pwc-archive/papers-with-abstracts huggingface dataset:
Spatioformer: A Geo-encoded Transformer for Large-Scale Plant Species Richness Prediction
Authors: Yiqing Guo, Karel Mokany, Shaun R. Levick, Jinyan Yang, Peyman Moghadam
Date: 2024-10-25 00:00:00
Tasks: Diversity, Earth Observation

Earth observation data have shown promise in predicting species richness of vascular plants ($\alpha$-diversity), but extending this approach to large spatial scales is challenging because geographically distant regions may exhibit different compositions of plant species ($\beta$-diversity), resulting in a location-dependent relationship between richness and spectral measurements. In order to handle such geolocation dependency, we propose Spatioformer, where a novel geolocation encoder is coupled with the transformer model to encode geolocation context into remote sensing imagery. The Spatioformer model compares favourably to state-of-the-art models in richness predictions on a large-scale ground-truth richness dataset (HAVPlot) that consists of 68,170 in-situ richness samples covering diverse landscapes across Australia. The results demonstrate that geolocational information is advantageous in predicting species richness from satellite observations over large spatial scales. With Spatioformer, plant species richness maps over Australia are compiled from Landsat archive for the years from 2015 to 2023. The richness maps produced in this study reveal the spatiotemporal dynamics of plant species richness in Australia, providing supporting evidence to inform effective planning and policy development for plant diversity conservation. Regions of high richness prediction uncertainties are identified, highlighting the need for future in-situ surveys to be conducted in these areas to enhance the prediction accuracy.
Enhancing Exchange Rate Forecasting with Explainable Deep Learning Models
Authors: Shuchen Meng, Andi Chen, Chihang Wang, Mengyao Zheng, Fangyu Wu, Xupeng Chen, Haowei Ni, Panfeng Li
Date: 2024-10-25 00:00:00
Tasks: Decision Making, Deep Learning, feature selection, Financial Analysis

Accurate exchange rate prediction is fundamental to financial stability and international trade, positioning it as a critical focus in economic and financial research. Traditional forecasting models often falter when addressing the inherent complexities and non-linearities of exchange rate data. This study explores the application of advanced deep learning models, including LSTM, CNN, and transformer-based architectures, to enhance the predictive accuracy of the RMB/USD exchange rate. Utilizing 40 features across 6 categories, the analysis identifies TSMixer as the most effective model for this task. A rigorous feature selection process emphasizes the inclusion of key economic indicators, such as China-U.S. trade volumes and exchange rates of other major currencies like the euro-RMB and yen-dollar pairs. The integration of grad-CAM visualization techniques further enhances model interpretability, allowing for clearer identification of the most influential features and bolstering the credibility of the predictions. These findings underscore the pivotal role of fundamental economic data in exchange rate forecasting and highlight the substantial potential of machine learning models to deliver more accurate and reliable predictions, thereby serving as a valuable tool for financial analysis and decision-making.
SHAP zero Explains Biological Sequence Models with Near-zero Marginal Cost for Future Queries
Authors: Darin Tsui, Aryan Musharaf, Yigit Efe Erginbas, Justin Singh Kang, Amirali Aghazadeh
Date: 2024-10-25 00:00:00

The growing adoption of machine learning models for biological sequences has intensified the need for interpretable predictions, with Shapley values emerging as a theoretically grounded standard for model explanation. While effective for local explanations of individual input sequences, scaling Shapley-based interpretability to extract global biological insights requires evaluating thousands of sequences--incurring exponential computational cost per query. We introduce SHAP zero, a novel algorithm that amortizes the cost of Shapley value computation across large-scale biological datasets. After a one-time model sketching step, SHAP zero enables near-zero marginal cost for future queries by uncovering an underexplored connection between Shapley values, high-order feature interactions, and the sparse Fourier transform of the model. Applied to models of guide RNA efficacy, DNA repair outcomes, and protein fitness, SHAP zero explains predictions orders of magnitude faster than existing methods, recovering rich combinatorial interactions previously inaccessible at scale. This work opens the door to principled, efficient, and scalable interpretability for black-box sequence models in biology.
Humanizing the Machine: Proxy Attacks to Mislead LLM Detectors
Authors: Tianchun Wang, Yuanzhou Chen, Zichuan Liu, Zhanwen Chen, Haifeng Chen, Xiang Zhang, Wei Cheng
Date: 2024-10-25 00:00:00
Tasks: Reinforcement Learning (RL), Small Language Model, Text Generation

