Spatial reasoning is a fundamental aspect of human cognition, enabling intuitive understanding and manipulation of objects in three-dimensional space. While foundation models demonstrate remarkable performance on some benchmarks, they still struggle with 3D reasoning tasks like arranging objects in space according to open-ended language instructions, particularly in dense and physically constrained environments. We introduce LayoutVLM, a framework and scene layout representation that exploits the semantic knowledge of Vision-Language Models (VLMs) and supports differentiable optimization to ensure physical plausibility. LayoutVLM employs VLMs to generate two mutually reinforcing representations from visually marked images, and a self-consistent decoding process to improve VLMs spatial planning. Our experiments show that LayoutVLM addresses the limitations of existing LLM and constraint-based approaches, producing physically plausible 3D layouts better aligned with the semantic intent of input language instructions. We also demonstrate that fine-tuning VLMs with the proposed scene layout representation extracted from existing scene datasets can improve their reasoning performance.

Explainable AI (XAI) has gained significant attention for providing insights into the decision-making processes of deep learning models, particularly for image classification tasks through saliency-based visual explanations. Despite their success, key challenges persist due to the scarcity of annotated datasets and the absence of standardized evaluation protocols. In this paper, we introduce Saliency-Bench, a novel benchmark designed to evaluate visual explanations generated by saliency methods across multiple datasets. We curated, constructed, and annotated eight datasets, each covering diverse tasks such as scene classification, cancer diagnosis, object classification, and action classification, with corresponding ground-truth explanation annotations. The benchmark includes a standardized and unified evaluation pipeline for assessing faithfulness and alignment of the visual explanation, providing a holistic visual explanation performance assessment. We benchmark these eight datasets with widely used saliency methods on different image classifier architectures to evaluate explanation quality. Additionally, we developed an user-friendly toolkit for automating the evaluation pipeline, from data accessing, and data loading, to result evaluation. The benchmark is available at https://github.com/XAIdataset/XAIdataset.github.io.

Geometric diffusion models have shown remarkable success in molecular dynamics and structure generation. However, efficiently fine-tuning them for downstream tasks with varying geometric controls remains underexplored. In this work, we propose an SE(3)-equivariant adapter framework (GeoAda) that enables flexible and parameter-efficient fine-tuning for controlled generative tasks without modifying the original model architecture. GeoAda introduces a structured adapter design: control signals are first encoded through coupling operators, then processed by a trainable copy of selected base model layers, and finally projected back via decoupling operators followed by an equivariant zero-initialized convolution. By fine-tuning only these lightweight adapter modules, GeoAda preserves the model’s geometric consistency while mitigating overfitting and catastrophic forgetting. We theoretically prove that the proposed adapters maintain SE(3)-equivariance, ensuring that the geometric inductive biases of the pretrained diffusion model remain intact during adaptation. We demonstrate the wide applicability of \method across diverse geometric control types, including frame control, global control, subgraph control, and a broad range of application domains such as particle dynamics, molecular dynamics, human motion prediction, and molecule generation. Empirical results show that GeoAda achieves state-of-the-art fine-tuning performance while preserving original task accuracy, whereas other baselines experience significant performance degradation due to overfitting and catastrophic forgetting.

Explanation supervision aims to enhance deep learning models by integrating additional signals to guide the generation of model explanations, showcasing notable improvements in both the predictability and explainability of the model. However, the application of explanation supervision to higher-dimensional data, such as 3D medical images, remains an under-explored domain. Challenges associated with supervising visual explanations in the presence of an additional dimension include: 1) spatial correlation changed, 2) lack of direct 3D annotations, and 3) uncertainty varies across different parts of the explanation. To address these challenges, we propose a Dynamic Uncertainty-aware Explanation supervision (DUE) framework for 3D explanation supervision that ensures uncertainty-aware explanation guidance when dealing with sparsely annotated 3D data with diffusion-based 3D interpolation. Our proposed framework is validated through comprehensive experiments on diverse real-world medical imaging datasets. The results demonstrate the effectiveness of our framework in enhancing the predictability and explainability of deep learning models in the context of medical imaging diagnosis applications.

Generating ligand molecules for specific protein targets, known as structure-based drug design, is a fundamental problem in therapeutics development and biological discovery. Recently, target-aware generative models, especially diffusion models, have shown great promise in modeling protein-ligand interactions and generating candidate drugs. However, existing models primarily focus on learning the chemical distribution of all drug candidates, which lacks effective steerability on the chemical quality of model generations. In this paper, we propose a novel and general alignment framework to align pretrained target diffusion models with preferred functional properties, named AliDiff. AliDiff shifts the target-conditioned chemical distribution towards regions with higher binding affinity and structural rationality, specified by user-defined reward functions, via the preference optimization approach. To avoid the overfitting problem in common preference optimization objectives, we further develop an improved Exact Energy Preference Optimization method to yield an exact and efficient alignment of the diffusion models, and provide the closed-form expression for the converged distribution. Empirical studies on the CrossDocked2020 benchmark show that AliDiff can generate molecules with state-of-the-art binding energies with up to -7.07 Avg. Vina Score, while maintaining strong molecular properties. Code is available at https://github.com/MinkaiXu/AliDiff.

