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 Deep Learning


A Graph-in-Graph Learning Framework for Drug-Target Interaction Prediction

arXiv.org Artificial Intelligence

Accurately predicting drug-target interactions (DTIs) is pivotal for advancing drug discovery and target validation techniques. While machine learning approaches including those that are based on Graph Neural Networks (GNN) have achieved notable success in DTI prediction, many of them have difficulties in effectively integrating the diverse features of drugs, targets and their interactions. To address this limitation, we introduce a novel framework to take advantage of the power of both transductive learning and inductive learning so that features at molecular level and drug-target interaction network level can be exploited. Within this framework is a GNN-based model called Graph-in-Graph (GiG) that represents graphs of drug and target molecular structures as meta-nodes in a drug-target interaction graph, enabling a detailed exploration of their intricate relationships. To evaluate the proposed model, we have compiled a special benchmark comprising drug SMILES, protein sequences, and their interaction data, which is interesting in its own right. Our experimental results demonstrate that the GiG model significantly outperforms existing approaches across all evaluation metrics, highlighting the benefits of integrating different learning paradigms and interaction data.


ArtifactsBench: Bridging the Visual-Interactive Gap in LLM Code Generation Evaluation

arXiv.org Artificial Intelligence

The generative capabilities of Large Language Models (LLMs) are rapidly expanding from static code to dynamic, interactive visual artifacts. This progress is bottlenecked by a critical evaluation gap: established benchmarks focus on algorithmic correctness and are blind to the visual fidelity and interactive integrity that define modern user experiences. To bridge this gap, we introduce ArtifactsBench, a new benchmark and paradigm for the automated, multimodal evaluation of visual code generation. Our framework programmatically renders each generated artifact and captures its dynamic behavior through temporal screenshots. This visual evidence, alongside the source code, is then assessed by a Multimodal LLM (MLLM)-as-Judge, which is rigorously guided by a fine-grained, per-task checklist to ensure holistic and reproducible scoring. We construct a new benchmark of 1,825 diverse tasks and evaluate over 30 leading LLMs. Our automated evaluation achieves a striking 94.4% ranking consistency with WebDev Arena, the gold-standard for human preference in web development, and over 90% pairwise agreement with human experts. This establishes ArtifactsBench as the first framework to reliably automate the assessment of human-perceived quality at scale. Our analysis provides a high-resolution map of the current SOTA, revealing that generalist models often outperform domain-specific ones. We open-source ArtifactsBench, including the benchmark, evaluation harness, and baseline results at https://artifactsbenchmark.github.io/, to provide the community with a scalable and accurate tool to accelerate the development of user-centric generative models.


Evaluating Compliance with Visualization Guidelines in Diagrams for Scientific Publications Using Large Vision Language Models

arXiv.org Artificial Intelligence

Diagrams are widely used to visualize data in publications. The research field of data visualization deals with defining principles and guidelines for the creation and use of these diagrams, which are often not known or adhered to by researchers, leading to misinformation caused by providing inaccurate or incomplete information. In this work, large Vision Language Models (VLMs) are used to analyze diagrams in order to identify potential problems in regards to selected data visualization principles and guidelines. To determine the suitability of VLMs for these tasks, five open source VLMs and five prompting strategies are compared using a set of questions derived from selected data visualization guidelines. The results show that the employed VLMs work well to accurately analyze diagram types (F1-score 82.49 %), 3D effects (F1-score 98.55 %), axes labels (F1-score 76.74 %), lines (RMSE 1.16), colors (RMSE 1.60) and legends (F1-score 96.64 %, RMSE 0.70), while they cannot reliably provide feedback about the image quality (F1-score 0.74 %) and tick marks/labels (F1-score 46.13 %). Among the employed VLMs, Qwen2.5VL performs best, and the summarizing prompting strategy performs best for most of the experimental questions. It is shown that VLMs can be used to automatically identify a number of potential issues in diagrams, such as missing axes labels, missing legends, and unnecessary 3D effects. The approach laid out in this work can be extended for further aspects of data visualization.