The advent of large language models (LLMs) has revolutionized the field of text generation, producing outputs that closely mimic human-like writing. Although academic and industrial institutions have developed detectors to prevent the malicious usage of LLM-generated texts, other research has doubt about the robustness of these systems. To stress test these detectors, we introduce a proxy-attack strategy that effortlessly compromises LLMs, causing them to produce outputs that align with human-written text and mislead detection systems. Our method attacks the source model by leveraging a reinforcement learning (RL) fine-tuned humanized small language model (SLM) in the decoding phase. Through an in-depth analysis, we demonstrate that our attack strategy is capable of generating responses that are indistinguishable to detectors, preventing them from differentiating between machine-generated and human-written text. We conduct systematic evaluations on extensive datasets using proxy-attacked open-source models, including Llama2-13B, Llama3-70B, and Mixtral-8*7B in both white- and black-box settings. Our findings show that the proxy-attack strategy effectively deceives the leading detectors, resulting in an average AUROC drop of 70.4% across multiple datasets, with a maximum drop of 90.3% on a single dataset. Furthermore, in cross-discipline scenarios, our strategy also bypasses these detectors, leading to a significant relative decrease of up to 90.9%, while in cross-language scenario, the drop reaches 91.3%. Despite our proxy-attack strategy successfully bypassing the detectors with such significant relative drops, we find that the generation quality of the attacked models remains preserved, even within a modest utility budget, when compared to the text produced by the original, unattacked source model.
Peptide-GPT: Generative Design of Peptides using Generative Pre-trained Transformers and Bio-informatic Supervision
Authors: Aayush Shah, Chakradhar Guntuboina, Amir Barati Farimani
Date: 2024-10-25 00:00:00
Tasks: Language Modelling, Protein Design, Protein Language Model, Text Generation

In recent years, natural language processing (NLP) models have demonstrated remarkable capabilities in various domains beyond traditional text generation. In this work, we introduce PeptideGPT, a protein language model tailored to generate protein sequences with distinct properties: hemolytic activity, solubility, and non-fouling characteristics. To facilitate a rigorous evaluation of these generated sequences, we established a comprehensive evaluation pipeline consisting of ideas from bioinformatics to retain valid proteins with ordered structures. First, we rank the generated sequences based on their perplexity scores, then we filter out those lying outside the permissible convex hull of proteins. Finally, we predict the structure using ESMFold and select the proteins with pLDDT values greater than 70 to ensure ordered structure. The properties of generated sequences are evaluated using task-specific classifiers - PeptideBERT and HAPPENN. We achieved an accuracy of 76.26% in hemolytic, 72.46% in non-hemolytic, 78.84% in non-fouling, and 68.06% in solubility protein generation. Our experimental results demonstrate the effectiveness of PeptideGPT in de novo protein design and underscore the potential of leveraging NLP-based approaches for paving the way for future innovations and breakthroughs in synthetic biology and bioinformatics. Codes, models, and data used in this study are freely available at: https://github.com/aayush-shah14/PeptideGPT.
Predicting Liquidity Coverage Ratio with Gated Recurrent Units: A Deep Learning Model for Risk Management
Authors: Zhen Xu, Jingming Pan, Siyuan Han, Hongju Ouyang, Yuan Chen, Mohan Jiang
Date: 2024-10-24 00:00:00
Tasks: Management

