pwc-archive/papers-with-abstracts huggingface dataset:
Question Answering for Electronic Health Records: A Scoping Review of datasets and models
Authors: Jayetri Bardhan, Kirk Roberts, Daisy Zhe Wang
Date: 2023-10-12 00:00:00
Tasks: Articles, Decision Making, Question Answering

Question Answering (QA) systems on patient-related data can assist both clinicians and patients. They can, for example, assist clinicians in decision-making and enable patients to have a better understanding of their medical history. Significant amounts of patient data are stored in Electronic Health Records (EHRs), making EHR QA an important research area. In EHR QA, the answer is obtained from the medical record of the patient. Because of the differences in data format and modality, this differs greatly from other medical QA tasks that employ medical websites or scientific papers to retrieve answers, making it critical to research EHR question answering. This study aimed to provide a methodological review of existing works on QA over EHRs. We searched for articles from January 1st, 2005 to September 30th, 2023 in four digital sources including Google Scholar, ACL Anthology, ACM Digital Library, and PubMed to collect relevant publications on EHR QA. 4111 papers were identified for our study, and after screening based on our inclusion criteria, we obtained a total of 47 papers for further study. Out of the 47 papers, 25 papers were about EHR QA datasets, and 37 papers were about EHR QA models. It was observed that QA on EHRs is relatively new and unexplored. Most of the works are fairly recent. Also, it was observed that emrQA is by far the most popular EHR QA dataset, both in terms of citations and usage in other papers. Furthermore, we identified the different models used in EHR QA along with the evaluation metrics used for these models.
Detection and prediction of clopidogrel treatment failures using longitudinal structured electronic health records
Authors: Samuel Kim, In Gu Sean Lee, Mijeong Irene Ban, Jane Chiang
Date: 2023-10-12 00:00:00
Tasks: Time Series

We propose machine learning algorithms to automatically detect and predict clopidogrel treatment failure using longitudinal structured electronic health records (EHR). By drawing analogies between natural language and structured EHR, we introduce various machine learning algorithms used in natural language processing (NLP) applications to build models for treatment failure detection and prediction. In this regard, we generated a cohort of patients with clopidogrel prescriptions from UK Biobank and annotated if the patients had treatment failure events within one year of the first clopidogrel prescription; out of 502,527 patients, 1,824 patients were identified as treatment failure cases, and 6,859 patients were considered as control cases. From the dataset, we gathered diagnoses, prescriptions, and procedure records together per patient and organized them into visits with the same date to build models. The models were built for two different tasks, i.e., detection and prediction, and the experimental results showed that time series models outperform bag-of-words approaches in both tasks. In particular, a Transformer-based model, namely BERT, could reach 0.928 AUC in detection tasks and 0.729 AUC in prediction tasks. BERT also showed competence over other time series models when there is not enough training data, because it leverages the pre-training procedure using large unlabeled data.
Tokenizer Choice For LLM Training: Negligible or Crucial?
Authors: Mehdi Ali, Michael Fromm, Klaudia Thellmann, Richard Rutmann, Max Lübbering, Johannes Leveling, Katrin Klug, Jan Ebert, Niclas Doll, Jasper Schulze Buschhoff, Charvi Jain, Alexander Arno Weber, Lena Jurkschat, Hammam Abdelwahab, Chelsea John, Pedro Ortiz Suarez, Malte Ostendorff, Samuel Weinbach, Rafet Sifa, Stefan Kesselheim, Nicolas Flores-Herr
Date: 2023-10-12 00:00:00

