VQSynery: Robust Drug Synergy Prediction With Vector Quantization Mechanism

The pursuit of optimizing cancer therapies is significantly advanced by the accurate prediction of drug synergy. Traditional methods, such as clinical trials, are reliable yet encumbered by extensive time and financial demands. The emergence of high-throughput screening and computational innovations has heralded a shift towards more efficient methodologies for exploring drug interactions. In this study, we present VQSynergy, a novel framework that employs the Vector Quantization (VQ) mechanism, integrated with gated residuals and a tailored attention mechanism, to enhance the precision and generalizability of drug synergy predictions. Our findings demonstrate that VQSynergy surpasses existing models in terms of robustness, particularly under Gaussian noise conditions, highlighting its superior performance and utility in the complex and often noisy domain of drug synergy research. This study underscores the potential of VQSynergy in revolutionizing the field through its advanced predictive capabilities, thereby contributing to the optimization of cancer treatment strategies.

Uncertainty-Based Extensible Codebook for Discrete Federated Learning in Heterogeneous Data Silos

Federated learning (FL), aimed at leveraging vast distributed datasets, confronts a crucial challenge: the heterogeneity of data across different silos. While previous studies have explored discrete representations to enhance model generalization across minor distributional shifts, these approaches often struggle to adapt to new data silos with significantly divergent distributions. In response, we have identified that models derived from FL exhibit markedly increased uncertainty when applied to data silos with unfamiliar distributions. Consequently, we propose an innovative yet straightforward iterative framework, termed Uncertainty-Based Extensible-Codebook Federated Learning (UEFL). This framework dynamically maps latent features to trainable discrete vectors, assesses the uncertainty, and specifically extends the discretization dictionary or codebook for silos exhibiting high uncertainty. Our approach aims to simultaneously enhance accuracy and reduce uncertainty by explicitly addressing the diversity of data distributions, all while maintaining minimal computational overhead in environments characterized by heterogeneous data silos. Through experiments conducted on five datasets, our method has demonstrated its superiority, achieving significant improvements in accuracy (by 3%--22.1%) and uncertainty reduction (by 38.83%--96.24%), thereby outperforming contemporary state-of-the-art methods. The source code is available at https://github.com/destiny301/uefl.

Unsupervised Concept Discovery Mitigates Spurious Correlations

Models prone to spurious correlations in training data often produce brittle predictions and introduce unintended biases. Addressing this challenge typically involves methods relying on prior knowledge and group annotation to remove spurious correlations, which may not be readily available in many applications. In this paper, we establish a novel connection between unsupervised object-centric learning and mitigation of spurious correlations. Instead of directly inferring sub-groups with varying correlations with labels, our approach focuses on discovering concepts: discrete ideas that are shared across input samples. Leveraging existing object-centric representation learning, we introduce CoBalT: a concept balancing technique that effectively mitigates spurious correlations without requiring human labeling of subgroups. Evaluation across the Waterbirds, CelebA and ImageNet-9 benchmark datasets for subpopulation shifts demonstrate superior or competitive performance compared state-of-the-art baselines, without the need for group annotation.

BarlowTwins-CXR : Enhancing Chest X-Ray abnormality localization in heterogeneous data with cross-domain self-supervised learning

Background: Chest X-ray imaging-based abnormality localization, essential in diagnosing various diseases, faces significant clinical challenges due to complex interpretations and the growing workload of radiologists. While recent advances in deep learning offer promising solutions, there is still a critical issue of domain inconsistency in cross-domain transfer learning, which hampers the efficiency and accuracy of diagnostic processes. This study aims to address the domain inconsistency problem and improve autonomic abnormality localization performance of heterogeneous chest X-ray image analysis, by developing a self-supervised learning strategy called "BarlwoTwins-CXR". Methods: We utilized two publicly available datasets: the NIH Chest X-ray Dataset and the VinDr-CXR. The BarlowTwins-CXR approach was conducted in a two-stage training process. Initially, self-supervised pre-training was performed using an adjusted Barlow Twins algorithm on the NIH dataset with a Resnet50 backbone pre-trained on ImageNet. This was followed by supervised fine-tuning on the VinDr-CXR dataset using Faster R-CNN with Feature Pyramid Network (FPN). Results: Our experiments showed a significant improvement in model performance with BarlowTwins-CXR. The approach achieved a 3% increase in mAP50 accuracy compared to traditional ImageNet pre-trained models. In addition, the Ablation CAM method revealed enhanced precision in localizing chest abnormalities. Conclusion: BarlowTwins-CXR significantly enhances the efficiency and accuracy of chest X-ray image-based abnormality localization, outperforming traditional transfer learning methods and effectively overcoming domain inconsistency in cross-domain scenarios. Our experiment results demonstrate the potential of using self-supervised learning to improve the generalizability of models in medical settings with limited amounts of heterogeneous data.