With the global economic integration and the high interconnection of financial markets, financial institutions are facing unprecedented challenges, especially liquidity risk. This paper proposes a liquidity coverage ratio (LCR) prediction model based on the gated recurrent unit (GRU) network to help financial institutions manage their liquidity risk more effectively. By utilizing the GRU network in deep learning technology, the model can automatically learn complex patterns from historical data and accurately predict LCR for a period of time in the future. The experimental results show that compared with traditional methods, the GRU model proposed in this study shows significant advantages in mean absolute error (MAE), proving its higher accuracy and robustness. This not only provides financial institutions with a more reliable liquidity risk management tool but also provides support for regulators to formulate more scientific and reasonable policies, which helps to improve the stability of the entire financial system.
Inference time LLM alignment in single and multidomain preference spectrum
Authors: Sadat Shahriar, Zheng Qi, Nikolaos Pappas, Srikanth Doss, Monica Sunkara, Kishaloy Halder, Manuel Mager, Yassine Benajiba
Date: 2024-10-24 00:00:00
Tasks: Model Editing, Prompt Engineering

Aligning Large Language Models (LLM) to address subjectivity and nuanced preference levels requires adequate flexibility and control, which can be a resource-intensive and time-consuming procedure. Existing training-time alignment methods require full re-training when a change is needed and inference-time ones typically require access to the reward model at each inference step. To address these limitations, we introduce inference-time model alignment method that learns encoded representations of preference dimensions, called \textit{Alignment Vectors} (AV). These representations are computed by subtraction of the base model from the aligned model as in model editing enabling dynamically adjusting the model behavior during inference through simple linear operations. Even though the preference dimensions can span various granularity levels, here we focus on three gradual response levels across three specialized domains: medical, legal, and financial, exemplifying its practical potential. This new alignment paradigm introduces adjustable preference knobs during inference, allowing users to tailor their LLM outputs while reducing the inference cost by half compared to the prompt engineering approach. Additionally, we find that AVs are transferable across different fine-tuning stages of the same model, demonstrating their flexibility. AVs also facilitate multidomain, diverse preference alignment, making the process 12x faster than the retraining approach.
Binary Classification: Is Boosting stronger than Bagging?
Authors: Dimitris Bertsimas, Vasiliki Stoumpou
Date: 2024-10-24 00:00:00
Tasks: Binary Classification, Classification

Random Forests have been one of the most popular bagging methods in the past few decades, especially due to their success at handling tabular datasets. They have been extensively studied and compared to boosting models, like XGBoost, which are generally considered more performant. Random Forests adopt several simplistic assumptions, such that all samples and all trees that form the forest are equally important for building the final model. We introduce Enhanced Random Forests, an extension of vanilla Random Forests with extra functionalities and adaptive sample and model weighting. We develop an iterative algorithm for adapting the training sample weights, by favoring the hardest examples, and an approach for finding personalized tree weighting schemes for each new sample. Our method significantly improves upon regular Random Forests across 15 different binary classification datasets and considerably outperforms other tree methods, including XGBoost, when run with default hyperparameters, which indicates the robustness of our approach across datasets, without the need for extensive hyperparameter tuning. Our tree-weighting methodology results in enhanced or comparable performance to the uniformly weighted ensemble, and is, more importantly, leveraged to define importance scores for trees based on their contributions to classifying each new sample. This enables us to only focus on a small number of trees as the main models that define the outcome of a new sample and, thus, to partially recover interpretability, which is critically missing from both bagging and boosting methods. In binary classification problems, the proposed extensions and the corresponding results suggest the equivalence of bagging and boosting methods in performance, and the edge of bagging in interpretability by leveraging a few learners of the ensemble, which is not an option in the less explainable boosting methods.
TEAM: Topological Evolution-aware Framework for Traffic Forecasting--Extended Version
Authors: Duc Kieu, Tung Kieu, Peng Han, Bin Yang, Christian S. Jensen, Bac Le
Date: 2024-10-24 00:00:00
Tasks: Continual Learning, Time Series

