pwc-archive/papers-with-abstracts huggingface dataset:
Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations
Authors: Jiarui Lu, Zuobai Zhang, Bozitao Zhong, Chence Shi, Jian Tang
Date: 2024-02-16 00:00:00
Tasks: Physical Simulations

The protein dynamics are common and important for their biological functions and properties, the study of which usually involves time-consuming molecular dynamics (MD) simulations in silico. Recently, generative models has been leveraged as a surrogate sampler to obtain conformation ensembles with orders of magnitude faster and without requiring any simulation data (a "zero-shot" inference). However, being agnostic of the underlying energy landscape, the accuracy of such generative model may still be limited. In this work, we explore the few-shot setting of such pre-trained generative sampler which incorporates MD simulations in a tractable manner. Specifically, given a target protein of interest, we first acquire some seeding conformations from the pre-trained sampler followed by a number of physical simulations in parallel starting from these seeding samples. Then we fine-tuned the generative model using the simulation trajectories above to become a target-specific sampler. Experimental results demonstrated the superior performance of such few-shot conformation sampler at a tractable computational cost.
Fixed Confidence Best Arm Identification in the Bayesian Setting
Authors: Kyoungseok Jang, Junpei Komiyama, Kazutoshi Yamazaki
Date: 2024-02-16 00:00:00

We consider the fixed-confidence best arm identification (FC-BAI) problem in the Bayesian setting. This problem aims to find the arm of the largest mean with a fixed confidence level when the bandit model has been sampled from the known prior. Most studies on the FC-BAI problem have been conducted in the frequentist setting, where the bandit model is predetermined before the game starts. We show that the traditional FC-BAI algorithms studied in the frequentist setting, such as track-and-stop and top-two algorithms, result in arbitrarily suboptimal performances in the Bayesian setting. We also obtain a lower bound of the expected number of samples in the Bayesian setting and introduce a variant of successive elimination that has a matching performance with the lower bound up to a logarithmic factor. Simulations verify the theoretical results.
Normalizing flow neural networks by JKO scheme
Authors: Chen Xu, Xiuyuan Cheng, Yao Xie
Date: 2022-12-29 00:00:00
Proceeding: NeurIPS 2023 11

Normalizing flow is a class of deep generative models for efficient sampling and likelihood estimation, which achieves attractive performance, particularly in high dimensions. The flow is often implemented using a sequence of invertible residual blocks. Existing works adopt special network architectures and regularization of flow trajectories. In this paper, we develop a neural ODE flow network called JKO-iFlow, inspired by the Jordan-Kinderleherer-Otto (JKO) scheme, which unfolds the discrete-time dynamic of the Wasserstein gradient flow. The proposed method stacks residual blocks one after another, allowing efficient block-wise training of the residual blocks, avoiding sampling SDE trajectories and score matching or variational learning, thus reducing the memory load and difficulty in end-to-end training. We also develop adaptive time reparameterization of the flow network with a progressive refinement of the induced trajectory in probability space to improve the model accuracy further. Experiments with synthetic and real data show that the proposed JKO-iFlow network achieves competitive performance compared with existing flow and diffusion models at a significantly reduced computational and memory cost.
LogELECTRA: Self-supervised Anomaly Detection for Unstructured Logs
Authors: Yuuki Yamanaka, Tomokatsu Takahashi, Takuya Minami, Yoshiaki Nakajima
Date: 2024-02-16 00:00:00
Tasks: Anomaly Detection, Self-Supervised Anomaly Detection, Supervised Anomaly Detection

