Do Protein Transformers Have Biological Intelligence?

Deep neural networks, particularly Transformers, have been widely adopted for predicting the functional properties of proteins. In this work, we focus on exploring whether Protein Transformers can capture biological intelligence among protein sequences. To achieve our goal, we first introduce a protein function dataset, namely Protein-FN, providing over 9000 protein data with meaningful labels. Second, we devise a new Transformer architecture, namely Sequence Protein Transformers (SPT), for computationally efficient protein function predictions. Third, we develop a novel Explainable Artificial Intelligence (XAI) technique called Sequence Score, which can efficiently interpret the decision-making processes of protein models, thereby overcoming the difficulty of deciphering biological intelligence bided in Protein Transformers. Remarkably, even our smallest SPT-Tiny model, which contains only 5.4M parameters, demonstrates impressive predictive accuracy, achieving 94.3% on the Antibiotic Resistance (AR) dataset and 99.6% on the Protein-FN dataset, all accomplished by training from scratch. Besides, our Sequence Score technique helps reveal that our SPT models can discover several meaningful patterns underlying the sequence structures of protein data, with these patterns aligning closely with the domain knowledge in the biology community. We have officially released our Protein-FN dataset on Hugging Face Datasets https://huggingface.co/datasets/Protein-FN/Protein-FN. Our code is available at https://github.com/fudong03/BioIntelligence.

Variational Autoencoder Framework for Hyperspectral Retrievals (Hyper-VAE) of Phytoplankton Absorption and Chlorophyll a in Coastal Waters for NASA's EMIT and PACE Missions

Phytoplankton absorb and scatter light in unique ways, subtly altering the color of water, changes that are often minor for human eyes to detect but can be captured by sensitive ocean color instruments onboard satellites from space. Hyperspectral sensors, paired with advanced algorithms, are expected to significantly enhance the characterization of phytoplankton community composition, especially in coastal waters where ocean color remote sensing applications have historically encountered significant challenges. This study presents novel machine learning-based solutions for NASA's hyperspectral missions, including EMIT and PACE, tackling high-fidelity retrievals of phytoplankton absorption coefficient and chlorophyll a from their hyperspectral remote sensing reflectance. Given that a single Rrs spectrum may correspond to varied combinations of inherent optical properties and associated concentrations, the Variational Autoencoder (VAE) is used as a backbone in this study to handle such multi-distribution prediction problems. We first time tailor the VAE model with innovative designs to achieve hyperspectral retrievals of aphy and of Chl-a from hyperspectral Rrs in optically complex estuarine-coastal waters. Validation with extensive experimental observation demonstrates superior performance of the VAE models with high precision and low bias. The in-depth analysis of VAE's advanced model structures and learning designs highlights the improvement and advantages of VAE-based solutions over the mixture density network (MDN) approach, particularly on high-dimensional data, such as PACE. Our study provides strong evidence that current EMIT and PACE hyperspectral data as well as the upcoming Surface Biology Geology mission will open new pathways toward a better understanding of phytoplankton community dynamics in aquatic ecosystems when integrated with AI technologies.

Resource Heterogeneity-Aware and Utilization-Enhanced Scheduling for Deep Learning Clusters

Scheduling deep learning (DL) models to train on powerful clusters with accelerators like GPUs and TPUs, presently falls short, either lacking fine-grained heterogeneity awareness or leaving resources substantially under-utilized. To fill this gap, we propose a novel design of a task-level heterogeneity-aware scheduler, {\em Hadar}, based on an optimization framework that can boost resource utilization. {\em Hadar} leverages the performance traits of DL jobs on a heterogeneous DL cluster, characterizes the task-level performance heterogeneity in the optimization problem, and makes scheduling decisions across both spatial and temporal dimensions. %with the objective to reduce the average job completion time of DL jobs. It involves the primal-dual framework employing a dual subroutine, to solve the optimization problem and guide the scheduling design. Our trace-driven simulation with representative DL model training workloads demonstrates that {\em Hadar} accelerates the total time duration by 1.20$\times$ when compared with its state-of-the-art heterogeneity-aware counterpart, Gavel. Further, our {\em Hadar} scheduler is enhanced to {\em HadarE} by forking each job into multiple copies to let a job train concurrently on heterogeneous GPUs resided on separate available nodes (i.e., machines or servers) for resource utilization enhancement. {\em HadarE} is evaluated extensively on physical DL clusters for comparison with {\em Hadar} and Gavel. With substantial enhancement in cluster resource utilization (by 1.45$\times$), {\em HadarE} exhibits considerable speed-ups in DL model training, reducing the total time duration by 50\% (or 80\%) on an Amazon's AWS (or our lab) cluster, while producing trained DL models with consistently better inference quality than those trained by \textit{Hadar}.