Explanation supervision is a technique in which the model is guided by human-generated explanations during training. This technique aims to improve the predictability of the model by incorporating human understanding of the prediction process into the training phase. This is a challenging task since it relies on the accuracy of human annotation labels. To obtain high-quality explanation annotations, using multiple annotations to do explanation supervision is a reasonable method. However, how to use multiple annotations to improve accuracy is particularly challenging due to the following: 1) The noisiness of annotations from different annotators; 2) The lack of pre-given information about the corresponding relationship between annotations and annotators; 3) Missing annotations since some images are not labeled by all annotators. To solve these challenges, we propose a Multi-annotated explanation-guided learning (MAGI) framework to do explanation supervision with comprehensive and high-quality generated annotations. We first propose a novel generative model to generate annotations from all annotators and infer them using a newly proposed variational inference-based technique by learning the characteristics of each annotator. We also incorporate an alignment mechanism into the generative model to infer the correspondence between annotations and annotators in the training process. Extensive experiments on two datasets from the medical imaging domain demonstrate the effectiveness of our proposed framework in handling noisy annotations while obtaining superior prediction performance compared with previous SOTA.

Inter-component communication (ICC) is a key mechanism in Android. It utilizes intents to achieve the communications between different components in the apps. Thus, the successful execution of ICCs (named ICC calls) is fundamental to the app operations. However, existing testing tools for Android seldom explicitly consider these ICC calls, which may fail to find those ICC-related bugs. To this end, we propose a novel ICC-guided exploration strategy to effectively find the ICC-related bugs. Our idea is that, we can (1) build an ICC call graph from the app under test, and (2) use this graph to guide the exploration toward exercising the ICC calls. To achieve this idea, we design this ICC-guided exploration strategy based on Q-learning, a classic reinforcement learning algorithm. Specifically, the reward function explicitly considers the number of explored intents, the number of promising-to-explore intents and the exploration order of explored intents to improve testing effectiveness. Moreover, to build a more complete ICC call graph, we design a graph enhancement exploration strategy also based on Q-learning to complement the call graph construction via static analysis. We have implemented our idea as an automated testing tool IccDroid. The evaluation on 28 real-word Android apps shows that IccDroid can effectively find the most number of ICC-related bugs within the same testing time, compared to existing testing tools — the bugs found by IccDroid are 1.7~2.7 times more than the others. So far, IccDroid has found 13 previously unknown ICC-related bugs, all of which have been confirmed by the app developers and five have already been fixed.

Explanation supervision is a technique in which the model is guided by human-generated explanations during training. This technique aims to improve both the interpretability and predictability of the model by incorporating human understanding into the training process. Since explanation supervision requires a large scale of training data, the data augmentation technique is necessary to be applied to increase the size and diversity of the original dataset. However, data augmentation on sophisticated data like medical images is particularly challenging due to the following: 1) scarcity of data in training the learning-based data augmenter, 2) difficulty in generating realistic and sophisticated images, and 3) difficulty in ensuring the augmented data indeed boosts the performance of explanation-guided learning. To solve these challenges, we propose an Explanation Iterative Supervision via Saliency-guided Data Augmentation (ESSA) framework for conducting explanation supervision and adversarial-trained image data augmentation via a synergized iterative loop that handles the translation from annotation to sophisticated images and the generation of synthetic image-annotation pairs with an alternating training strategy. Extensive experiments on two datasets from the medical imaging domain demonstrate the effectiveness of our proposed framework in improving both the predictability and explainability of the model.

Despite the fast progress of explanation techniques in modern Deep Neural Networks (DNNs) where the main focus is handling "how to generate the explanations", advanced research questions that examine the quality of the explanation itself (e.g., "whether the explanations are accurate") and improve the explanation quality (e.g., "how to adjust the model to generate more accurate explanations when explanations are inaccurate") are still relatively under-explored. To guide the model toward better explanations, techniques in explanation supervision - which add supervision signals on the model explanation - have started to show promising effects on improving both the generalizability as and intrinsic interpretability of Deep Neural Networks. However, the research on supervising explanations, especially in vision-based applications represented through saliency maps, is in its early stage due to several inherent challenges: 1) inaccuracy of the human explanation annotation boundary, 2) incompleteness of the human explanation annotation region, and 3) inconsistency of the data distribution between human annotation and model explanation maps. To address the challenges, we propose a generic RES framework for guiding visual explanation by developing a novel objective that handles inaccurate boundary, incomplete region, and inconsistent distribution of human annotations, with a theoretical justification on model generalizability. Extensive experiments on two real-world image datasets demonstrate the effectiveness of the proposed framework on enhancing both the reasonability of the explanation and the performance of the backbone DNNs model.