The recent success of Large Language Models (LLMs) has been predominantly driven by curating the training dataset composition, scaling of model architectures and dataset sizes and advancements in pretraining objectives, leaving tokenizer influence as a blind spot. Shedding light on this underexplored area, we conduct a comprehensive study on the influence of tokenizer choice on LLM downstream performance by training 24 mono- and multilingual LLMs at a 2.6B parameter scale, ablating different tokenizer algorithms and parameterizations. Our studies highlight that the tokenizer choice can significantly impact the model's downstream performance and training costs. In particular, we find that the common tokenizer evaluation metrics fertility and parity are not always predictive of model downstream performance, rendering these metrics a questionable proxy for the model's downstream performance. Furthermore, we show that multilingual tokenizers trained on the five most frequent European languages require vocabulary size increases of factor three in comparison to English. While English-centric tokenizers have been applied to the training of multi-lingual LLMs in the past, we find that this approach results in a severe downstream performance degradation and additional training costs of up to 68%, due to an inefficient tokenization vocabulary.
Search-Adaptor: Embedding Customization for Information Retrieval
Authors: Jinsung Yoon, Sercan O Arik, Yanfei Chen, Tomas Pfister
Date: 2023-10-12 00:00:00
Tasks: Information Retrieval, Retrieval

Embeddings extracted by pre-trained Large Language Models (LLMs) have significant potential to improve information retrieval and search. Beyond the zero-shot setup in which they are being conventionally used, being able to take advantage of the information from the relevant query-corpus paired data can further boost the LLM capabilities. In this paper, we propose a novel method, Search-Adaptor, for customizing LLMs for information retrieval in an efficient and robust way. Search-Adaptor modifies the embeddings generated by pre-trained LLMs, and can be integrated with any LLM, including those only available via prediction APIs. On multiple English, multilingual, and multimodal retrieval datasets, we show consistent and significant performance benefits for Search-Adaptor -- e.g., more than 5% improvements for Google Embedding APIs in nDCG@10 averaged over 14 BEIR datasets.
Evolutionary Dynamic Optimization and Machine Learning
Authors: Abdennour Boulesnane
Date: 2023-10-12 00:00:00
Tasks: Diversity, Evolutionary Algorithms, feature selection

Evolutionary Computation (EC) has emerged as a powerful field of Artificial Intelligence, inspired by nature's mechanisms of gradual development. However, EC approaches often face challenges such as stagnation, diversity loss, computational complexity, population initialization, and premature convergence. To overcome these limitations, researchers have integrated learning algorithms with evolutionary techniques. This integration harnesses the valuable data generated by EC algorithms during iterative searches, providing insights into the search space and population dynamics. Similarly, the relationship between evolutionary algorithms and Machine Learning (ML) is reciprocal, as EC methods offer exceptional opportunities for optimizing complex ML tasks characterized by noisy, inaccurate, and dynamic objective functions. These hybrid techniques, known as Evolutionary Machine Learning (EML), have been applied at various stages of the ML process. EC techniques play a vital role in tasks such as data balancing, feature selection, and model training optimization. Moreover, ML tasks often require dynamic optimization, for which Evolutionary Dynamic Optimization (EDO) is valuable. This paper presents the first comprehensive exploration of reciprocal integration between EDO and ML. The study aims to stimulate interest in the evolutionary learning community and inspire innovative contributions in this domain.
Robustness to Multi-Modal Environment Uncertainty in MARL using Curriculum Learning
Authors: Aakriti Agrawal, Rohith Aralikatti, Yanchao Sun, Furong Huang
Date: 2023-10-12 00:00:00
Tasks: Multi-agent Reinforcement Learning

Multi-agent reinforcement learning (MARL) plays a pivotal role in tackling real-world challenges. However, the seamless transition of trained policies from simulations to real-world requires it to be robust to various environmental uncertainties. Existing works focus on finding Nash Equilibrium or the optimal policy under uncertainty in one environment variable (i.e. action, state or reward). This is because a multi-agent system itself is highly complex and unstationary. However, in real-world situation uncertainty can occur in multiple environment variables simultaneously. This work is the first to formulate the generalised problem of robustness to multi-modal environment uncertainty in MARL. To this end, we propose a general robust training approach for multi-modal uncertainty based on curriculum learning techniques. We handle two distinct environmental uncertainty simultaneously and present extensive results across both cooperative and competitive MARL environments, demonstrating that our approach achieves state-of-the-art levels of robustness.
Circuit Component Reuse Across Tasks in Transformer Language Models
Authors: Jack Merullo, Carsten Eickhoff, Ellie Pavlick
Date: 2023-10-12 00:00:00