System logs are some of the most important information for the maintenance of software systems, which have become larger and more complex in recent years. The goal of log-based anomaly detection is to automatically detect system anomalies by analyzing the large number of logs generated in a short period of time, which is a critical challenge in the real world. Previous studies have used a log parser to extract templates from unstructured log data and detect anomalies on the basis of patterns of the template occurrences. These methods have limitations for logs with unknown templates. Furthermore, since most log anomalies are known to be point anomalies rather than contextual anomalies, detection methods based on occurrence patterns can cause unnecessary delays in detection. In this paper, we propose LogELECTRA, a new log anomaly detection model that analyzes a single line of log messages more deeply on the basis of self-supervised anomaly detection. LogELECTRA specializes in detecting log anomalies as point anomalies by applying ELECTRA, a natural language processing model, to analyze the semantics of a single line of log messages. LogELECTRA outperformed existing state-of-the-art methods in experiments on the public benchmark log datasets BGL, Sprit, and Thunderbird.
MFBind: a Multi-Fidelity Approach for Evaluating Drug Compounds in Practical Generative Modeling
Authors: Peter Eckmann, Dongxia Wu, Germano Heinzelmann, Michael K Gilson, Rose Yu
Date: 2024-02-16 00:00:00
Tasks: Active Learning, Activity Prediction, Drug Discovery, Molecular Docking

Current generative models for drug discovery primarily use molecular docking to evaluate the quality of generated compounds. However, such models are often not useful in practice because even compounds with high docking scores do not consistently show experimental activity. More accurate methods for activity prediction exist, such as molecular dynamics based binding free energy calculations, but they are too computationally expensive to use in a generative model. We propose a multi-fidelity approach, Multi-Fidelity Bind (MFBind), to achieve the optimal trade-off between accuracy and computational cost. MFBind integrates docking and binding free energy simulators to train a multi-fidelity deep surrogate model with active learning. Our deep surrogate model utilizes a pretraining technique and linear prediction heads to efficiently fit small amounts of high-fidelity data. We perform extensive experiments and show that MFBind (1) outperforms other state-of-the-art single and multi-fidelity baselines in surrogate modeling, and (2) boosts the performance of generative models with markedly higher quality compounds.
DataDreamer: A Tool for Synthetic Data Generation and Reproducible LLM Workflows
Authors: Ajay Patel, Colin Raffel, Chris Callison-Burch
Date: 2024-02-16 00:00:00
Tasks: Synthetic Data Generation

Large language models (LLMs) have become a dominant and important tool for NLP researchers in a wide range of tasks. Today, many researchers use LLMs in synthetic data generation, task evaluation, fine-tuning, distillation, and other model-in-the-loop research workflows. However, challenges arise when using these models that stem from their scale, their closed source nature, and the lack of standardized tooling for these new and emerging workflows. The rapid rise to prominence of these models and these unique challenges has had immediate adverse impacts on open science and on the reproducibility of work that uses them. In this paper, we introduce DataDreamer, an open source Python library that allows researchers to write simple code to implement powerful LLM workflows. DataDreamer also helps researchers adhere to best practices that we propose to encourage open science and reproducibility. The library and documentation are available at https://github.com/datadreamer-dev/DataDreamer .
Revisiting Experience Replayable Conditions
Authors: Taisuke Kobayashi
Date: 2024-02-15 00:00:00
Tasks: Deep Reinforcement Learning, Metric Learning

Experience replay (ER) used in (deep) reinforcement learning is considered to be applicable only to off-policy algorithms. However, there have been some cases in which ER has been applied for on-policy algorithms, suggesting that off-policyness might be a sufficient condition for applying ER. This paper reconsiders more strict "experience replayable conditions" (ERC) and proposes the way of modifying the existing algorithms to satisfy ERC. In light of this, it is postulated that the instability of policy improvements represents a pivotal factor in ERC. The instability factors are revealed from the viewpoint of metric learning as i) repulsive forces from negative samples and ii) replays of inappropriate experiences. Accordingly, the corresponding stabilization tricks are derived. As a result, it is confirmed through numerical simulations that the proposed stabilization tricks make ER applicable to an advantage actor-critic, an on-policy algorithm. Moreover, its learning performance is comparable to that of a soft actor-critic, a state-of-the-art off-policy algorithm.
Transductive Learning Is Compact
Authors: Julian Asilis, Siddartha Devic, Shaddin Dughmi, Vatsal Sharan, Shang-Hua Teng
Date: 2024-02-15 00:00:00
Tasks: Learning Theory, PAC learning, Transductive Learning