HiBench: Benchmarking LLMs Capability on Hierarchical Structure Reasoning

Structure reasoning is a fundamental capability of large language models (LLMs), enabling them to reason about structured commonsense and answer multi-hop questions. However, existing benchmarks for structure reasoning mainly focus on horizontal and coordinate structures (\emph{e.g.} graphs), overlooking the hierarchical relationships within them. Hierarchical structure reasoning is crucial for human cognition, particularly in memory organization and problem-solving. It also plays a key role in various real-world tasks, such as information extraction and decision-making. To address this gap, we propose HiBench, the first framework spanning from initial structure generation to final proficiency assessment, designed to benchmark the hierarchical reasoning capabilities of LLMs systematically. HiBench encompasses six representative scenarios, covering both fundamental and practical aspects, and consists of 30 tasks with varying hierarchical complexity, totaling 39,519 queries. To evaluate LLMs comprehensively, we develop five capability dimensions that depict different facets of hierarchical structure understanding. Through extensive evaluation of 20 LLMs from 10 model families, we reveal key insights into their capabilities and limitations: 1) existing LLMs show proficiency in basic hierarchical reasoning tasks; 2) they still struggle with more complex structures and implicit hierarchical representations, especially in structural modification and textual reasoning. Based on these findings, we create a small yet well-designed instruction dataset, which enhances LLMs' performance on HiBench by an average of 88.84\% (Llama-3.1-8B) and 31.38\% (Qwen2.5-7B) across all tasks. The HiBench dataset and toolkit are available here, https://github.com/jzzzzh/HiBench, to encourage evaluation.

GRID: Protecting Training Graph from Link Stealing Attacks on GNN Models

Graph neural networks (GNNs) have exhibited superior performance in various classification tasks on graph-structured data. However, they encounter the potential vulnerability from the link stealing attacks, which can infer the presence of a link between two nodes via measuring the similarity of its incident nodes' prediction vectors produced by a GNN model. Such attacks pose severe security and privacy threats to the training graph used in GNN models. In this work, we propose a novel solution, called Graph Link Disguise (GRID), to defend against link stealing attacks with the formal guarantee of GNN model utility for retaining prediction accuracy. The key idea of GRID is to add carefully crafted noises to the nodes' prediction vectors for disguising adjacent nodes as n-hop indirect neighboring nodes. We take into account the graph topology and select only a subset of nodes (called core nodes) covering all links for adding noises, which can avert the noises offset and have the further advantages of reducing both the distortion loss and the computation cost. Our crafted noises can ensure 1) the noisy prediction vectors of any two adjacent nodes have their similarity level like that of two non-adjacent nodes and 2) the model prediction is unchanged to ensure zero utility loss. Extensive experiments on five datasets are conducted to show the effectiveness of our proposed GRID solution against different representative link-stealing attacks under transductive settings and inductive settings respectively, as well as two influence-based attacks. Meanwhile, it achieves a much better privacy-utility trade-off than existing methods when extended to GNNs.

Regional Weather Variable Predictions by Machine Learning with Near-Surface Observational and Atmospheric Numerical Data

Accurate and timely regional weather prediction is vital for sectors dependent on weather-related decisions. Traditional prediction methods, based on atmospheric equations, often struggle with coarse temporal resolutions and inaccuracies. This paper presents a novel machine learning (ML) model, called MiMa (short for Micro-Macro), that integrates both near-surface observational data from Kentucky Mesonet stations (collected every five minutes, known as Micro data) and hourly atmospheric numerical outputs (termed as Macro data) for fine-resolution weather forecasting. The MiMa model employs an encoder-decoder transformer structure, with two encoders for processing multivariate data from both datasets and a decoder for forecasting weather variables over short time horizons. Each instance of the MiMa model, called a modelet, predicts the values of a specific weather parameter at an individual Mesonet station. The approach is extended with Re-MiMa modelets, which are designed to predict weather variables at ungauged locations by training on multivariate data from a few representative stations in a region, tagged with their elevations. Re-MiMa (short for Regional-MiMa) can provide highly accurate predictions across an entire region, even in areas without observational stations. Experimental results show that MiMa significantly outperforms current models, with Re-MiMa offering precise short-term forecasts for ungauged locations, marking a significant advancement in weather forecasting accuracy and applicability.

BadCM: Invisible Backdoor Attack Against Cross-Modal Learning

Despite remarkable successes in unimodal learning tasks, backdoor attacks against cross-modal learning are still underexplored due to the limited generalization and inferior stealthiness when involving multiple modalities. Notably, since works in this area mainly inherit ideas from unimodal visual attacks, they struggle with dealing with diverse cross-modal attack circumstances and manipulating imperceptible trigger samples, which hinders their practicability in real-world applications. In this paper, we introduce a novel bilateral backdoor to fill in the missing pieces of the puzzle in the cross-modal backdoor and propose a generalized invisible backdoor framework against cross-modal learning (BadCM). Specifically, a cross-modal mining scheme is developed to capture the modality-invariant components as target poisoning areas, where well-designed trigger patterns injected into these regions can be efficiently recognized by the victim models. This strategy is adapted to different image-text cross-modal models, making our framework available to various attack scenarios. Furthermore, for generating poisoned samples of high stealthiness, we conceive modality-specific generators for visual and linguistic modalities that facilitate hiding explicit trigger patterns in modality-invariant regions. To the best of our knowledge, BadCM is the first invisible backdoor method deliberately designed for diverse cross-modal attacks within one unified framework. Comprehensive experimental evaluations on two typical applications, i.e., cross-modal retrieval and VQA, demonstrate the effectiveness and generalization of our method under multiple kinds of attack scenarios. Moreover, we show that BadCM can robustly evade existing backdoor defenses. Our code is available at https://github.com/xandery-geek/BadCM.