Recent work in mechanistic interpretability has shown that behaviors in language models can be successfully reverse-engineered through circuit analysis. A common criticism, however, is that each circuit is task-specific, and thus such analysis cannot contribute to understanding the models at a higher level. In this work, we present evidence that insights (both low-level findings about specific heads and higher-level findings about general algorithms) can indeed generalize across tasks. Specifically, we study the circuit discovered in Wang et al. (2022) for the Indirect Object Identification (IOI) task and 1.) show that it reproduces on a larger GPT2 model, and 2.) that it is mostly reused to solve a seemingly different task: Colored Objects (Ippolito & Callison-Burch, 2023). We provide evidence that the process underlying both tasks is functionally very similar, and contains about a 78% overlap in in-circuit attention heads. We further present a proof-of-concept intervention experiment, in which we adjust four attention heads in middle layers in order to 'repair' the Colored Objects circuit and make it behave like the IOI circuit. In doing so, we boost accuracy from 49.6% to 93.7% on the Colored Objects task and explain most sources of error. The intervention affects downstream attention heads in specific ways predicted by their interactions in the IOI circuit, indicating that this subcircuit behavior is invariant to the different task inputs. Overall, our results provide evidence that it may yet be possible to explain large language models' behavior in terms of a relatively small number of interpretable task-general algorithmic building blocks and computational components.
Splicing Up Your Predictions with RNA Contrastive Learning
Authors: Philip Fradkin, Ruian Shi, Bo wang, Brendan Frey, Leo J. Lee
Date: 2023-10-12 00:00:00
Tasks: Contrastive Learning, Property Prediction, Sentence

In the face of rapidly accumulating genomic data, our understanding of the RNA regulatory code remains incomplete. Recent self-supervised methods in other domains have demonstrated the ability to learn rules underlying the data-generating process such as sentence structure in language. Inspired by this, we extend contrastive learning techniques to genomic data by utilizing functional similarities between sequences generated through alternative splicing and gene duplication. Our novel dataset and contrastive objective enable the learning of generalized RNA isoform representations. We validate their utility on downstream tasks such as RNA half-life and mean ribosome load prediction. Our pre-training strategy yields competitive results using linear probing on both tasks, along with up to a two-fold increase in Pearson correlation in low-data conditions. Importantly, our exploration of the learned latent space reveals that our contrastive objective yields semantically meaningful representations, underscoring its potential as a valuable initialization technique for RNA property prediction.
Provably Cost-Sensitive Adversarial Defense via Randomized Smoothing
Authors: Yuan Xin, Dingfan Chen, Michael Backes, Xiao Zhang
Date: 2023-10-12 00:00:00
Tasks: Adversarial Defense

As ML models are increasingly deployed in critical applications, robustness against adversarial perturbations is crucial. While numerous defenses have been proposed to counter such attacks, they typically assume that all adversarial transformations are equally important, an assumption that rarely aligns with real-world applications. To address this, we study the problem of robust learning against adversarial perturbations under cost-sensitive scenarios, where the potential harm of different types of misclassifications is encoded in a cost matrix. Our solution introduces a provably robust learning algorithm to certify and optimize for cost-sensitive robustness, building on the scalable certification framework of randomized smoothing. Specifically, we formalize the definition of cost-sensitive certified radius and propose our novel adaptation of the standard certification algorithm to generate tight robustness certificates tailored to any cost matrix. In addition, we design a robust training method that improves certified cost-sensitive robustness without compromising model accuracy. Extensive experiments on benchmark datasets, including challenging ones unsolvable by existing methods, demonstrate the effectiveness of our certification algorithm and training method across various cost-sensitive scenarios.
Heterophily-Based Graph Neural Network for Imbalanced Classification
Authors: Zirui Liang, Yuntao Li, Tianjin Huang, Akrati Saxena, Yulong Pei, Mykola Pechenizkiy
Date: 2023-10-12 00:00:00
Tasks: Classification, Graph Neural Network, imbalanced classification, Node Classification