We demonstrate a compactness result holding broadly across supervised learning with a general class of loss functions: Any hypothesis class $H$ is learnable with transductive sample complexity $m$ precisely when all of its finite projections are learnable with sample complexity $m$. We prove that this exact form of compactness holds for realizable and agnostic learning with respect to any proper metric loss function (e.g., any norm on $\mathbb{R}^d$) and any continuous loss on a compact space (e.g., cross-entropy, squared loss). For realizable learning with improper metric losses, we show that exact compactness of sample complexity can fail, and provide matching upper and lower bounds of a factor of 2 on the extent to which such sample complexities can differ. We conjecture that larger gaps are possible for the agnostic case. Furthermore, invoking the equivalence between sample complexities in the PAC and transductive models (up to lower order factors, in the realizable case) permits us to directly port our results to the PAC model, revealing an almost-exact form of compactness holding broadly in PAC learning.
Can we Soft Prompt LLMs for Graph Learning Tasks?
Authors: Zheyuan Liu, Xiaoxin He, Yijun Tian, Nitesh V. Chawla
Date: 2024-02-15 00:00:00
Tasks: Graph Learning, Graph Neural Network, Link Prediction, Node Classification

Graph plays an important role in representing complex relationships in real-world applications such as social networks, biological data and citation networks. In recent years, Large Language Models (LLMs) have achieved tremendous success in various domains, which makes applying LLMs to graphs particularly appealing. However, directly applying LLMs to graph modalities presents unique challenges due to the discrepancy and mismatch between the graph and text modalities. Hence, to further investigate LLMs' potential for comprehending graph information, we introduce GraphPrompter, a novel framework designed to align graph information with LLMs via soft prompts. Specifically, GraphPrompter consists of two main components: a graph neural network to encode complex graph information and an LLM that effectively processes textual information. Comprehensive experiments on various benchmark datasets under node classification and link prediction tasks demonstrate the effectiveness of our proposed method. The GraphPrompter framework unveils the substantial capabilities of LLMs as predictors in graph-related tasks, enabling researchers to utilize LLMs across a spectrum of real-world graph scenarios more effectively.
Efficient Sampling on Riemannian Manifolds via Langevin MCMC
Authors: Xiang Cheng, Jingzhao Zhang, Suvrit Sra
Date: 2024-02-15 00:00:00

We study the task of efficiently sampling from a Gibbs distribution $d \pi^* = e^{-h} d {vol}_g$ over a Riemannian manifold $M$ via (geometric) Langevin MCMC; this algorithm involves computing exponential maps in random Gaussian directions and is efficiently implementable in practice. The key to our analysis of Langevin MCMC is a bound on the discretization error of the geometric Euler-Murayama scheme, assuming $\nabla h$ is Lipschitz and $M$ has bounded sectional curvature. Our error bound matches the error of Euclidean Euler-Murayama in terms of its stepsize dependence. Combined with a contraction guarantee for the geometric Langevin Diffusion under Kendall-Cranston coupling, we prove that the Langevin MCMC iterates lie within $\epsilon$-Wasserstein distance of $\pi^*$ after $\tilde{O}(\epsilon^{-2})$ steps, which matches the iteration complexity for Euclidean Langevin MCMC. Our results apply in general settings where $h$ can be nonconvex and $M$ can have negative Ricci curvature. Under additional assumptions that the Riemannian curvature tensor has bounded derivatives, and that $\pi^*$ satisfies a $CD(\cdot,\infty)$ condition, we analyze the stochastic gradient version of Langevin MCMC, and bound its iteration complexity by $\tilde{O}(\epsilon^{-2})$ as well.
Prompt-Based Bias Calibration for Better Zero/Few-Shot Learning of Language Models
Authors: Kang He, Yinghan Long, Kaushik Roy
Date: 2024-02-15 00:00:00
Tasks: Fairness, Few-Shot Learning, In-Context Learning, Language Modeling, Language Modelling, Sentiment Analysis, Topic Classification

