pwc-archive/papers-with-abstracts huggingface dataset:
Generating Drug Repurposing Hypotheses through the Combination of Disease-Specific Hypergraphs
Authors: Ayush Jain, Marie Laure-Charpignon, Irene Y. Chen, Anthony Philippakis, Ahmed Alaa
Date: 2023-11-16 00:00:00
Tasks: All, Representation Learning

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph representations have recently yielded new drug repurposing hypotheses. In this study, we present a novel, disease-specific hypergraph representation learning technique to derive contextual embeddings of biological pathways of various lengths but that all start at any given drug and all end at the disease of interest. Further, we extend this method to multi-disease hypergraphs. To determine the repurposing potential of each of the 1,522 drugs, we derive drug-specific distributions of cosine similarity values and ultimately consider the median for ranking. Cosine similarity values are computed between (1) all biological pathways starting at the considered drug and ending at the disease of interest and (2) all biological pathways starting at drugs currently prescribed against that disease and ending at the disease of interest. We illustrate our approach with Alzheimer's disease (AD) and two of its risk factors: hypertension (HTN) and type 2 diabetes (T2D). We compare each drug's rank across four hypergraph settings (single- or multi-disease): AD only, AD + HTN, AD + T2D, and AD + HTN + T2D. Notably, our framework led to the identification of two promising drugs whose repurposing potential was significantly higher in hypergraphs combining two diseases: dapagliflozin (antidiabetic; moved up, from top 32$\%$ to top 7$\%$, across all considered drugs) and debrisoquine (antihypertensive; moved up, from top 76$\%$ to top 23$\%$). Our approach serves as a hypothesis generation tool, to be paired with a validation pipeline relying on laboratory experiments and semi-automated parsing of the biomedical literature.
Accelerating material discovery with a threshold-driven hybrid acquisition policy-based Bayesian optimization
Authors: Ahmed Shoyeb Raihan, Hamed Khosravi, Srinjoy Das, Imtiaz Ahmed
Date: 2023-11-16 00:00:00
Tasks: Bayesian Optimization

Advancements in materials play a crucial role in technological progress. However, the process of discovering and developing materials with desired properties is often impeded by substantial experimental costs, extensive resource utilization, and lengthy development periods. To address these challenges, modern approaches often employ machine learning (ML) techniques such as Bayesian Optimization (BO), which streamline the search for optimal materials by iteratively selecting experiments that are most likely to yield beneficial results. However, traditional BO methods, while beneficial, often struggle with balancing the trade-off between exploration and exploitation, leading to sub-optimal performance in material discovery processes. This paper introduces a novel Threshold-Driven UCB-EI Bayesian Optimization (TDUE-BO) method, which dynamically integrates the strengths of Upper Confidence Bound (UCB) and Expected Improvement (EI) acquisition functions to optimize the material discovery process. Unlike the classical BO, our method focuses on efficiently navigating the high-dimensional material design space (MDS). TDUE-BO begins with an exploration-focused UCB approach, ensuring a comprehensive initial sweep of the MDS. As the model gains confidence, indicated by reduced uncertainty, it transitions to the more exploitative EI method, focusing on promising areas identified earlier. The UCB-to-EI switching policy dictated guided through continuous monitoring of the model uncertainty during each step of sequential sampling results in navigating through the MDS more efficiently while ensuring rapid convergence. The effectiveness of TDUE-BO is demonstrated through its application on three different material datasets, showing significantly better approximation and optimization performance over the EI and UCB-based BO methods in terms of the RMSE scores and convergence efficiency, respectively.
Group-Aware Interest Disentangled Dual-Training for Personalized Recommendation
Authors: Xiaolong Liu, Liangwei Yang, Zhiwei Liu, Xiaohan Li, Mingdai Yang, Chen Wang, Philip S. Yu
Date: 2023-11-16 00:00:00
Tasks: Informativeness, Recommendation Systems