Graph neural networks (GNNs) have shown promise in addressing graph-related problems, including node classification. However, conventional GNNs assume an even distribution of data across classes, which is often not the case in real-world scenarios, where certain classes are severely underrepresented. This leads to suboptimal performance of standard GNNs on imbalanced graphs. In this paper, we introduce a unique approach that tackles imbalanced classification on graphs by considering graph heterophily. We investigate the intricate relationship between class imbalance and graph heterophily, revealing that minority classes not only exhibit a scarcity of samples but also manifest lower levels of homophily, facilitating the propagation of erroneous information among neighboring nodes. Drawing upon this insight, we propose an efficient method, called Fast Im-GBK, which integrates an imbalance classification strategy with heterophily-aware GNNs to effectively address the class imbalance problem while significantly reducing training time. Our experiments on real-world graphs demonstrate our model's superiority in classification performance and efficiency for node classification tasks compared to existing baselines.
Designing Observables for Measurements with Deep Learning
Authors: Owen Long, Benjamin Nachman
Date: 2023-10-12 00:00:00
Tasks: Deep Learning

Many analyses in particle and nuclear physics use simulations to infer fundamental, effective, or phenomenological parameters of the underlying physics models. When the inference is performed with unfolded cross sections, the observables are designed using physics intuition and heuristics. We propose to design targeted observables with machine learning. Unfolded, differential cross sections in a neural network output contain the most information about parameters of interest and can be well-measured by construction. The networks are trained using a custom loss function that rewards outputs that are sensitive to the parameter(s) of interest while simultaneously penalizing outputs that are different between particle-level and detector-level (to minimize detector distortions). We demonstrate this idea in simulation using two physics models for inclusive measurements in deep inelastic scattering. We find that the new approach is more sensitive than classical observables at distinguishing the two models and also has a reduced unfolding uncertainty due to the reduced detector distortions.
Waymax: An Accelerated, Data-Driven Simulator for Large-Scale Autonomous Driving Research
Date: 2023-10-12 00:00:00
Proceeding: NeurIPS 2023 11
Tasks: Autonomous Driving

Simulation is an essential tool to develop and benchmark autonomous vehicle planning software in a safe and cost-effective manner. However, realistic simulation requires accurate modeling of nuanced and complex multi-agent interactive behaviors. To address these challenges, we introduce Waymax, a new data-driven simulator for autonomous driving in multi-agent scenes, designed for large-scale simulation and testing. Waymax uses publicly-released, real-world driving data (e.g., the Waymo Open Motion Dataset) to initialize or play back a diverse set of multi-agent simulated scenarios. It runs entirely on hardware accelerators such as TPUs/GPUs and supports in-graph simulation for training, making it suitable for modern large-scale, distributed machine learning workflows. To support online training and evaluation, Waymax includes several learned and hard-coded behavior models that allow for realistic interaction within simulation. To supplement Waymax, we benchmark a suite of popular imitation and reinforcement learning algorithms with ablation studies on different design decisions, where we highlight the effectiveness of routes as guidance for planning agents and the ability of RL to overfit against simulated agents.
Polynomial Time Cryptanalytic Extraction of Neural Network Models
Authors: Adi Shamir, Isaac Canales-Martinez, Anna Hambitzer, Jorge Chavez-Saab, Francisco Rodrigez-Henriquez, Nitin Satpute
Date: 2023-10-12 00:00:00
Tasks: GPU

