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Navigating protein landscapes with a machine-learned transferable coarse-grained model

arXiv.org Machine Learning

The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model with similar prediction performance has been a long-standing challenge. By combining recent deep learning methods with a large and diverse training set of all-atom protein simulations, we here develop a bottom-up CG force field with chemical transferability, which can be used for extrapolative molecular dynamics on new sequences not used during model parametrization. We demonstrate that the model successfully predicts folded structures, intermediates, metastable folded and unfolded basins, and the fluctuations of intrinsically disordered proteins while it is several orders of magnitude faster than an all-atom model. This showcases the feasibility of a universal and computationally efficient machine-learned CG model for proteins.


A Global Multi-Unit Calibration as a Method for Large Scale IoT Particulate Matter Monitoring Systems Deployments

arXiv.org Artificial Intelligence

Scalable and effective calibration is a fundamental requirement for Low Cost Air Quality Monitoring Systems and will enable accurate and pervasive monitoring in cities. Suffering from environmental interferences and fabrication variance, these devices need to encompass sensors specific and complex calibration processes for reaching a sufficient accuracy to be deployed as indicative measurement devices in Air Quality (AQ) monitoring networks. Concept and sensor drift often force calibration process to be frequently repeated. These issues lead to unbearable calibration costs which denies their massive deployment when accuracy is a concern. In this work, We propose a zero transfer samples, global calibration methodology as a technological enabler for IoT AQ multisensory devices which relies on low cost Particulate Matter (PM) sensors. This methodology is based on field recorded responses from a limited number of IoT AQ multisensors units and machine learning concepts and can be universally applied to all units of the same type. A multi season test campaign shown that, when applied to different sensors, this methodology performances match those of state of the art methodology which requires to derive different calibration parameters for each different unit. If confirmed, these results show that, when properly derived, a global calibration law can be exploited for a large number of networked devices with dramatic cost reduction eventually allowing massive deployment of accurate IoT AQ monitoring devices. Furthermore, this calibration model could be easily embedded on board of the device or implemented on the edge allowing immediate access to accurate readings for personal exposure monitor applications as well as reducing long range data transfer needs.


How Well Do Feature-Additive Explainers Explain Feature-Additive Predictors?

arXiv.org Artificial Intelligence

Surging interest in deep learning from high-stakes domains has precipitated concern over the inscrutable nature of black box neural networks. Explainable AI (XAI) research has led to an abundance of explanation algorithms for these black boxes. Such post hoc explainers produce human-comprehensible explanations, however, their fidelity with respect to the model is not well understood - explanation evaluation remains one of the most challenging issues in XAI. In this paper, we ask a targeted but important question: can popular feature-additive explainers (e.g., LIME, SHAP, SHAPR, MAPLE, and PDP) explain feature-additive predictors? Herein, we evaluate such explainers on ground truth that is analytically derived from the additive structure of a model. We demonstrate the efficacy of our approach in understanding these explainers applied to symbolic expressions, neural networks, and generalized additive models on thousands of synthetic and several real-world tasks. Our results suggest that all explainers eventually fail to correctly attribute the importance of features, especially when a decision-making process involves feature interactions.


T5 meets Tybalt: Author Attribution in Early Modern English Drama Using Large Language Models

arXiv.org Artificial Intelligence

Large language models have shown breakthrough potential in many NLP domains. Here we consider their use for stylometry, specifically authorship identification in Early Modern English drama. We find both promising and concerning results; LLMs are able to accurately predict the author of surprisingly short passages but are also prone to confidently misattribute texts to specific authors. A fine-tuned t5-large model outperforms all tested baselines, including logistic regression, SVM with a linear kernel, and cosine delta, at attributing small passages. However, we see indications that the presence of certain authors in the model's pre-training data affects predictive results in ways that are difficult to assess.


State-Action Similarity-Based Representations for Off-Policy Evaluation

arXiv.org Artificial Intelligence

In reinforcement learning, off-policy evaluation (OPE) is the problem of estimating the expected return of an evaluation policy given a fixed dataset that was collected by running one or more different policies. One of the more empirically successful algorithms for OPE has been the fitted q-evaluation (FQE) algorithm that uses temporal difference updates to learn an action-value function, which is then used to estimate the expected return of the evaluation policy. Typically, the original fixed dataset is fed directly into FQE to learn the action-value function of the evaluation policy. Instead, in this paper, we seek to enhance the data-efficiency of FQE by first transforming the fixed dataset using a learned encoder, and then feeding the transformed dataset into FQE. To learn such an encoder, we introduce an OPE-tailored state-action behavioral similarity metric, and use this metric and the fixed dataset to learn an encoder that models this metric. Theoretically, we show that this metric allows us to bound the error in the resulting OPE estimate. Empirically, we show that other state-action similarity metrics lead to representations that cannot represent the action-value function of the evaluation policy, and that our state-action representation method boosts the data-efficiency of FQE and lowers OPE error relative to other OPE-based representation learning methods on challenging OPE tasks. We also empirically show that the learned representations significantly mitigate divergence of FQE under varying distribution shifts. Our code is available here: https://github.com/Badger-RL/ROPE.