Personalized recommender systems aim to predict users' preferences for items. It has become an indispensable part of online services. Online social platforms enable users to form groups based on their common interests. The users' group participation on social platforms reveals their interests and can be utilized as side information to mitigate the data sparsity and cold-start problem in recommender systems. Users join different groups out of different interests. In this paper, we generate group representation from the user's interests and propose IGRec (Interest-based Group enhanced Recommendation) to utilize the group information accurately. It consists of four modules. (1) Interest disentangler via self-gating that disentangles users' interests from their initial embedding representation. (2) Interest aggregator that generates the interest-based group representation by Gumbel-Softmax aggregation on the group members' interests. (3) Interest-based group aggregation that fuses user's representation with the participated group representation. (4) A dual-trained rating prediction module to utilize both user-item and group-item interactions. We conduct extensive experiments on three publicly available datasets. Results show IGRec can effectively alleviate the data sparsity problem and enhance the recommender system with interest-based group representation. Experiments on the group recommendation task further show the informativeness of interest-based group representation.
A Knowledge Distillation Approach for Sepsis Outcome Prediction from Multivariate Clinical Time Series
Authors: Anna Wong, Shu Ge, Nassim Oufattole, Adam Dejl, Megan Su, Ardavan Saeedi, Li-wei H. Lehman
Date: 2023-11-16 00:00:00
Tasks: Knowledge Distillation, Time Series, Variational Inference

Sepsis is a life-threatening condition triggered by an extreme infection response. Our objective is to forecast sepsis patient outcomes using their medical history and treatments, while learning interpretable state representations to assess patients' risks in developing various adverse outcomes. While neural networks excel in outcome prediction, their limited interpretability remains a key issue. In this work, we use knowledge distillation via constrained variational inference to distill the knowledge of a powerful "teacher" neural network model with high predictive power to train a "student" latent variable model to learn interpretable hidden state representations to achieve high predictive performance for sepsis outcome prediction. Using real-world data from the MIMIC-IV database, we trained an LSTM as the "teacher" model to predict mortality for sepsis patients, given information about their recent history of vital signs, lab values and treatments. For our student model, we use an autoregressive hidden Markov model (AR-HMM) to learn interpretable hidden states from patients' clinical time series, and use the posterior distribution of the learned state representations to predict various downstream outcomes, including hospital mortality, pulmonary edema, need for diuretics, dialysis, and mechanical ventilation. Our results show that our approach successfully incorporates the constraint to achieve high predictive power similar to the teacher model, while maintaining the generative performance.
A Speed Odyssey for Deployable Quantization of LLMs
Authors: Qingyuan Li, Ran Meng, Yiduo Li, Bo Zhang, Liang Li, Yifan Lu, Xiangxiang Chu, Yerui Sun, Yuchen Xie
Date: 2023-11-16 00:00:00
Tasks: Language Modeling, Language Modelling, Large Language Model, Model Compression, Quantization

The large language model era urges faster and less costly inference. Prior model compression works on LLMs tend to undertake a software-centric approach primarily focused on the simulated quantization performance. By neglecting the feasibility of deployment, these approaches are typically disabled in real practice. They used to drastically push down the quantization bit range for a reduced computation which might not be supported by the mainstream hardware, or involve sophisticated algorithms that introduce extra computation or memory access overhead. We argue that pursuing a hardware-centric approach in the construction of quantization algorithms is crucial. In this regard, we are driven to build our compression method on top of hardware awareness, eliminating impractical algorithm choices while maximizing the benefit of hardware acceleration. Our method, OdysseyLLM, comes with a novel W4A8 kernel implementation called FastGEMM and a combined recipe of quantization strategies. Extensive experiments manifest the superiority of our W4A8 method which brings the actual speed boosting up to \textbf{4$\times$} compared to Hugging Face FP16 inference and \textbf{2.23$\times$} vs. the state-of-the-art inference engine TensorRT-LLM in FP16, and \textbf{1.45$\times$} vs. TensorRT-LLM in INT8, yet without substantially harming the performance.
Know Thy Neighbors: A Graph Based Approach for Effective Sensor-Based Human Activity Recognition in Smart Homes
Authors: Srivatsa P, Thomas Plötz
Date: 2023-11-16 00:00:00
Tasks: Activity Recognition, Human Activity Recognition

