Representation learning of drug and disease terms for drug repositioning

Drug repositioning (DR) refers to identification of novel indications for the approved drugs. The requirement of huge investment of time as well as money and risk of failure in clinical trials have led to surge in interest in drug repositioning. DR exploits two major aspects associated with drugs and diseases: existence of similarity among drugs and among diseases due to their shared involved genes or pathways or common biological effects. Existing methods of identifying drug-disease association majorly rely on the information available in the structured databases only. On the other hand, abundant information available in form of free texts in biomedical research articles are not being fully exploited. Word-embedding or obtaining vector representation of words from a large corpora of free texts using neural network methods have been shown to give significant performance for several natural language processing tasks. In this work we propose a novel way of representation learning to obtain features of drugs and diseases by combining complementary information available in unstructured texts and structured datasets. Next we use matrix completion approach on these feature vectors to learn projection matrix between drug and disease vector spaces. The proposed method has shown competitive performance with state-of-the-art methods. Further, the case studies on Alzheimer's and Hypertension diseases have shown that the predicted associations are matching with the existing knowledge.Comment: Accepted to appear in 3rd IEEE International Conference on Cybernetics (Spl Session: Deep Learning for Prediction and Estimation

GRAFENNE: Learning on Graphs with Heterogeneous and Dynamic Feature Sets

Graph neural networks (GNNs), in general, are built on the assumption of a static set of features characterizing each node in a graph. This assumption is often violated in practice. Existing methods partly address this issue through feature imputation. However, these techniques (i) assume uniformity of feature set across nodes, (ii) are transductive by nature, and (iii) fail to work when features are added or removed over time. In this work, we address these limitations through a novel GNN framework called GRAFENNE. GRAFENNE performs a novel allotropic transformation on the original graph, wherein the nodes and features are decoupled through a bipartite encoding. Through a carefully chosen message passing framework on the allotropic transformation, we make the model parameter size independent of the number of features and thereby inductive to both unseen nodes and features. We prove that GRAFENNE is at least as expressive as any of the existing message-passing GNNs in terms of Weisfeiler-Leman tests, and therefore, the additional inductivity to unseen features does not come at the cost of expressivity. In addition, as demonstrated over four real-world graphs, GRAFENNE empowers the underlying GNN with high empirical efficacy and the ability to learn in continual fashion over streaming feature sets.Comment: 17 pages, 4 figures and 9 tables. Accepted in ICML 2023, DOI will be updated once it is availabl

GSHOT: Few-shot Generative Modeling of Labeled Graphs

Deep graph generative modeling has gained enormous attraction in recent years due to its impressive ability to directly learn the underlying hidden graph distribution. Despite their initial success, these techniques, like much of the existing deep generative methods, require a large number of training samples to learn a good model. Unfortunately, large number of training samples may not always be available in scenarios such as drug discovery for rare diseases. At the same time, recent advances in few-shot learning have opened door to applications where available training data is limited. In this work, we introduce the hitherto unexplored paradigm of few-shot graph generative modeling. Towards this, we develop GSHOT, a meta-learning based framework for few-shot labeled graph generative modeling. GSHOT learns to transfer meta-knowledge from similar auxiliary graph datasets. Utilizing these prior experiences, GSHOT quickly adapts to an unseen graph dataset through self-paced fine-tuning. Through extensive experiments on datasets from diverse domains having limited training samples, we establish that GSHOT generates graphs of superior fidelity compared to existing baselines

NeuroCUT: A Neural Approach for Robust Graph Partitioning

Graph partitioning aims to divide a graph into $k$ disjoint subsets while optimizing a specific partitioning objective. The majority of formulations related to graph partitioning exhibit NP-hardness due to their combinatorial nature. As a result, conventional approximation algorithms rely on heuristic methods, sometimes with approximation guarantees and sometimes without. Unfortunately, traditional approaches are tailored for specific partitioning objectives and do not generalize well across other known partitioning objectives from the literature. To overcome this limitation, and learn heuristics from the data directly, neural approaches have emerged, demonstrating promising outcomes. In this study, we extend this line of work through a novel framework, NeuroCut. NeuroCut introduces two key innovations over prevailing methodologies. First, it is inductive to both graph topology and the partition count, which is provided at query time. Second, by leveraging a reinforcement learning based framework over node representations derived from a graph neural network, NeuroCut can accommodate any optimization objective, even those encompassing non-differentiable functions. Through empirical evaluation, we demonstrate that NeuroCut excels in identifying high-quality partitions, showcases strong generalization across a wide spectrum of partitioning objectives, and exhibits resilience to topological modifications