Billions of dollars and countless GPU hours are currently spent on training Deep Neural Networks (DNNs) for a variety of tasks. Thus, it is essential to determine the difficulty of extracting all the parameters of such neural networks when given access to their black-box implementations. Many versions of this problem have been studied over the last 30 years, and the best current attack on ReLU-based deep neural networks was presented at Crypto 2020 by Carlini, Jagielski, and Mironov. It resembles a differential chosen plaintext attack on a cryptosystem, which has a secret key embedded in its black-box implementation and requires a polynomial number of queries but an exponential amount of time (as a function of the number of neurons). In this paper, we improve this attack by developing several new techniques that enable us to extract with arbitrarily high precision all the real-valued parameters of a ReLU-based DNN using a polynomial number of queries and a polynomial amount of time. We demonstrate its practical efficiency by applying it to a full-sized neural network for classifying the CIFAR10 dataset, which has 3072 inputs, 8 hidden layers with 256 neurons each, and over million neuronal parameters. An attack following the approach by Carlini et al. requires an exhaustive search over 2 to the power 256 possibilities. Our attack replaces this with our new techniques, which require only 30 minutes on a 256-core computer.
Kernel-Elastic Autoencoder for Molecular Design
Authors: Haote Li, Yu Shee, Brandon Allen, Federica Maschietto, Victor Batista
Date: 2023-10-12 00:00:00
Tasks: Diversity, valid

We introduce the Kernel-Elastic Autoencoder (KAE), a self-supervised generative model based on the transformer architecture with enhanced performance for molecular design. KAE is formulated based on two novel loss functions: modified maximum mean discrepancy and weighted reconstruction. KAE addresses the long-standing challenge of achieving valid generation and accurate reconstruction at the same time. KAE achieves remarkable diversity in molecule generation while maintaining near-perfect reconstructions on the independent testing dataset, surpassing previous molecule-generating models. KAE enables conditional generation and allows for decoding based on beam search resulting in state-of-the-art performance in constrained optimizations. Furthermore, KAE can generate molecules conditional to favorable binding affinities in docking applications as confirmed by AutoDock Vina and Glide scores, outperforming all existing candidates from the training dataset. Beyond molecular design, we anticipate KAE could be applied to solve problems by generation in a wide range of applications.
Machine Learning Who to Nudge: Causal vs Predictive Targeting in a Field Experiment on Student Financial Aid Renewal
Authors: Susan Athey, Niall Keleher, Jann Spiess
Date: 2023-10-12 00:00:00

In many settings, interventions may be more effective for some individuals than others, so that targeting interventions may be beneficial. We analyze the value of targeting in the context of a large-scale field experiment with over 53,000 college students, where the goal was to use "nudges" to encourage students to renew their financial-aid applications before a non-binding deadline. We begin with baseline approaches to targeting. First, we target based on a causal forest that estimates heterogeneous treatment effects and then assigns students to treatment according to those estimated to have the highest treatment effects. Next, we evaluate two alternative targeting policies, one targeting students with low predicted probability of renewing financial aid in the absence of the treatment, the other targeting those with high probability. The predicted baseline outcome is not the ideal criterion for targeting, nor is it a priori clear whether to prioritize low, high, or intermediate predicted probability. Nonetheless, targeting on low baseline outcomes is common in practice, for example because the relationship between individual characteristics and treatment effects is often difficult or impossible to estimate with historical data. We propose hybrid approaches that incorporate the strengths of both predictive approaches (accurate estimation) and causal approaches (correct criterion); we show that targeting intermediate baseline outcomes is most effective in our specific application, while targeting based on low baseline outcomes is detrimental. In one year of the experiment, nudging all students improved early filing by an average of 6.4 percentage points over a baseline average of 37% filing, and we estimate that targeting half of the students using our preferred policy attains around 75% of this benefit.
Counting and Algorithmic Generalization with Transformers
Authors: Simon Ouellette, Rolf Pfister, Hansueli Jud
Date: 2023-10-12 00:00:00

Algorithmic generalization in machine learning refers to the ability to learn the underlying algorithm that generates data in a way that generalizes out-of-distribution. This is generally considered a difficult task for most machine learning algorithms. Here, we analyze algorithmic generalization when counting is required, either implicitly or explicitly. We show that standard Transformers are based on architectural decisions that hinder out-of-distribution performance for such tasks. In particular, we discuss the consequences of using layer normalization and of normalizing the attention weights via softmax. With ablation of the problematic operations, we demonstrate that a modified transformer can exhibit a good algorithmic generalization performance on counting while using a very lightweight architecture.