Evolution Guided Generative Flow Networks

Generative Flow Networks (GFlowNets) are a family of probabilistic generative models that learn to sample compositional objects proportional to their rewards. One big challenge of GFlowNets is training them effectively when dealing with long time horizons and sparse rewards. To address this, we propose Evolution guided generative flow networks (EGFN), a simple but powerful augmentation to the GFlowNets training using Evolutionary algorithms (EA). Our method can work on top of any GFlowNets training objective, by training a set of agent parameters using EA, storing the resulting trajectories in the prioritized replay buffer, and training the GFlowNets agent using the stored trajectories. We present a thorough investigation over a wide range of toy and real-world benchmark tasks showing the effectiveness of our method in handling long trajectories and sparse rewards.

Discrete Messages Improve Communication Efficiency among Isolated Intelligent Agents

Individuals, despite having varied life experiences and learning processes, can communicate effectively through languages. This study aims to explore the efficiency of language as a communication medium. We put forth two specific hypotheses: First, discrete messages are more effective than continuous ones when agents have diverse personal experiences. Second, communications using multiple discrete tokens are more advantageous than those using a single token. To valdate these hypotheses, we designed multi-agent machine learning experiments to assess communication efficiency using various information transmission methods between speakers and listeners. Our empirical findings indicate that, in scenarios where agents are exposed to different data, communicating through sentences composed of discrete tokens offers the best inter-agent communication efficiency. The limitations of our finding include lack of systematic advantages over other more sophisticated encoder-decoder model such as variational autoencoder and lack of evluation on non-image dataset, which we will leave for future studies.

Physical Reasoning and Object Planning for Household Embodied Agents

In this study, we explore the sophisticated domain of task planning for robust household embodied agents, with a particular emphasis on the intricate task of selecting substitute objects. We introduce the CommonSense Object Affordance Task (COAT), a novel framework designed to analyze reasoning capabilities in commonsense scenarios. This approach is centered on understanding how these agents can effectively identify and utilize alternative objects when executing household tasks, thereby offering insights into the complexities of practical decision-making in real-world environments.Drawing inspiration from human decision-making, we explore how large language models tackle this challenge through three meticulously crafted commonsense question-and-answer datasets, featuring refined rules and human annotations. Our evaluation of state-of-the-art language models on these datasets sheds light on three pivotal considerations: 1) aligning an object's inherent utility with the task at hand, 2) navigating contextual dependencies (societal norms, safety, appropriateness, and efficiency), and 3) accounting for the current physical state of the object. To maintain accessibility, we introduce five abstract variables reflecting an object's physical condition, modulated by human insights to simulate diverse household scenarios. Our contributions include insightful Object-Utility mappings addressing the first consideration and two extensive QA datasets (15k and 130k questions) probing the intricacies of contextual dependencies and object states. The datasets, along with our findings, are accessible at: \url{https://github.com/com-phy-affordance/COAT}. This research not only advances our understanding of physical commonsense reasoning in language models but also paves the way for future improvements in household agent intelligence.

Probabilistic Generative Modeling for Procedural Roundabout Generation for Developing Countries

Due to limited resources and fast economic growth, designing optimal transportation road networks with traffic simulation and validation in a cost-effective manner is vital for developing countries, where extensive manual testing is expensive and often infeasible. Current rule-based road design generators lack diversity, a key feature for design robustness. Generative Flow Networks (GFlowNets) learn stochastic policies to sample from an unnormalized reward distribution, thus generating high-quality solutions while preserving their diversity. In this work, we formulate the problem of linking incident roads to the circular junction of a roundabout by a Markov decision process, and we leverage GFlowNets as the Junction-Art road generator. We compare our method with related methods and our empirical results show that our method achieves better diversity while preserving a high validity score.