nils-herrmann/clean_scirepeval huggingface dataset:
Diffusion Schrödinger Bridge with Applications to Score-Based Generative Modeling
Authors: Valentin De Bortoli, James Thornton, Jeremy Heng, Arnaud Doucet

Progressively applying Gaussian noise transforms complex data distributions to approximately Gaussian. Reversing this dynamic defines a generative model. When the forward noising process is given by a Stochastic Differential Equation (SDE), Song et al (2021) demonstrate how the time inhomogeneous drift of the associated reverse-time SDE may be estimated using score-matching. A limitation of this approach is that the forward-time SDE must be run for a sufficiently long time for the final distribution to be approximately Gaussian. In contrast, solving the Schrödinger Bridge (SB) problem, i.e. an entropy-regularized optimal transport problem on path spaces, yields diffusions which generate samples from the data distribution in finite time. We present Diffusion SB (DSB), an original approximation of the Iterative Proportional Fitting (IPF) procedure to solve the SB problem, and provide theoretical analysis along with generative modeling experiments. The first DSB iteration recovers the methodology proposed by Song et al. (2021), with the flexibility of using shorter time intervals, as subsequent DSB iterations reduce the discrepancy between the final-time marginal of the forward (resp. backward) SDE with respect to the prior (resp. data) distribution. Beyond generative modeling, DSB offers a widely applicable computational optimal transport tool as the continuous state-space analogue of the popular Sinkhorn algorithm (Cuturi, 2013).
Beyond Pinball Loss: Quantile Methods for Calibrated Uncertainty Quantification
Authors: Youngseog Chung, Willie Neiswanger, Ian Char, Jeff Schneider

Among the many ways of quantifying uncertainty in a regression setting, specifying the full quantile function is attractive, as quantiles are amenable to interpretation and evaluation. A model that predicts the true conditional quantiles for each input, at all quantile levels, presents a correct and efficient representation of the underlying uncertainty. To achieve this, many current quantile-based methods focus on optimizing the pinball loss. However, this loss restricts the scope of applicable regression models, limits the ability to target many desirable properties (e.g. calibration, sharpness, centered intervals), and may produce poor conditional quantiles. In this work, we develop new quantile methods that address these shortcomings. In particular, we propose methods that can apply to any class of regression model, select an explicit balance between calibration and sharpness, optimize for calibration of centered intervals, and produce more accurate conditional quantiles. We provide a thorough experimental evaluation of our methods, which includes a high dimensional uncertainty quantification task in nuclear fusion.
Increasing Liquid State Machine Performance with Edge-of-Chaos Dynamics Organized by Astrocyte-modulated Plasticity
Authors: Vladimir A Ivanov, Konstantinos P. Michmizos

The liquid state machine (LSM) combines low training complexity and biological plausibility, which has made it an attractive machine learning framework for edge and neuromorphic computing paradigms. Originally proposed as a model of brain computation, the LSM tunes its internal weights without backpropagation of gradients, which results in lower performance compared to multi-layer neural networks. Recent findings in neuroscience suggest that astrocytes, a long-neglected non-neuronal brain cell, modulate synaptic plasticity and brain dynamics, tuning brain networks to the vicinity of the computationally optimal critical phase transition between order and chaos. Inspired by this disruptive understanding of how brain networks self-tune, we propose the neuron-astrocyte liquid state machine (NALSM) that addresses under-performance through self-organized near-critical dynamics. Similar to its biological counterpart, the astrocyte model integrates neuronal activity and provides global feedback to spike-timing-dependent plasticity (STDP), which self-organizes NALSM dynamics around a critical branching factor that is associated with the edge-of-chaos. We demonstrate that NALSM achieves state-of-the-art accuracy versus comparable LSM methods, without the need for data-specific hand-tuning. With a top accuracy of $97.61\%$ on MNIST, $97.51\%$ on N-MNIST, and $85.84\%$ on Fashion-MNIST, NALSM achieved comparable performance to current fully-connected multi-layer spiking neural networks trained via backpropagation. Our findings suggest that the further development of brain-inspired machine learning methods has the potential to reach the performance of deep learning, with the added benefits of supporting robust and energy-efficient neuromorphic computing on the edge.
Accelerating Quadratic Optimization with Reinforcement Learning
Authors: Jeffrey Ichnowski, Paras Jain, Bartolomeo Stellato, Goran Banjac, Michael Luo, Francesco Borrelli, Joseph E. Gonzalez, Ion Stoica, Ken Goldberg