Prompt-based learning is susceptible to intrinsic bias present in pre-trained language models (LMs), leading to sub-optimal performance in prompt-based zero/few-shot settings. In this work, we propose a null-input prompting method to calibrate intrinsic bias encoded in pre-trained LMs. Different from prior efforts that address intrinsic bias primarily for social fairness and often involve excessive computational cost, our objective is to explore enhancing LMs' performance in downstream zero/few-shot learning while emphasizing the efficiency of intrinsic bias calibration. Specifically, we leverage a diverse set of auto-selected null-meaning inputs generated from GPT-4 to probe intrinsic bias of pre-trained LMs. Utilizing the bias-reflected probability distribution, we formulate a distribution disparity loss for bias calibration, where we exclusively update bias parameters ($0.1\%$ of total parameters) of LMs towards equal probability distribution. Experimental results show that the calibration promotes an equitable starting point for LMs while preserving language modeling abilities. Across a wide range of datasets, including sentiment analysis and topic classification, our method significantly improves zero/few-shot learning performance of LMs for both in-context learning and prompt-based fine-tuning (on average $9\%$ and $2\%$, respectively).
Exploration-Driven Policy Optimization in RLHF: Theoretical Insights on Efficient Data Utilization
Authors: Yihan Du, Anna Winnicki, Gal Dalal, Shie Mannor, R. Srikant
Date: 2024-02-15 00:00:00

Reinforcement Learning from Human Feedback (RLHF) has achieved impressive empirical successes while relying on a small amount of human feedback. However, there is limited theoretical justification for this phenomenon. Additionally, most recent studies focus on value-based algorithms despite the recent empirical successes of policy-based algorithms. In this work, we consider an RLHF algorithm based on policy optimization (PO-RLHF). The algorithm is based on the popular Policy Cover-Policy Gradient (PC-PG) algorithm, which assumes knowledge of the reward function. In PO-RLHF, knowledge of the reward function is not assumed, and the algorithm uses trajectory-based comparison feedback to infer the reward function. We provide performance bounds for PO-RLHF with low query complexity, which provides insight into why a small amount of human feedback may be sufficient to achieve good performance with RLHF. A key novelty is a trajectory-level elliptical potential analysis, which bounds the reward estimation error when comparison feedback (rather than numerical reward observation) is given. We provide and analyze algorithms PG-RLHF and NN-PG-RLHF for two settings: linear and neural function approximation, respectively.
What to Do When Your Discrete Optimization Is the Size of a Neural Network?
Authors: Hugo Silva, Martha White
Date: 2024-02-15 00:00:00
Tasks: Continual Learning, image-classification, Image Classification, Network Pruning

Oftentimes, machine learning applications using neural networks involve solving discrete optimization problems, such as in pruning, parameter-isolation-based continual learning and training of binary networks. Still, these discrete problems are combinatorial in nature and are also not amenable to gradient-based optimization. Additionally, classical approaches used in discrete settings do not scale well to large neural networks, forcing scientists and empiricists to rely on alternative methods. Among these, two main distinct sources of top-down information can be used to lead the model to good solutions: (1) extrapolating gradient information from points outside of the solution set (2) comparing evaluations between members of a subset of the valid solutions. We take continuation path (CP) methods to represent using purely the former and Monte Carlo (MC) methods to represent the latter, while also noting that some hybrid methods combine the two. The main goal of this work is to compare both approaches. For that purpose, we first overview the two classes while also discussing some of their drawbacks analytically. Then, on the experimental section, we compare their performance, starting with smaller microworld experiments, which allow more fine-grained control of problem variables, and gradually moving towards larger problems, including neural network regression and neural network pruning for image classification, where we additionally compare against magnitude-based pruning.
Interpretable Generative Adversarial Imitation Learning
Authors: Wenliang Liu, Danyang Li, Erfan Aasi, Roberto Tron, Calin Belta
Date: 2024-02-15 00:00:00
Tasks: Generative Adversarial Network, Imitation Learning