StriderNET: A Graph Reinforcement Learning Approach to Optimize Atomic Structures on Rough Energy Landscapes

Optimization of atomic structures presents a challenging problem, due to their highly rough and non-convex energy landscape, with wide applications in the fields of drug design, materials discovery, and mechanics. Here, we present a graph reinforcement learning approach, StriderNET, that learns a policy to displace the atoms towards low energy configurations. We evaluate the performance of StriderNET on three complex atomic systems, namely, binary Lennard-Jones particles, calcium silicate hydrates gel, and disordered silicon. We show that StriderNET outperforms all classical optimization algorithms and enables the discovery of a lower energy minimum. In addition, StriderNET exhibits a higher rate of reaching minima with energies, as confirmed by the average over multiple realizations. Finally, we show that StriderNET exhibits inductivity to unseen system sizes that are an order of magnitude different from the training system

Ten golden rules for optimal antibiotic use in hospital settings: the WARNING call to action

Antibiotics are recognized widely for their benefits when used appropriately. However, they are often used inappropriately despite the importance of responsible use within good clinical practice. Effective antibiotic treatment is an essential component of universal healthcare, and it is a global responsibility to ensure appropriate use. Currently, pharmaceutical companies have little incentive to develop new antibiotics due to scientific, regulatory, and financial barriers, further emphasizing the importance of appropriate antibiotic use. To address this issue, the Global Alliance for Infections in Surgery established an international multidisciplinary task force of 295 experts from 115 countries with different backgrounds. The task force developed a position statement called WARNING (Worldwide Antimicrobial Resistance National/International Network Group) aimed at raising awareness of antimicrobial resistance and improving antibiotic prescribing practices worldwide. The statement outlined is 10 axioms, or “golden rules,” for the appropriate use of antibiotics that all healthcare workers should consistently adhere in clinical practice

LIMIP: Lifelong Learning to Solve Mixed Integer Programs

Mixed Integer programs (MIPs) are typically solved by the Branch-and-Bound algorithm. Recently, Learning to imitate fast approximations of the expert strong branching heuristic has gained attention due to its success in reducing the running time for solving MIPs. However, existing learning-to-branch methods assume that the entire training data is available in a single session of training. This assumption is often not true, and if the training data is supplied in continual fashion over time, existing techniques suffer from catastrophic forgetting. In this work, we study the hitherto unexplored paradigm of Lifelong Learning to Branch on Mixed Integer Programs. To mitigate catastrophic forgetting, we propose LIMIP, which is powered by the idea of modeling an MIP instance in the form of a bipartite graph, which we map to an embedding space using a bipartite Graph Attention Network. This rich embedding space avoids catastrophic forgetting through the application of knowledge distillation and elastic weight consolidation, wherein we learn the parameters key towards retaining efficacy and are therefore protected from significant drift. We evaluate LIMIP on a series of NP-hard problems and establish that in comparison to existing baselines, LIMIP is up to 50% better when confronted with lifelong learnin

On the Generalization of Neural Combinatorial Optimization Heuristics

Neural Combinatorial Optimization approaches have recently leveraged the expressiveness and flexibility of deep neural networks to learn efficient heuristics for hard Combinatorial Optimization (CO) problems. However, most of the current methods lack generalization: for a given CO problem, heuristics which are trained on instances with certain characteristics underperform when tested on instances with different characteristics. While some previous works have focused on varying the training instances properties, we postulate that a one-size-fit-all model is out of reach. Instead, we formalize solving a CO problem over a given instance distribution as a separate learning task and investigate meta-learning techniques to learn a model on a variety of tasks, in order to optimize its capacity to adapt to new tasks. Through extensive experiments, on two CO problems, using both synthetic and realistic instances, we show that our proposed meta-learning approach significantly improves the generalization of two state-of-the-art models.Comment: Published in ECML PKDD 202