First-order methods for quadratic optimization such as OSQP are widely used for large-scale machine learning and embedded optimal control, where many related problems must be rapidly solved. These methods face two persistent challenges: manual hyperparameter tuning and convergence time to high-accuracy solutions. To address these, we explore how Reinforcement Learning (RL) can learn a policy to tune parameters to accelerate convergence. In experiments with well-known QP benchmarks we find that our RL policy, RLQP, significantly outperforms state-of-the-art QP solvers by up to 3x. RLQP generalizes surprisingly well to previously unseen problems with varying dimension and structure from different applications, including the QPLIB, Netlib LP and Maros-M{\'e}sz{\'a}ros problems. Code, models, and videos are available at https://berkeleyautomation.github.io/rlqp/.
Non-Asymptotic Analysis for Two Time-scale TDC with General Smooth Function Approximation
Authors: Yue Wang, Shaofeng Zou, Yi Zhou

Temporal-difference learning with gradient correction (TDC) is a two time-scale algorithm for policy evaluation in reinforcement learning. This algorithm was initially proposed with linear function approximation, and was later extended to the one with general smooth function approximation. The asymptotic convergence for the on-policy setting with general smooth function approximation was established in [Bhatnagar et al., 2009], however, the non-asymptotic convergence analysis remains unsolved due to challenges in the non-linear and two-time-scale update structure, non-convex objective function and the projection onto a time-varying tangent plane. In this paper, we develop novel techniques to address the above challenges and explicitly characterize the non-asymptotic error bound for the general off-policy setting with i.i.d. or Markovian samples, and show that it converges as fast as $\mathcal O(1/\sqrt T)$ (up to a factor of $\mathcal O(\log T)$). Our approach can be applied to a wide range of value-based reinforcement learning algorithms with general smooth function approximation.
Closing the loop in medical decision support by understanding clinical decision-making: A case study on organ transplantation
Authors: Yuchao Qin, Fergus Imrie, Alihan Hüyük, Daniel Jarrett, Alexander Edward Gimson, Mihaela van der Schaar

Significant effort has been placed on developing decision support tools to improve patient care. However, drivers of real-world clinical decisions in complex medical scenarios are not yet well-understood, resulting in substantial gaps between these tools and practical applications. In light of this, we highlight that more attention on understanding clinical decision-making is required both to elucidate current clinical practices and to enable effective human-machine interactions. This is imperative in high-stakes scenarios with scarce available resources. Using organ transplantation as a case study, we formalize the desiderata of methods for understanding clinical decision-making. We show that most existing machine learning methods are insufficient to meet these requirements and propose iTransplant, a novel data-driven framework to learn the factors affecting decisions on organ offers in an instance-wise fashion directly from clinical data, as a possible solution. Through experiments on real-world liver transplantation data from OPTN, we demonstrate the use of iTransplant to: (1) discover which criteria are most important to clinicians for organ offer acceptance; (2) identify patient-specific organ preferences of clinicians allowing automatic patient stratification;  and (3) explore variations in transplantation practices between different transplant centers. Finally, we emphasize that the insights gained by iTransplant can be used to inform the development of future decision support tools.
Credit Assignment in Neural Networks through Deep Feedback Control
Authors: Alexander Meulemans, Matilde Tristany Farinha, Javier Garcia Ordonez, Pau Vilimelis Aceituno, Joao Sacramento, Benjamin F Grewe

The success of deep learning sparked interest in whether the brain learns by using similar techniques for assigning credit to each synaptic weight for its contribution to the network output. However, the majority of current attempts at biologically-plausible learning methods are either non-local in time, require highly specific connectivity motifs, or have no clear link to any known mathematical optimization method. Here, we introduce Deep Feedback Control (DFC), a new learning method that uses a feedback controller to drive a deep neural network to match a desired output target and whose control signal can be used for credit assignment. The resulting learning rule is fully local in space and time and approximates Gauss-Newton optimization for a wide range of feedback connectivity patterns. To further underline its biological plausibility, we relate DFC to a multi-compartment model of cortical pyramidal neurons with a local voltage-dependent synaptic plasticity rule, consistent with recent theories of dendritic processing. By combining dynamical system theory with mathematical optimization theory, we provide a strong theoretical foundation for DFC that we corroborate with detailed results on toy experiments and standard computer-vision benchmarks.
A Probabilistic State Space Model for Joint Inference from Differential Equations and Data
Authors: Jonathan Schmidt, Nicholas Krämer, Philipp Hennig

Mechanistic models with differential equations are a key component of scientific applications of machine learning. Inference in such models is usually computationally demanding because it involves repeatedly solving the differential equation. The main problem here is that the numerical solver is hard to combine with standard inference techniques. Recent work in probabilistic numerics has developed a new class of solvers for ordinary differential equations (ODEs) that phrase the solution process directly in terms of Bayesian filtering. We here show that this allows such methods to be combined very directly, with conceptual and numerical ease, with latent force models in the ODE itself. It then becomes possible to perform approximate Bayesian inference on the latent force as well as the ODE solution in a single, linear complexity pass of an extended Kalman filter / smoother — that is, at the cost of computing a single ODE solution. We demonstrate the expressiveness and performance of the algorithm by training, among others, a non-parametric SIRD model on data from the COVID-19 outbreak.
Auto-Encoding Knowledge Graph for Unsupervised Medical Report Generation
Authors: Fenglin Liu, Chenyu You, Xian Wu, Shen Ge, Sheng Wang, Xu Sun