Imitation learning methods have demonstrated considerable success in teaching autonomous systems complex tasks through expert demonstrations. However, a limitation of these methods is their lack of interpretability, particularly in understanding the specific task the learning agent aims to accomplish. In this paper, we propose a novel imitation learning method that combines Signal Temporal Logic (STL) inference and control synthesis, enabling the explicit representation of the task as an STL formula. This approach not only provides a clear understanding of the task but also allows for the incorporation of human knowledge and adaptation to new scenarios through manual adjustments of the STL formulae. Additionally, we employ a Generative Adversarial Network (GAN)-inspired training approach for both the inference and the control policy, effectively narrowing the gap between the expert and learned policies. The effectiveness of our algorithm is demonstrated through two case studies, showcasing its practical applicability and adaptability.
Discrete Probabilistic Inference as Control in Multi-path Environments
Authors: Tristan Deleu, Padideh Nouri, Nikolay Malkin, Doina Precup, Yoshua Bengio
Date: 2024-02-15 00:00:00

We consider the problem of sampling from a discrete and structured distribution as a sequential decision problem, where the objective is to find a stochastic policy such that objects are sampled at the end of this sequential process proportionally to some predefined reward. While we could use maximum entropy Reinforcement Learning (MaxEnt RL) to solve this problem for some distributions, it has been shown that in general, the distribution over states induced by the optimal policy may be biased in cases where there are multiple ways to generate the same object. To address this issue, Generative Flow Networks (GFlowNets) learn a stochastic policy that samples objects proportionally to their reward by approximately enforcing a conservation of flows across the whole Markov Decision Process (MDP). In this paper, we extend recent methods correcting the reward in order to guarantee that the marginal distribution induced by the optimal MaxEnt RL policy is proportional to the original reward, regardless of the structure of the underlying MDP. We also prove that some flow-matching objectives found in the GFlowNet literature are in fact equivalent to well-established MaxEnt RL algorithms with a corrected reward. Finally, we study empirically the performance of multiple MaxEnt RL and GFlowNet algorithms on multiple problems involving sampling from discrete distributions.
An Evaluation of Real-time Adaptive Sampling Change Point Detection Algorithm using KCUSUM
Authors: Vijayalakshmi Saravanan, Perry Siehien, Shinjae Yoo, Hubertus van Dam, Thomas Flynn, Christopher Kelly, Khaled Z Ibrahim
Date: 2024-02-15 00:00:00
Tasks: Change Detection, Change Point Detection, Protein Folding

Detecting abrupt changes in real-time data streams from scientific simulations presents a challenging task, demanding the deployment of accurate and efficient algorithms. Identifying change points in live data stream involves continuous scrutiny of incoming observations for deviations in their statistical characteristics, particularly in high-volume data scenarios. Maintaining a balance between sudden change detection and minimizing false alarms is vital. Many existing algorithms for this purpose rely on known probability distributions, limiting their feasibility. In this study, we introduce the Kernel-based Cumulative Sum (KCUSUM) algorithm, a non-parametric extension of the traditional Cumulative Sum (CUSUM) method, which has gained prominence for its efficacy in online change point detection under less restrictive conditions. KCUSUM splits itself by comparing incoming samples directly with reference samples and computes a statistic grounded in the Maximum Mean Discrepancy (MMD) non-parametric framework. This approach extends KCUSUM's pertinence to scenarios where only reference samples are available, such as atomic trajectories of proteins in vacuum, facilitating the detection of deviations from the reference sample without prior knowledge of the data's underlying distribution. Furthermore, by harnessing MMD's inherent random-walk structure, we can theoretically analyze KCUSUM's performance across various use cases, including metrics like expected delay and mean runtime to false alarms. Finally, we discuss real-world use cases from scientific simulations such as NWChem CODAR and protein folding data, demonstrating KCUSUM's practical effectiveness in online change point detection.