There has been a resurgence of applications focused on Human Activity Recognition (HAR) in smart homes, especially in the field of ambient intelligence and assisted living technologies. However, such applications present numerous significant challenges to any automated analysis system operating in the real world, such as variability, sparsity, and noise in sensor measurements. Although state-of-the-art HAR systems have made considerable strides in addressing some of these challenges, they especially suffer from a practical limitation: they require successful pre-segmentation of continuous sensor data streams before automated recognition, i.e., they assume that an oracle is present during deployment, which is capable of identifying time windows of interest across discrete sensor events. To overcome this limitation, we propose a novel graph-guided neural network approach that performs activity recognition by learning explicit co-firing relationships between sensors. We accomplish this by learning a more expressive graph structure representing the sensor network in a smart home, in a data-driven manner. Our approach maps discrete input sensor measurements to a feature space through the application of attention mechanisms and hierarchical pooling of node embeddings. We demonstrate the effectiveness of our proposed approach by conducting several experiments on CASAS datasets, showing that the resulting graph-guided neural network outperforms the state-of-the-art method for HAR in smart homes across multiple datasets and by large margins. These results are promising because they push HAR for smart homes closer to real-world applications.
Identifying Systems with Symmetries using Equivariant Autoregressive Reservoir Computers
Authors: Fredy Vides, Idelfonso B. R. Nogueira, Lendy Banegas, Evelyn Flores
Date: 2023-11-16 00:00:00
Tasks: Time Series

The investigation reported in this document focuses on identifying systems with symmetries using equivariant autoregressive reservoir computers. General results in structured matrix approximation theory are presented, exploring a two-fold approach. Firstly, a comprehensive examination of generic symmetry-preserving nonlinear time delay embedding is conducted. This involves analyzing time series data sampled from an equivariant system under study. Secondly, sparse least-squares methods are applied to discern approximate representations of the output coupling matrices. These matrices play a pivotal role in determining the nonlinear autoregressive representation of an equivariant system. The structural characteristics of these matrices are dictated by the set of symmetries inherent in the system. The document outlines prototypical algorithms derived from the described techniques, offering insight into their practical applications. Emphasis is placed on their effectiveness in the identification and predictive simulation of equivariant nonlinear systems, regardless of whether such systems exhibit chaotic behavior.
Investigating the Impact of Weight Sharing Decisions on Knowledge Transfer in Continual Learning
Authors: Josh Andle, Ali Payani, Salimeh Yasaei-Sekeh
Date: 2023-11-16 00:00:00
Tasks: Continual Learning, Decision Making, Transfer Learning

Continual Learning (CL) has generated attention as a method of avoiding Catastrophic Forgetting (CF) in the sequential training of neural networks, improving network efficiency and adaptability to different tasks. Additionally, CL serves as an ideal setting for studying network behavior and Forward Knowledge Transfer (FKT) between tasks. Pruning methods for CL train subnetworks to handle the sequential tasks which allows us to take a structured approach to investigating FKT. Sharing prior subnetworks' weights leverages past knowledge for the current task through FKT. Understanding which weights to share is important as sharing all weights can yield sub-optimal accuracy. This paper investigates how different sharing decisions affect the FKT between tasks. Through this lens we demonstrate how task complexity and similarity influence the optimal weight sharing decisions, giving insights into the relationships between tasks and helping inform decision making in similar CL methods. We implement three sequential datasets designed to emphasize variation in task complexity and similarity, reporting results for both ResNet-18 and VGG-16. By sharing in accordance with the decisions supported by our findings, we show that we can improve task accuracy compared to other sharing decisions.
Network Wide Evacuation Traffic Prediction in a Rapidly Intensifying Hurricane from Traffic Detectors and Facebook Movement Data: A Deep Learning Approach
Authors: Md Mobasshir Rashid, Rezaur Rahman, Samiul Hasan
Date: 2023-11-16 00:00:00
Tasks: Prediction, Traffic Prediction, Transfer Learning

