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GlycoNMR: Dataset and benchmarks for NMR chemical shift prediction of carbohydrates with graph neural networks

arXiv.org Artificial Intelligence

Molecular representation learning (MRL) is a powerful tool for bridging the gap between machine learning and chemical sciences, as it converts molecules into numerical representations while preserving their chemical features. These encoded representations serve as a foundation for various downstream biochemical studies, including property prediction and drug design. MRL has had great success with proteins and general biomolecule datasets. Yet, in the growing sub-field of glycoscience (the study of carbohydrates, where longer carbohydrates are also called glycans), MRL methods have been barely explored. This under-exploration can be primarily attributed to the limited availability of comprehensive and well-curated carbohydrate-specific datasets and a lack of Machine learning (ML) pipelines specifically tailored to meet the unique problems presented by carbohydrate data. Since interpreting and annotating carbohydrate-specific data is generally more complicated than protein data, domain experts are usually required to get involved. The existing MRL methods, predominately optimized for proteins and small biomolecules, also cannot be directly used in carbohydrate applications without special modifications. To address this challenge, accelerate progress in glycoscience, and enrich the data resources of the MRL community, we introduce GlycoNMR. GlycoNMR contains two laboriously curated datasets with 2,609 carbohydrate structures and 211,543 annotated nuclear magnetic resonance (NMR) chemical shifts for precise atomic-level prediction. We tailored carbohydrate-specific features and adapted existing MRL models to tackle this problem effectively. For illustration, we benchmark four modified MRL models on our new datasets.


Viral Costco item sparks mixed reviews -- plus dermatologists reveal how often you should wash your face daily

FOX News

Fans of Costco have joined in on the conversation and are sharing their thoughts about viral glass containers that are available for purchase at the wholesaler. MIXED REVIEWS – Costco shoppers are igniting a conversation about a set of glass storage containers that are reportedly selling out fast. WEDDING DRAMA – Sisters are pitted against each other as the bride wants a "child-free" event. FACING FACTS – How often should you wash your face? If you want to avoid dullness, breakouts, inflammation and irritation, wash your face two times a day for overall skin health.


Comparative Analysis of Shear Strength Prediction Models for Reinforced Concrete Slab-Column Connections

arXiv.org Artificial Intelligence

This research aims at comparative analysis of shear strength prediction at slab-column connection, unifying machine learning, design codes and Finite Element Analysis. Current design codes (CDCs) of ACI 318-19 (ACI), Eurocode 2 (EC2), Compressive Force Path (CFP) method, Feed Forward Neural Network (FNN) based Artificial Neural Network (ANN), PSO-based FNN (PSOFNN), and BAT algorithm-based BATFNN are used. The study is complemented with FEA of slab for validating the experimental results and machine learning predictions.In the case of hybrid models of PSOFNN and BATFNN, mean square error is used as an objective function to obtain the optimized values of the weights, that are used by Feed Forward Neural Network to perform predictions on the slab data. Seven different models of PSOFNN, BATFNN, and FNN are trained on this data and the results exhibited that PSOFNN is the best model overall. PSOFNN has the best results for SCS=1 with highest value of R as 99.37% and lowest of MSE, and MAE values of 0.0275%, and 1.214% respectively which are better than the best FNN model for SCS=4 having the values of R, MSE, and MAE as 97.464%, 0.0492%, and 1.43%, respectively.


Scalable Extraction of Training Data from (Production) Language Models

arXiv.org Artificial Intelligence

This paper studies extractable memorization: training data that an adversary can efficiently extract by querying a machine learning model without prior knowledge of the training dataset. We show an adversary can extract gigabytes of training data from open-source language models like Pythia or GPT-Neo, semi-open models like LLaMA or Falcon, and closed models like ChatGPT. Existing techniques from the literature suffice to attack unaligned models; in order to attack the aligned ChatGPT, we develop a new divergence attack that causes the model to diverge from its chatbot-style generations and emit training data at a rate 150x higher than when behaving properly. Our methods show practical attacks can recover far more data than previously thought, and reveal that current alignment techniques do not eliminate memorization.


Gaussian Processes for Monitoring Air-Quality in Kampala

arXiv.org Machine Learning

Monitoring air pollution is of vital importance to the overall health of the population. Unfortunately, devices that can measure air quality can be expensive, and many cities in low and middle-income countries have to rely on a sparse allocation of them. In this paper, we investigate the use of Gaussian Processes for both nowcasting the current air-pollution in places where there are no sensors and forecasting the air-pollution in the future at the sensor locations. In particular, we focus on the city of Kampala in Uganda, using data from AirQo's network of sensors. We demonstrate the advantage of removing outliers, compare different kernel functions and additional inputs. We also compare two sparse approximations to allow for the large amounts of temporal data in the dataset.


GROOT: Learning to Follow Instructions by Watching Gameplay Videos

arXiv.org Artificial Intelligence

We study the problem of building a controller that can follow open-ended instructions in open-world environments. We propose to follow reference videos as instructions, which offer expressive goal specifications while eliminating the need for expensive text-gameplay annotations. A new learning framework is derived to allow learning such instruction-following controllers from gameplay videos while producing a video instruction encoder that induces a structured goal space. We implement our agent GROOT in a simple yet effective encoder-decoder architecture based on causal transformers. We evaluate GROOT against open-world counterparts and human players on a proposed Minecraft SkillForge benchmark. The Elo ratings clearly show that GROOT is closing the human-machine gap as well as exhibiting a 70% winning rate over the best generalist agent baseline. Qualitative analysis of the induced goal space further demonstrates some interesting emergent properties, including the goal composition and complex gameplay behavior synthesis. The project page is available at https://craftjarvis-groot.github.io.