PlantPlotGAN: A Physics-Informed Generative Adversarial Network for Plant Disease Prediction

arXiv.org Artificial Intelligence

Monitoring plantations is crucial for crop management and producing healthy harvests. Unmanned Aerial Vehicles (UAVs) have been used to collect multispectral images that aid in this monitoring. However, given the number of hectares to be monitored and the limitations of flight, plant disease signals become visually clear only in the later stages of plant growth and only if the disease has spread throughout a significant portion of the plantation. This limited amount of relevant data hampers the prediction models, as the algorithms struggle to generalize patterns with unbalanced or unrealistic augmented datasets effectively. To address this issue, we propose PlantPlotGAN, a physics-informed generative model capable of creating synthetic multispectral plot images with realistic vegetation indices. These indices served as a proxy for disease detection and were used to evaluate if our model could help increase the accuracy of prediction models. The results demonstrate that the synthetic imagery generated from PlantPlotGAN outperforms state-of-the-art methods regarding the Fr\'echet inception distance. Moreover, prediction models achieve higher accuracy metrics when trained with synthetic and original imagery for earlier plant disease detection compared to the training processes based solely on real imagery.


MalFake: A Multimodal Fake News Identification for Malayalam using Recurrent Neural Networks and VGG-16

arXiv.org Artificial Intelligence

The amount of news being consumed online has substantially expanded in recent years. Fake news has become increasingly common, especially in regional languages like Malayalam, due to the rapid publication and lack of editorial standards on some online sites. Fake news may have a terrible effect on society, causing people to make bad judgments, lose faith in authorities, and even engage in violent behavior. When we take into the context of India, there are many regional languages, and fake news is spreading in every language. Therefore, providing efficient techniques for identifying false information in regional tongues is crucial. Until now, little to no work has been done in Malayalam, extracting features from multiple modalities to classify fake news. Multimodal approaches are more accurate in detecting fake news, as features from multiple modalities are extracted to build the deep learning classification model. As far as we know, this is the first piece of work in Malayalam that uses multimodal deep learning to tackle false information. Models trained with more than one modality typically outperform models taught with only one modality. Our study in the Malayalam language utilizing multimodal deep learning is a significant step toward more effective misinformation detection and mitigation.


Revising with a Backward Glance: Regressions and Skips during Reading as Cognitive Signals for Revision Policies in Incremental Processing

arXiv.org Artificial Intelligence

In NLP, incremental processors produce output in instalments, based on incoming prefixes of the linguistic input. Some tokens trigger revisions, causing edits to the output hypothesis, but little is known about why models revise when they revise. A policy that detects the time steps where revisions should happen can improve efficiency. Still, retrieving a suitable signal to train a revision policy is an open problem, since it is not naturally available in datasets. In this work, we investigate the appropriateness of regressions and skips in human reading eye-tracking data as signals to inform revision policies in incremental sequence labelling. Using generalised mixed-effects models, we find that the probability of regressions and skips by humans can potentially serve as useful predictors for revisions in BiLSTMs and Transformer models, with consistent results for various languages.


Lost in Translation -- Multilingual Misinformation and its Evolution

arXiv.org Artificial Intelligence

Misinformation and disinformation are growing threats in the digital age, spreading rapidly across languages and borders. This paper investigates the prevalence and dynamics of multilingual misinformation through an analysis of over 250,000 unique fact-checks spanning 95 languages. First, we find that while the majority of misinformation claims are only fact-checked once, 11.7%, corresponding to more than 21,000 claims, are checked multiple times. Using fact-checks as a proxy for the spread of misinformation, we find 33% of repeated claims cross linguistic boundaries, suggesting that some misinformation permeates language barriers. However, spreading patterns exhibit strong homophily, with misinformation more likely to spread within the same language. To study the evolution of claims over time and mutations across languages, we represent fact-checks with multilingual sentence embeddings and cluster semantically similar claims. We analyze the connected components and shortest paths connecting different versions of a claim finding that claims gradually drift over time and undergo greater alteration when traversing languages. Overall, this novel investigation of multilingual misinformation provides key insights. It quantifies redundant fact-checking efforts, establishes that some claims diffuse across languages, measures linguistic homophily, and models the temporal and cross-lingual evolution of claims. The findings advocate for expanded information sharing between fact-checkers globally while underscoring the importance of localized verification.


ViCLEVR: A Visual Reasoning Dataset and Hybrid Multimodal Fusion Model for Visual Question Answering in Vietnamese

arXiv.org Artificial Intelligence

In recent years, Visual Question Answering (VQA) has gained significant attention for its diverse applications, including intelligent car assistance, aiding visually impaired individuals, and document image information retrieval using natural language queries. VQA requires effective integration of information from questions and images to generate accurate answers. Neural models for VQA have made remarkable progress on large-scale datasets, with a primary focus on resource-rich languages like English. To address this, we introduce the ViCLEVR dataset, a pioneering collection for evaluating various visual reasoning capabilities in Vietnamese while mitigating biases. The dataset comprises over 26,000 images and 30,000 question-answer pairs (QAs), each question annotated to specify the type of reasoning involved. Leveraging this dataset, we conduct a comprehensive analysis of contemporary visual reasoning systems, offering valuable insights into their strengths and limitations. Furthermore, we present PhoVIT, a comprehensive multimodal fusion that identifies objects in images based on questions. The architecture effectively employs transformers to enable simultaneous reasoning over textual and visual data, merging both modalities at an early model stage. The experimental findings demonstrate that our proposed model achieves state-of-the-art performance across four evaluation metrics. The accompanying code and dataset have been made publicly accessible at \url{https://github.com/kvt0012/ViCLEVR}. This provision seeks to stimulate advancements within the research community, fostering the development of more multimodal fusion algorithms, specifically tailored to address the nuances of low-resource languages, exemplified by Vietnamese.