Due to the global trend towards urbanization, people increasingly move to and live in cities that then continue to grow. Traffic forecasting plays an important role in the intelligent transportation systems of cities as well as in spatio-temporal data mining. State-of-the-art forecasting is achieved by deep-learning approaches due to their ability to contend with complex spatio-temporal dynamics. However, existing methods assume the input is fixed-topology road networks and static traffic time series. These assumptions fail to align with urbanization, where time series are collected continuously and road networks evolve over time. In such settings, deep-learning models require frequent re-initialization and re-training, imposing high computational costs. To enable much more efficient training without jeopardizing model accuracy, we propose the Topological Evolution-aware Framework (TEAM) for traffic forecasting that incorporates convolution and attention. This combination of mechanisms enables better adaptation to newly collected time series, while being able to maintain learned knowledge from old time series. TEAM features a continual learning module based on the Wasserstein metric that acts as a buffer that can identify the most stable and the most changing network nodes. Then, only data related to stable nodes is employed for re-training when consolidating a model. Further, only data of new nodes and their adjacent nodes as well as data pertaining to changing nodes are used to re-train the model. Empirical studies with two real-world traffic datasets offer evidence that TEAM is capable of much lower re-training costs than existing methods are, without jeopardizing forecasting accuracy.
Reinforcement Learning the Chromatic Symmetric Function
Authors: Gergely Bérczi, Jonas Klüver
Date: 2024-10-24 00:00:00
Tasks: reinforcement-learning, Reinforcement Learning

We propose a conjectural counting formula for the coefficients of the chromatic symmetric function of unit interval graphs using reinforcement learning. The formula counts specific disjoint cycle-tuples in the graphs, referred to as Eschers, which satisfy certain concatenation conditions. These conditions are identified by a reinforcement learning model and are independent of the particular unit interval graph, resulting a universal counting expression.
Cascading Failure Prediction via Causal Inference
Authors: Shiuli Subhra Ghosh, Anmol Dwivedi, Ali Tajer, Kyongmin Yeo, Wesley M. Gifford
Date: 2024-10-24 00:00:00
Tasks: Causal Inference, Prediction

Causal inference provides an analytical framework to identify and quantify cause-and-effect relationships among a network of interacting agents. This paper offers a novel framework for analyzing cascading failures in power transmission networks. This framework generates a directed latent graph in which the nodes represent the transmission lines and the directed edges encode the cause-effect relationships. This graph has a structure distinct from the system's topology, signifying the intricate fact that both local and non-local interdependencies exist among transmission lines, which are more general than only the local interdependencies that topological graphs can present. This paper formalizes a causal inference framework for predicting how an emerging anomaly propagates throughout the system. Using this framework, two algorithms are designed, providing an analytical framework to identify the most likely and most costly cascading scenarios. The framework's effectiveness is evaluated compared to the pertinent literature on the IEEE 14-bus, 39-bus, and 118-bus systems.
Perturbation-based Graph Active Learning for Weakly-Supervised Belief Representation Learning
Authors: Dachun Sun, Ruijie Wang, Jinning Li, Ruipeng Han, Xinyi Liu, You Lyu, Tarek Abdelzaher
Date: 2024-10-24 00:00:00
Tasks: Active Learning, Data Augmentation, Graph Learning, Representation Learning