Traffic prediction during hurricane evacuation is essential for optimizing the use of transportation infrastructures. It can reduce evacuation time by providing information on future congestion in advance. However, evacuation traffic prediction can be challenging as evacuation traffic patterns is significantly different than regular period traffic. A data-driven traffic prediction model is developed in this study by utilizing traffic detector and Facebook movement data during Hurricane Ian, a rapidly intensifying hurricane. We select 766 traffic detectors from Florida's 4 major interstates to collect traffic features. Additionally, we use Facebook movement data collected during Hurricane Ian's evacuation period. The deep-learning model is first trained on regular period (May-August 2022) data to understand regular traffic patterns and then Hurricane Ian's evacuation period data is used as test data. The model achieves 95% accuracy (RMSE = 356) during regular period, but it underperforms with 55% accuracy (RMSE = 1084) during the evacuation period. Then, a transfer learning approach is adopted where a pretrained model is used with additional evacuation related features to predict evacuation period traffic. After transfer learning, the model achieves 89% accuracy (RMSE = 514). Adding Facebook movement data further reduces model's RMSE value to 393 and increases accuracy to 93%. The proposed model is capable to forecast traffic up to 6-hours in advance. Evacuation traffic management officials can use the developed traffic prediction model to anticipate future traffic congestion in advance and take proactive measures to reduce delays during evacuation.
Spatial Bayesian Neural Networks
Authors: Andrew Zammit-Mangion, Michael D. Kaminski, Ba-Hien Tran, Maurizio Filippone, Noel Cressie
Date: 2023-11-16 00:00:00
Tasks: Gaussian Processes

interpretable, and well understood models that are routinely employed even though, as is revealed through prior and posterior predictive checks, these can poorly characterise the spatial heterogeneity in the underlying process of interest. Here, we propose a new, flexible class of spatial-process models, which we refer to as spatial Bayesian neural networks (SBNNs). An SBNN leverages the representational capacity of a Bayesian neural network; it is tailored to a spatial setting by incorporating a spatial ``embedding layer'' into the network and, possibly, spatially-varying network parameters. An SBNN is calibrated by matching its finite-dimensional distribution at locations on a fine gridding of space to that of a target process of interest. That process could be easy to simulate from or we may have many realisations from it. We propose several variants of SBNNs, most of which are able to match the finite-dimensional distribution of the target process at the selected grid better than conventional BNNs of similar complexity. We also show that an SBNN can be used to represent a variety of spatial processes often used in practice, such as Gaussian processes, lognormal processes, and max-stable processes. We briefly discuss the tools that could be used to make inference with SBNNs, and we conclude with a discussion of their advantages and limitations.
Show Your Work with Confidence: Confidence Bands for Tuning Curves
Authors: Nicholas Lourie, Kyunghyun Cho, He He
Date: 2023-11-16 00:00:00

The choice of hyperparameters greatly impacts performance in natural language processing. Often, it is hard to tell if a method is better than another or just better tuned. Tuning curves fix this ambiguity by accounting for tuning effort. Specifically, they plot validation performance as a function of the number of hyperparameter choices tried so far. While several estimators exist for these curves, it is common to use point estimates, which we show fail silently and give contradictory results when given too little data. Beyond point estimates, confidence bands are necessary to rigorously establish the relationship between different approaches. We present the first method to construct valid confidence bands for tuning curves. The bands are exact, simultaneous, and distribution-free, thus they provide a robust basis for comparing methods. Empirical analysis shows that while bootstrap confidence bands, which serve as a baseline, fail to approximate their target confidence, ours achieve it exactly. We validate our design with ablations, analyze the effect of sample size, and provide guidance on comparing models with our method. To promote confident comparisons in future work, we release opda: an easy-to-use library that you can install with pip. https://github.com/nicholaslourie/opda
Soft Matching Distance: A metric on neural representations that captures single-neuron tuning
Authors: Meenakshi Khosla, Alex H. Williams
Date: 2023-11-16 00:00:00

