Fragment-Masked Molecular Optimization

Molecular optimization is a crucial aspect of drug discovery, aimed at refining molecular structures to enhance drug efficacy and minimize side effects, ultimately accelerating the overall drug development process. Many target-based molecular optimization methods have been proposed, significantly advancing drug discovery. These methods primarily on understanding the specific drug target structures or their hypothesized roles in combating diseases. However, challenges such as a limited number of available targets and a difficulty capturing clear structures hinder innovative drug development. In contrast, phenotypic drug discovery (PDD) does not depend on clear target structures and can identify hits with novel and unbiased polypharmacology signatures. As a result, PDD-based molecular optimization can reduce potential safety risks while optimizing phenotypic activity, thereby increasing the likelihood of clinical success. Therefore, we propose a fragment-masked molecular optimization method based on PDD (FMOP). FMOP employs a regression-free diffusion model to conditionally optimize the molecular masked regions without training, effectively generating new molecules with similar scaffolds. On the large-scale drug response dataset GDSCv2, we optimize the potential molecules across all 945 cell lines. The overall experiments demonstrate that the in-silico optimization success rate reaches 94.4%, with an average efficacy increase of 5.3%. Additionally, we conduct extensive ablation and visualization experiments, confirming that FMOP is an effective and robust molecular optimization method. The code is available at:https://anonymous.4open.science/r/FMOP-98C2.

TextIM: Part-aware Interactive Motion Synthesis from Text

In this work, we propose TextIM, a novel framework for synthesizing TEXT-driven human Interactive Motions, with a focus on the precise alignment of part-level semantics. Existing methods often overlook the critical roles of interactive body parts and fail to adequately capture and align part-level semantics, resulting in inaccuracies and even erroneous movement outcomes. To address these issues, TextIM utilizes a decoupled conditional diffusion framework to enhance the detailed alignment between interactive movements and corresponding semantic intents from textual descriptions. Our approach leverages large language models, functioning as a human brain, to identify interacting human body parts and to comprehend interaction semantics to generate complicated and subtle interactive motion. Guided by the refined movements of the interacting parts, TextIM further extends these movements into a coherent whole-body motion. We design a spatial coherence module to complement the entire body movements while maintaining consistency and harmony across body parts using a part graph convolutional network. For training and evaluation, we carefully selected and re-labeled interactive motions from HUMANML3D to develop a specialized dataset. Experimental results demonstrate that TextIM produces semantically accurate human interactive motions, significantly enhancing the realism and applicability of synthesized interactive motions in diverse scenarios, even including interactions with deformable and dynamically changing objects.

Dual-perspective Cross Contrastive Learning in Graph Transformers

Graph contrastive learning (GCL) is a popular method for leaning graph representations by maximizing the consistency of features across augmented views. Traditional GCL methods utilize single-perspective i.e. data or model-perspective) augmentation to generate positive samples, restraining the diversity of positive samples. In addition, these positive samples may be unreliable due to uncontrollable augmentation strategies that potentially alter the semantic information. To address these challenges, this paper proposed a innovative framework termed dual-perspective cross graph contrastive learning (DC-GCL), which incorporates three modifications designed to enhance positive sample diversity and reliability: 1) We propose dual-perspective augmentation strategy that provide the model with more diverse training data, enabling the model effective learning of feature consistency across different views. 2) From the data perspective, we slightly perturb the original graphs using controllable data augmentation, effectively preserving their semantic information. 3) From the model perspective, we enhance the encoder by utilizing more powerful graph transformers instead of graph neural networks. Based on the model's architecture, we propose three pruning-based strategies to slightly perturb the encoder, providing more reliable positive samples. These modifications collectively form the DC-GCL's foundation and provide more diverse and reliable training inputs, offering significant improvements over traditional GCL methods. Extensive experiments on various benchmarks demonstrate that DC-GCL consistently outperforms different baselines on various datasets and tasks.

Multi-modal Latent Space Learning for Chain-of-Thought Reasoning in Language Models

Chain-of-thought (CoT) reasoning has exhibited impressive performance in language models for solving complex tasks and answering questions. However, many real-world questions require multi-modal information, such as text and images. Previous research on multi-modal CoT has primarily focused on extracting fixed image features from off-the-shelf vision models and then fusing them with text using attention mechanisms. This approach has limitations because these vision models were not designed for complex reasoning tasks and do not align well with language thoughts. To overcome this limitation, we introduce a novel approach for multi-modal CoT reasoning that utilizes latent space learning via diffusion processes to generate effective image features that align with language thoughts. Our method fuses image features and text representations at a deep level and improves the complex reasoning ability of multi-modal CoT. We demonstrate the efficacy of our proposed method on multi-modal ScienceQA and machine translation benchmarks, achieving state-of-the-art performance on ScienceQA. Overall, our approach offers a more robust and effective solution for multi-modal reasoning in language models, enhancing their ability to tackle complex real-world problems.

Enhancing Visually-Rich Document Understanding via Layout Structure Modeling

In recent years, the use of multi-modal pre-trained Transformers has led to significant advancements in visually-rich document understanding. However, existing models have mainly focused on features such as text and vision while neglecting the importance of layout relationship between text nodes. In this paper, we propose GraphLayoutLM, a novel document understanding model that leverages the modeling of layout structure graph to inject document layout knowledge into the model. GraphLayoutLM utilizes a graph reordering algorithm to adjust the text sequence based on the graph structure. Additionally, our model uses a layout-aware multi-head self-attention layer to learn document layout knowledge. The proposed model enables the understanding of the spatial arrangement of text elements, improving document comprehension. We evaluate our model on various benchmarks, including FUNSD, XFUND and CORD, and achieve state-of-the-art results among these datasets. Our experimental results demonstrate that our proposed method provides a significant improvement over existing approaches and showcases the importance of incorporating layout information into document understanding models. We also conduct an ablation study to investigate the contribution of each component of our model. The results show that both the graph reordering algorithm and the layout-aware multi-head self-attention layer play a crucial role in achieving the best performance.