This paper addresses the problem of optimizing the allocation of labeling resources for semi-supervised belief representation learning in social networks. The objective is to strategically identify valuable messages on social media graphs that are worth labeling within a constrained budget, ultimately maximizing the task's performance. Despite the progress in unsupervised or semi-supervised methods in advancing belief and ideology representation learning on social networks and the remarkable efficacy of graph learning techniques, the availability of high-quality curated labeled social data can greatly benefit and further improve performances. Consequently, allocating labeling efforts is a critical research problem in scenarios where labeling resources are limited. This paper proposes a graph data augmentation-inspired perturbation-based active learning strategy (PerbALGraph) that progressively selects messages for labeling according to an automatic estimator, obviating human guidance. This estimator is based on the principle that messages in the network that exhibit heightened sensitivity to structural features of the observational data indicate landmark quality that significantly influences semi-supervision processes. We design the estimator to be the prediction variance under a set of designed graph perturbations, which is model-agnostic and application-independent. Extensive experiment results demonstrate the effectiveness of the proposed strategy for belief representation learning tasks.
Indication Finding: a novel use case for representation learning
Authors: Maren Eckhoff, Valmir Selimi, Alexander Aranovitch, Ian Lyons, Emily Briggs, Jennifer Hou, Alex Devereson, Matej Macak, David Champagne, Chris Anagnostopoulos
Date: 2024-10-24 00:00:00
Tasks: Representation Learning

Many therapies are effective in treating multiple diseases. We present an approach that leverages methods developed in natural language processing and real-world data to prioritize potential, new indications for a mechanism of action (MoA). We specifically use representation learning to generate embeddings of indications and prioritize them based on their proximity to the indications with the strongest available evidence for the MoA. We demonstrate the successful deployment of our approach for anti-IL-17A using embeddings generated with SPPMI and present an evaluation framework to determine the quality of indication finding results and the derived embeddings.
Cross Spline Net and a Unified World
Authors: Linwei Hu, Ye Jin Choi, Vijayan N. Nair
Date: 2024-10-24 00:00:00

In today's machine learning world for tabular data, XGBoost and fully connected neural network (FCNN) are two most popular methods due to their good model performance and convenience to use. However, they are highly complicated, hard to interpret, and can be overfitted. In this paper, we propose a new modeling framework called cross spline net (CSN) that is based on a combination of spline transformation and cross-network (Wang et al. 2017, 2021). We will show CSN is as performant and convenient to use, and is less complicated, more interpretable and robust. Moreover, the CSN framework is flexible, as the spline layer can be configured differently to yield different models. With different choices of the spline layer, we can reproduce or approximate a set of non-neural network models, including linear and spline-based statistical models, tree, rule-fit, tree-ensembles (gradient boosting trees, random forest), oblique tree/forests, multi-variate adaptive regression spline (MARS), SVM with polynomial kernel, etc. Therefore, CSN provides a unified modeling framework that puts the above set of non-neural network models under the same neural network framework. By using scalable and powerful gradient descent algorithms available in neural network libraries, CSN avoids some pitfalls (such as being ad-hoc, greedy or non-scalable) in the case-specific optimization methods used in the above non-neural network models. We will use a special type of CSN, TreeNet, to illustrate our point. We will compare TreeNet with XGBoost and FCNN to show the benefits of TreeNet. We believe CSN will provide a flexible and convenient framework for practitioners to build performant, robust and more interpretable models.
Learning Coupled Subspaces for Multi-Condition Spike Data
Authors: Yididiya Y. Nadew, Xuhui Fan, Christopher J. Quinn
Date: 2024-10-24 00:00:00

In neuroscience, researchers typically conduct experiments under multiple conditions to acquire neural responses in the form of high-dimensional spike train datasets. Analysing high-dimensional spike data is a challenging statistical problem. To this end, Gaussian process factor analysis (GPFA), a popular class of latent variable models has been proposed. GPFA extracts smooth, low-dimensional latent trajectories underlying high-dimensional spike train datasets. However, such analyses are often done separately for each experimental condition, contrary to the nature of neural datasets, which contain recordings under multiple experimental conditions. Exploiting the parametric nature of these conditions, we propose a multi-condition GPFA model and inference procedure to learn the underlying latent structure in the corresponding datasets in sample-efficient manner. In particular, we propose a non-parametric Bayesian approach to learn a smooth tuning function over the experiment condition space. Our approach not only boosts model accuracy and is faster, but also improves model interpretability compared to approaches that separately fit models for each experimental condition.