Recognizing Conditional Causal Relationships about Emotions and Their Corresponding Conditions

arXiv.org Artificial Intelligence

The study of causal relationships between emotions and causes in texts has recently received much attention. Most works focus on extracting causally related clauses from documents. However, none of these works has considered that the causal relationships among the extracted emotion and cause clauses can only be valid under some specific context clauses. To highlight the context in such special causal relationships, we propose a new task to determine whether or not an input pair of emotion and cause has a valid causal relationship under different contexts and extract the specific context clauses that participate in the causal relationship. Since the task is new for which no existing dataset is available, we conduct manual annotation on a benchmark dataset to obtain the labels for our tasks and the annotations of each context clause's type that can also be used in some other applications. We adopt negative sampling to construct the final dataset to balance the number of documents with and without causal relationships. Based on the constructed dataset, we propose an end-to-end multi-task framework, where we design two novel and general modules to handle the two goals of our task. Specifically, we propose a context masking module to extract the context clauses participating in the causal relationships. We propose a prediction aggregation module to fine-tune the prediction results according to whether the input emotion and causes depend on specific context clauses. Results of extensive comparative experiments and ablation studies demonstrate the effectiveness and generality of our proposed framework.


Autonomous Restructuring of Asteroids into Rotating Space Stations

arXiv.org Artificial Intelligence

Asteroid restructuring uses robotics, self replication, and mechanical automatons to autonomously restructure an asteroid into a large rotating space station. The restructuring process makes structures from asteroid oxide materials; uses productive self-replication to make replicators, helpers, and products; and creates a multiple floor station to support a large population. In an example simulation, it takes 12 years to autonomously restructure a large asteroid into the space station. This is accomplished with a single rocket launch. The single payload contains a base station, 4 robots (spiders), and a modest set of supplies. Our simulation creates 3000 spiders and over 23,500 other pieces of equipment. Only the base station and spiders (replicators) have advanced microprocessors and algorithms. These represent 21st century technologies created and trans-ported from Earth. The equipment and tools are built using in-situ materials and represent 18th or 19th century technologies. The equipment and tools (helpers) have simple mechanical programs to perform repetitive tasks. The resulting example station would be a rotating framework almost 5 kilometers in diameter. Once completed, it could support a population of over 700,000 people. Many researchers identify the high launch costs, the harsh space environment, and the lack of gravity as the key obstacles hindering the development of space stations. The single probe addresses the high launch cost. The autonomous construction eliminates the harsh space environment for construction crews. The completed rotating station provides radiation protection and centripetal gravity for the first work crews and colonists.


The Open DAC 2023 Dataset and Challenges for Sorbent Discovery in Direct Air Capture

arXiv.org Artificial Intelligence

New methods for carbon dioxide removal are urgently needed to combat global climate change. Direct air capture (DAC) is an emerging technology to capture carbon dioxide directly from ambient air. Metal-organic frameworks (MOFs) have been widely studied as potentially customizable adsorbents for DAC. However, discovering promising MOF sorbents for DAC is challenging because of the vast chemical space to explore and the need to understand materials as functions of humidity and temperature. We explore a computational approach benefiting from recent innovations in machine learning (ML) and present a dataset named Open DAC 2023 (ODAC23) consisting of more than 38M density functional theory (DFT) calculations on more than 8,400 MOF materials containing adsorbed $CO_2$ and/or $H_2O$. ODAC23 is by far the largest dataset of MOF adsorption calculations at the DFT level of accuracy currently available. In addition to probing properties of adsorbed molecules, the dataset is a rich source of information on structural relaxation of MOFs, which will be useful in many contexts beyond specific applications for DAC. A large number of MOFs with promising properties for DAC are identified directly in ODAC23. We also trained state-of-the-art ML models on this dataset to approximate calculations at the DFT level. This open-source dataset and our initial ML models will provide an important baseline for future efforts to identify MOFs for a wide range of applications, including DAC.


Tabular Two-Dimensional Correlation Analysis for Multifaceted Characterization Data

arXiv.org Artificial Intelligence

We propose tabular two-dimensional correlation analysis for extracting features from multifaceted characterization data, essential for understanding material properties. This method visualizes similarities and phase lags in structural parameter changes through heatmaps, combining hierarchical clustering and asynchronous correlations. We applied the proposed method to datasets of carbon nanotube (CNTs) films annealed at various temperatures and revealed the complexity of their hierarchical structures, which include elements like voids, bundles, and amorphous carbon. Our analysis addresses the challenge of attempting to understand the sequence of structural changes, especially in multifaceted characterization data where 11 structural parameters derived from 8 characterization methods interact with complex behavior. The results show how phase lags (asynchronous changes from stimuli) and parameter similarities can illuminate the sequence of structural changes in materials, providing insights into phenomena like the removal of amorphous carbon and graphitization in annealed CNTs. This approach is beneficial even with limited data and holds promise for a wide range of material analyses, demonstrating its potential in elucidating complex material behaviors and properties.