GRAF: Multi-turn Jailbreaking via Global Refinement and Active Fabrication

arXiv.org Artificial Intelligence

Large Language Models (LLMs) have demonstrated remarkable performance across diverse tasks. Nevertheless, they still pose notable safety risks due to potential misuse for malicious purposes. Jailbreaking, which seeks to induce models to generate harmful content through single-turn or multi-turn attacks, plays a crucial role in uncovering underlying security vulnerabilities. However, prior methods, including sophisticated multi-turn approaches, often struggle to adapt to the evolving dynamics of dialogue as interactions progress. To address this challenge, we propose \ours (JailBreaking via \textbf{G}lobally \textbf{R}efining and \textbf{A}daptively \textbf{F}abricating), a novel multi-turn jailbreaking method that globally refines the attack trajectory at each interaction. In addition, we actively fabricate model responses to suppress safety-related warnings, thereby increasing the likelihood of eliciting harmful outputs in subsequent queries. Extensive experiments across six state-of-the-art LLMs demonstrate the superior effectiveness of our approach compared to existing single-turn and multi-turn jailbreaking methods. Our code will be released at https://github.com/Ytang520/Multi-Turn_jailbreaking_Global-Refinment_and_Active-Fabrication.


Reward-Agnostic Prompt Optimization for Text-to-Image Diffusion Models

arXiv.org Artificial Intelligence

We investigate a general approach for improving user prompts in text-to-image (T2I) diffusion models by finding prompts that maximize a reward function specified at test-time. Although diverse reward models are used for evaluating image generation, existing automated prompt engineering methods typically target specific reward configurations. Consequently, these specialized designs exhibit suboptimal performance when applied to new prompt engineering scenarios involving different reward models. To address this limitation, we introduce RATTPO (Reward-Agnostic Test-Time Prompt Optimization), a flexible test-time optimization method applicable across various reward scenarios without modification. RATTPO iteratively searches for optimized prompts by querying large language models (LLMs) \textit{without} requiring reward-specific task descriptions. Instead, it uses the optimization trajectory and a novel reward-aware feedback signal (termed a "hint") as context. Empirical results demonstrate the versatility of RATTPO, effectively enhancing user prompts across diverse reward setups that assess various generation aspects, such as aesthetics, general human preference, or spatial relationships between objects. RATTPO surpasses other test-time search baselines in search efficiency, running 4.8 times faster than naive reward-agnostic test-time search baseline on average. Furthermore, with sufficient inference budget, it can achieve comparable performance to learning-based baselines that require reward-specific fine-tuning. The code is available at https://github.com/seminkim/RATTPO.


FindingDory: A Benchmark to Evaluate Memory in Embodied Agents

arXiv.org Artificial Intelligence

Large vision-language models have recently demonstrated impressive performance in planning and control tasks, driving interest in their application to real-world robotics. However, deploying these models for reasoning in embodied contexts is limited by their ability to incorporate long-term experience collected across multiple days and represented by vast collections of images. Current VLMs typically struggle to process more than a few hundred images concurrently, highlighting the need for more efficient mechanisms to handle long-term memory in embodied settings. To effectively evaluate these models for long-horizon control, a benchmark must specifically target scenarios where memory is crucial for success. Existing long-video QA benchmarks overlook embodied challenges like object manipulation and navigation, which demand low-level skills and fine-grained reasoning over past interactions. Moreover, effective memory integration in embodied agents involves both recalling relevant historical information and executing actions based on that information, making it essential to study these aspects together rather than in isolation. In this work, we introduce a new benchmark for long-range embodied tasks in the Habitat simulator. This benchmark evaluates memory-based capabilities across 60 tasks requiring sustained engagement and contextual awareness in an environment. The tasks can also be procedurally extended to longer and more challenging versions, enabling scalable evaluation of memory and reasoning. We also present baselines that integrate state-of-the-art VLMs with low level navigation policies, assessing their performance on these memory-intensive tasks and highlight areas for improvement.


StorySage: Conversational Autobiography Writing Powered by a Multi-Agent Framework

arXiv.org Artificial Intelligence

Every individual carries a unique and personal life story shaped by their memories and experiences. However, these memories are often scattered and difficult to organize into a coherent narrative, a challenge that defines the task of autobiography writing. Existing conversational writing assistants tend to rely on generic user interactions and pre-defined guidelines, making it difficult for these systems to capture personal memories and develop a complete biography over time. We introduce StorySage, a user-driven software system designed to meet the needs of a diverse group of users that supports a flexible conversation and a structured approach to autobiography writing. Powered by a multi-agent framework composed of an Interviewer, Session Scribe, Planner, Section Writer, and Session Coordinator, our system iteratively collects user memories, updates their autobiography, and plans for future conversations. In experimental simulations, StorySage demonstrates its ability to navigate multiple sessions and capture user memories across many conversations. User studies (N=28) highlight how StorySage maintains improved conversational flow, narrative completeness, and higher user satisfaction when compared to a baseline. In summary, StorySage contributes both a novel architecture for autobiography writing and insights into how multi-agent systems can enhance human-AI creative partnerships.


