Weighted Diversified Sampling for Efficient Data-Driven Single-Cell Gene-Gene Interaction Discovery

Gene-gene interactions play a crucial role in the manifestation of complex human diseases. Uncovering significant gene-gene interactions is a challenging task. Here, we present an innovative approach utilizing data-driven computational tools, leveraging an advanced Transformer model, to unearth noteworthy gene-gene interactions. Despite the efficacy of Transformer models, their parameter intensity presents a bottleneck in data ingestion, hindering data efficiency. To mitigate this, we introduce a novel weighted diversified sampling algorithm. This algorithm computes the diversity score of each data sample in just two passes of the dataset, facilitating efficient subset generation for interaction discovery. Our extensive experimentation demonstrates that by sampling a mere 1\% of the single-cell dataset, we achieve performance comparable to that of utilizing the entire dataset.

InfiniBench: A Comprehensive Benchmark for Large Multimodal Models in Very Long Video Understanding

Understanding long videos, ranging from tens of minutes to several hours, presents unique challenges in video comprehension. Despite the increasing importance of long-form video content, existing benchmarks primarily focus on shorter clips. To address this gap, we introduce InfiniBench a comprehensive benchmark for very long video understanding which presents 1)The longest video duration, averaging 76.34 minutes; 2) The largest number of question-answer pairs, 108.2K; 3) Diversity in questions that examine nine different skills and include both multiple-choice questions and open-ended questions; 4) Humancentric, as the video sources come from movies and daily TV shows, with specific human-level question designs such as Movie Spoiler Questions that require critical thinking and comprehensive understanding. Using InfiniBench, we comprehensively evaluate existing Large MultiModality Models (LMMs) on each skill, including the commercial model Gemini 1.5 Flash and the open-source models. The evaluation shows significant challenges in our benchmark.Our results show that the best AI models such Gemini struggles to perform well with 42.72% average accuracy and 2.71 out of 5 average score. We hope this benchmark will stimulate the LMMs community towards long video and human-level understanding. Our benchmark can be accessed at https://vision-cair.github.io/InfiniBench/

GNNX-BENCH: Unravelling the Utility of Perturbation-based GNN Explainers through In-depth Benchmarking

Numerous explainability methods have been proposed to shed light on the inner workings of GNNs. Despite the inclusion of empirical evaluations in all the proposed algorithms, the interrogative aspects of these evaluations lack diversity. As a result, various facets of explainability pertaining to GNNs, such as a comparative analysis of counterfactual reasoners, their stability to variational factors such as different GNN architectures, noise, stochasticity in non-convex loss surfaces, feasibility amidst domain constraints, and so forth, have yet to be formally investigated. Motivated by this need, we present a benchmarking study on perturbation-based explainability methods for GNNs, aiming to systematically evaluate and compare a wide range of explainability techniques. Among the key findings of our study, we identify the Pareto-optimal methods that exhibit superior efficacy and stability in the presence of noise. Nonetheless, our study reveals that all algorithms are affected by stability issues when faced with noisy data. Furthermore, we have established that the current generation of counterfactual explainers often fails to provide feasible recourses due to violations of topological constraints encoded by domain-specific considerations. Overall, this benchmarking study empowers stakeholders in the field of GNNs with a comprehensive understanding of the state-of-the-art explainability methods, potential research problems for further enhancement, and the implications of their application in real-world scenarios.

Scaling Distributed Multi-task Reinforcement Learning with Experience Sharing

Recently, DARPA launched the ShELL program, which aims to explore how experience sharing can benefit distributed lifelong learning agents in adapting to new challenges. In this paper, we address this issue by conducting both theoretical and empirical research on distributed multi-task reinforcement learning (RL), where a group of $N$ agents collaboratively solves $M$ tasks without prior knowledge of their identities. We approach the problem by formulating it as linearly parameterized contextual Markov decision processes (MDPs), where each task is represented by a context that specifies the transition dynamics and rewards. To tackle this problem, we propose an algorithm called DistMT-LSVI. First, the agents identify the tasks, and then they exchange information through a central server to derive $\epsilon$-optimal policies for the tasks. Our research demonstrates that to achieve $\epsilon$-optimal policies for all $M$ tasks, a single agent using DistMT-LSVI needs to run a total number of episodes that is at most $\tilde{\mathcal{O}}({d^3H^6(\epsilon^{-2}+c_{\rm sep}^{-2})}\cdot M/N)$, where $c_{\rm sep}>0$ is a constant representing task separability, $H$ is the horizon of each episode, and $d$ is the feature dimension of the dynamics and rewards. Notably, DistMT-LSVI improves the sample complexity of non-distributed settings by a factor of $1/N$, as each agent independently learns $\epsilon$-optimal policies for all $M$ tasks using $\tilde{\mathcal{O}}(d^3H^6M\epsilon^{-2})$ episodes. Additionally, we provide numerical experiments conducted on OpenAI Gym Atari environments that validate our theoretical findings.

Variance of Twitter Embeddings and Temporal Trends of COVID-19 cases

The severity of the coronavirus pandemic necessitates the need of effective administrative decisions. Over 4 lakh people in India succumbed to COVID-19, with over 3 crore confirmed cases, and still counting. The threat of a plausible third wave continues to haunt millions. In this ever changing dynamic of the virus, predictive modeling methods can serve as an integral tool. The pandemic has further triggered an unprecedented usage of social media. This paper aims to propose a method for harnessing social media, specifically Twitter, to predict the upcoming scenarios related to COVID-19 cases. In this study, we seek to understand how the surges in COVID-19 related tweets can indicate rise in the cases. This prospective analysis can be utilised to aid administrators about timely resource allocation to lessen the severity of the damage. Using word embeddings to capture the semantic meaning of tweets, we identify Significant Dimensions (SDs).Our methodology predicts the rise in cases with a lead time of 15 days and 30 days with R2 scores of 0.80 and 0.62 respectively. Finally, we explain the thematic utility of the SDs.

WiseR: An end-to-end structure learning and deployment framework for causal graphical models

Structure learning offers an expressive, versatile and explainable approach to causal and mechanistic modeling of complex biological data. We present wiseR, an open source application for learning, evaluating and deploying robust causal graphical models using graph neural networks and Bayesian networks. We demonstrate the utility of this application through application on for biomarker discovery in a COVID-19 clinical dataset.