Towards Robust Vision Transformer via Masked Adaptive Ensemble

Adversarial training (AT) can help improve the robustness of Vision Transformers (ViT) against adversarial attacks by intentionally injecting adversarial examples into the training data. However, this way of adversarial injection inevitably incurs standard accuracy degradation to some extent, thereby calling for a trade-off between standard accuracy and robustness. Besides, the prominent AT solutions are still vulnerable to adaptive attacks. To tackle such shortcomings, this paper proposes a novel ViT architecture, including a detector and a classifier bridged by our newly developed adaptive ensemble. Specifically, we empirically discover that detecting adversarial examples can benefit from the Guided Backpropagation technique. Driven by this discovery, a novel Multi-head Self-Attention (MSA) mechanism is introduced to enhance our detector to sniff adversarial examples. Then, a classifier with two encoders is employed for extracting visual representations respectively from clean images and adversarial examples, with our adaptive ensemble to adaptively adjust the proportion of visual representations from the two encoders for accurate classification. This design enables our ViT architecture to achieve a better trade-off between standard accuracy and robustness. Besides, our adaptive ensemble technique allows us to mask off a random subset of image patches within input data, boosting our ViT's robustness against adaptive attacks, while maintaining high standard accuracy. Experimental results exhibit that our ViT architecture, on CIFAR-10, achieves the best standard accuracy and adversarial robustness of 90.3% and 49.8%, respectively.

FedClust: Tackling Data Heterogeneity in Federated Learning through Weight-Driven Client Clustering

Federated learning (FL) is an emerging distributed machine learning paradigm that enables collaborative training of machine learning models over decentralized devices without exposing their local data. One of the major challenges in FL is the presence of uneven data distributions across client devices, violating the well-known assumption of independent-and-identically-distributed (IID) training samples in conventional machine learning. To address the performance degradation issue incurred by such data heterogeneity, clustered federated learning (CFL) shows its promise by grouping clients into separate learning clusters based on the similarity of their local data distributions. However, state-of-the-art CFL approaches require a large number of communication rounds to learn the distribution similarities during training until the formation of clusters is stabilized. Moreover, some of these algorithms heavily rely on a predefined number of clusters, thus limiting their flexibility and adaptability. In this paper, we propose {\em FedClust}, a novel approach for CFL that leverages the correlation between local model weights and the data distribution of clients. {\em FedClust} groups clients into clusters in a one-shot manner by measuring the similarity degrees among clients based on the strategically selected partial weights of locally trained models. We conduct extensive experiments on four benchmark datasets with different non-IID data settings. Experimental results demonstrate that {\em FedClust} achieves higher model accuracy up to $\sim$45\% as well as faster convergence with a significantly reduced communication cost up to 2.7$\times$ compared to its state-of-the-art counterparts.

An Open and Large-Scale Dataset for Multi-Modal Climate Change-aware Crop Yield Predictions

Precise crop yield predictions are of national importance for ensuring food security and sustainable agricultural practices. While AI-for-science approaches have exhibited promising achievements in solving many scientific problems such as drug discovery, precipitation nowcasting, etc., the development of deep learning models for predicting crop yields is constantly hindered by the lack of an open and large-scale deep learning-ready dataset with multiple modalities to accommodate sufficient information. To remedy this, we introduce the CropNet dataset, the first terabyte-sized, publicly available, and multi-modal dataset specifically targeting climate change-aware crop yield predictions for the contiguous United States (U.S.) continent at the county level. Our CropNet dataset is composed of three modalities of data, i.e., Sentinel-2 Imagery, WRF-HRRR Computed Dataset, and USDA Crop Dataset, for over 2200 U.S. counties spanning 6 years (2017-2022), expected to facilitate researchers in developing versatile deep learning models for timely and precisely predicting crop yields at the county-level, by accounting for the effects of both short-term growing season weather variations and long-term climate change on crop yields. Besides, we develop the CropNet package, offering three types of APIs, for facilitating researchers in downloading the CropNet data on the fly over the time and region of interest, and flexibly building their deep learning models for accurate crop yield predictions. Extensive experiments have been conducted on our CropNet dataset via employing various types of deep learning solutions, with the results validating the general applicability and the efficacy of the CropNet dataset in climate change-aware crop yield predictions.