Foundation Models for Causal Inference via Prior-Data Fitted Networks

arXiv.org Artificial Intelligence

Prior-data fitted networks (PFNs) have recently been proposed as a promising way to train tabular foundation models. PFNs are transformers that are pre-trained on synthetic data generated from a prespecified prior distribution and that enable Bayesian inference through in-context learning. In this paper, we introduce CausalFM, a comprehensive framework for training PFN-based foundation models in various causal inference settings. First, we formalize the construction of Bayesian priors for causal inference based on structural causal models (SCMs) in a principled way and derive necessary criteria for the validity of such priors. Building on this, we propose a novel family of prior distributions using causality-inspired Bayesian neural networks that enable CausalFM to perform Bayesian causal inference in various settings, including for back-door, front-door, and instrumental variable adjustment. Finally, we instantiate CausalFM and explicitly train models to perform in-context learning in these settings. We show that CausalFM achieves competitive in-context learning performance even when compared to baselines that are specifically trained for the task at hand. In sum, our framework can be used as a general recipe to train foundation models for various causal inference settings. In contrast to the current state-of-the-art in causal inference, CausalFM offers a novel paradigm with the potential to fundamentally change how practitioners perform causal inference in medicine, economics, and other disciplines.


ReCogDrive: A Reinforced Cognitive Framework for End-to-End Autonomous Driving

arXiv.org Artificial Intelligence

Recent studies have explored leveraging the world knowledge and cognitive capabilities of Vision-Language Models (VLMs) to address the long-tail problem in end-to-end autonomous driving. However, existing methods typically formulate trajectory planning as a language modeling task, where physical actions are output in the language space, potentially leading to issues such as format-violating outputs, infeasible actions, and slow inference speeds. In this paper, we propose ReCogDrive, a novel Reinforced Cognitive framework for end-to-end autonomous Driving, unifying driving understanding and planning by integrating an autoregressive model with a diffusion planner. First, to instill human driving cognition into the VLM, we introduce a hierarchical data pipeline that mimics the sequential cognitive process of human drivers through three stages: generation, refinement, and quality control. Building on this cognitive foundation, we then address the language-action mismatch by injecting the VLM's learned driving priors into a diffusion planner to efficiently generate continuous and stable trajectories. Furthermore, to enhance driving safety and reduce collisions, we introduce a Diffusion Group Relative Policy Optimization (DiffGRPO) stage, reinforcing the planner for enhanced safety and comfort. Extensive experiments on the NAVSIM and Bench2Drive benchmarks demonstrate that ReCogDrive achieves state-of-the-art performance. Additionally, qualitative results across diverse driving scenarios and DriveBench highlight the model's scene comprehension. All code, model weights, and datasets will be made publicly available to facilitate subsequent research.


Towards Better Generalization via Distributional Input Projection Network

arXiv.org Artificial Intelligence

As overparameterized models become increasingly prevalent, training loss alone offers limited insight into generalization performance. While smoothness has been linked to improved generalization across various settings, directly enforcing smoothness in neural networks remains challenging. To address this, we introduce Distributional Input Projection Networks (DIPNet), a novel framework that projects inputs into learnable distributions at each layer. This distributional representation induces a smoother loss landscape with respect to the input, promoting better generalization. We provide theoretical analysis showing that DIPNet reduces both local smoothness measures and the Lipschitz constant of the network, contributing to improved generalization performance. Empirically, we validate DIPNet across a wide range of architectures and tasks, including Vision Transformers (ViTs), Large Language Models (LLMs), ResNet and MLPs. Our method consistently enhances test performance under standard settings, adversarial attacks, out-of-distribution inputs, and reasoning benchmarks. We demonstrate that the proposed input projection strategy can be seamlessly integrated into existing models, providing a general and effective approach for boosting generalization performance in modern deep learning.