activation similarity, which may help explain their surprising mergeability.

Categorical Schrödinger Bridge Matching

The Schr\"odinger Bridge (SB) is a powerful framework for solving generative modeling tasks such as unpaired domain translation. Most SB-related research focuses on continuous data space $\mathbb{R}^{D}$ and leaves open theoretical and algorithmic questions about applying SB methods to discrete data, e.g, on finite spaces $\mathbb{S}^{D}$. Notable examples of such sets $\mathbb{S}$ are codebooks of vector-quantized (VQ) representations of modern autoencoders, tokens in texts, categories of atoms in molecules, etc. In this paper, we provide a theoretical and algorithmic foundation for solving SB in discrete spaces using the recently introduced Iterative Markovian Fitting (IMF) procedure. Specifically, we theoretically justify the convergence of discrete-time IMF (D-IMF) to SB in discrete spaces. This enables us to develop a practical computational algorithm for SB which we call Categorical Schr\"odinger Bridge Matching (CSBM). We show the performance of CSBM via a series of experiments with synthetic data and VQ representations of images.

CF-CGN: Channel Fingerprints Extrapolation for Multi-band Massive MIMO Transmission based on Cycle-Consistent Generative Networks

Multi-band massive multiple-input multiple-output (MIMO) communication can promote the cooperation of licensed and unlicensed spectra, effectively enhancing spectrum efficiency for Wi-Fi and other wireless systems. As an enabler for multi-band transmission, channel fingerprints (CF), also known as the channel knowledge map or radio environment map, are used to assist channel state information (CSI) acquisition and reduce computational complexity. In this paper, we propose CF-CGN (Channel Fingerprints with Cycle-consistent Generative Networks) to extrapolate CF for multi-band massive MIMO transmission where licensed and unlicensed spectra cooperate to provide ubiquitous connectivity. Specifically, we first model CF as a multichannel image and transform the extrapolation problem into an image translation task, which converts CF from one frequency to another by exploring the shared characteristics of statistical CSI in the beam domain. Then, paired generative networks are designed and coupled by variable-weight cycle consistency losses to fit the reciprocal relationship at different bands. Matched with the coupled networks, a joint training strategy is developed accordingly, supporting synchronous optimization of all trainable parameters. During the inference process, we also introduce a refining scheme to improve the extrapolation accuracy based on the resolution of CF. Numerical results illustrate that our proposed CF-CGN can achieve bidirectional extrapolation with an error of 5-17 dB lower than the benchmarks in different communication scenarios, demonstrating its excellent generalization ability. We further show that the sum rate performance assisted by CF-CGN-based CF is close to that with perfect CSI for multi-band massive MIMO transmission.