Common measures of neural representational (dis)similarity are designed to be insensitive to rotations and reflections of the neural activation space. Motivated by the premise that the tuning of individual units may be important, there has been recent interest in developing stricter notions of representational (dis)similarity that require neurons to be individually matched across networks. When two networks have the same size (i.e. same number of neurons), a distance metric can be formulated by optimizing over neuron index permutations to maximize tuning curve alignment. However, it is not clear how to generalize this metric to measure distances between networks with different sizes. Here, we leverage a connection to optimal transport theory to derive a natural generalization based on "soft" permutations. The resulting metric is symmetric, satisfies the triangle inequality, and can be interpreted as a Wasserstein distance between two empirical distributions. Further, our proposed metric avoids counter-intuitive outcomes suffered by alternative approaches, and captures complementary geometric insights into neural representations that are entirely missed by rotation-invariant metrics.
Labeled Interactive Topic Models
Authors: Kyle Seelman, Mozhi Zhang, Jordan Boyd-Graber
Date: 2023-11-15 00:00:00
Tasks: Topic Models

Topic models are valuable for understanding extensive document collections, but they don't always identify the most relevant topics. Classical probabilistic and anchor-based topic models offer interactive versions that allow users to guide the models towards more pertinent topics. However, such interactive features have been lacking in neural topic models. To correct this lacuna, we introduce a user-friendly interaction for neural topic models. This interaction permits users to assign a word label to a topic, leading to an update in the topic model where the words in the topic become closely aligned with the given label. Our approach encompasses two distinct kinds of neural topic models. The first includes models where topic embeddings are trainable and evolve during the training process. The second kind involves models where topic embeddings are integrated post-training, offering a different approach to topic refinement. To facilitate user interaction with these neural topic models, we have developed an interactive interface. This interface enables users to engage with and re-label topics as desired. We evaluate our method through a human study, where users can relabel topics to find relevant documents. Using our method, user labeling improves document rank scores, helping to find more relevant documents to a given query when compared to no user labeling.
Striped Attention: Faster Ring Attention for Causal Transformers
Authors: William Brandon, Aniruddha Nrusimha, Kevin Qian, Zachary Ankner, Tian Jin, Zhiye Song, Jonathan Ragan-Kelley
Date: 2023-11-15 00:00:00

To help address the growing demand for ever-longer sequence lengths in transformer models, Liu et al. recently proposed Ring Attention, an exact attention algorithm capable of overcoming per-device memory bottle- necks by distributing self-attention across multiple devices. In this paper, we study the performance characteristics of Ring Attention in the important special case of causal transformer models, and identify a key workload imbal- ance due to triangular structure of causal attention computations. We propose a simple extension to Ring Attention, which we call Striped Attention to fix this imbalance. Instead of devices having contiguous subsequences, each device has a subset of tokens distributed uniformly throughout the sequence, which we demonstrate leads to more even workloads. In experiments running Striped Attention on A100 GPUs and TPUv4s, we are able to achieve up to 1.45x end-to-end throughput improvements over the original Ring Attention algorithm on causal transformer training at a sequence length of 256k. Furthermore, on 16 TPUv4 chips, we were able to achieve 1.65x speedups at sequence lengths of 786k. We release the code for our experiments as open source
Alternatives to the Scaled Dot Product for Attention in the Transformer Neural Network Architecture
Authors: James Bernhard
Date: 2023-11-15 00:00:00

The transformer neural network architecture uses a form of attention in which the dot product of query and key is divided by the square root of the key dimension before applying softmax. This scaling of the dot product is designed to avoid the absolute value of the dot products becoming so large that applying softmax leads to vanishing gradients. In this paper, we propose some alternative scalings, including dividing the dot product instead by the sum of the key lengths before applying softmax. We use simulated keys and queries to show that in many situations this appears to be more effective at avoiding regions where applying softmax leads to vanishing gradients.