Medical report generation, which aims to automatically generate a long and coherent report of a given medical image, has been receiving growing research interests. Existing approaches mainly adopt a supervised manner and heavily rely on coupled image-report pairs. However, in the medical domain, building a large-scale image-report paired dataset is both time-consuming and expensive. To relax the dependency on paired data, we propose an unsupervised model Knowledge Graph Auto-Encoder (KGAE) which accepts independent sets of images and reports in training. KGAE consists of a pre-constructed knowledge graph, a knowledge-driven encoder and a knowledge-driven decoder. The knowledge graph works as the shared latent space to bridge the visual and textual domains; The knowledge-driven encoder projects medical images and reports to the corresponding coordinates in this latent space and the knowledge-driven decoder generates a medical report given a coordinate in this space. Since the knowledge-driven encoder and decoder can be trained with independent sets of images and reports, KGAE is unsupervised. The experiments show that the unsupervised KGAE generates desirable medical reports without using any image-report training pairs. Moreover, KGAE can also work in both semi-supervised and supervised settings, and accept paired images and reports in training. By further fine-tuning with image-report pairs, KGAE consistently outperforms the current state-of-the-art models on two datasets.
Coordinated Proximal Policy Optimization
Authors: Zifan Wu, Chao Yu, Deheng Ye, Junge Zhang, haiyin piao, Hankz Hankui Zhuo

We present Coordinated Proximal Policy Optimization (CoPPO), an algorithm that extends the original Proximal Policy Optimization (PPO) to the multi-agent setting. The key idea lies in the coordinated adaptation of step size during the policy update process among multiple agents. We prove the monotonicity of policy improvement when optimizing a theoretically-grounded joint objective, and derive a simplified optimization objective based on a set of approximations. We then interpret that such an objective in CoPPO can achieve dynamic credit assignment among agents, thereby alleviating the high variance issue during the concurrent update of agent policies. Finally, we demonstrate that CoPPO outperforms several strong baselines and is competitive with the latest multi-agent PPO method (i.e. MAPPO) under typical multi-agent settings, including cooperative matrix games and the StarCraft II micromanagement tasks.
Scaling Neural Tangent Kernels via Sketching and Random Features
Authors: Amir Zandieh, Insu Han, Haim Avron, Neta Shoham, Chaewon Kim, Jinwoo Shin

The Neural Tangent Kernel (NTK) characterizes the behavior of infinitely-wide neural networks trained under least squares loss by gradient descent. Recent works also report that NTK regression can outperform finitely-wide neural networks trained on small-scale datasets. However, the computational complexity of kernel methods has limited its use in large-scale learning tasks. To accelerate learning with NTK, we design a near input-sparsity time approximation algorithm for NTK, by sketching the polynomial expansions of arc-cosine kernels: our sketch for the convolutional counterpart of NTK (CNTK) can transform any image using a linear runtime in the number of pixels. Furthermore, we prove a spectral approximation guarantee for the NTK matrix, by combining random features (based on leverage score sampling) of the arc-cosine kernels with a sketching algorithm. We benchmark our methods on various large-scale regression and classification tasks and show that a linear regressor trained on our CNTK features matches the accuracy of exact CNTK on CIFAR-10 dataset while achieving 150x speedup.
Score-based Generative Neural Networks for Large-Scale Optimal Transport
Authors: Max Daniels, Tyler Maunu, PAul HAnd

We consider the fundamental problem of sampling the optimal transport coupling between given source and target distributions. In certain cases, the optimal transport plan takes the form of a one-to-one mapping from the source support to the target support, but learning or even approximating such a map is computationally challenging for large and high-dimensional datasets due to the high cost of linear programming routines and an intrinsic curse of dimensionality. We study instead the Sinkhorn problem, a regularized form of optimal transport whose solutions are couplings between the source and the target distribution. We introduce a novel framework for learning the Sinkhorn coupling between two distributions in the form of a score-based generative model. Conditioned on source data, our procedure iterates Langevin Dynamics to sample target data according to the regularized optimal coupling. Key to this approach is a neural network parametrization of the Sinkhorn problem, and we prove convergence of gradient descent with respect to network parameters in this formulation. We demonstrate its empirical success on a variety of large scale optimal transport tasks.
Contrastive Mixture of Posteriors for Counterfactual Inference, Data Integration and Fairness
Authors: Adam Foster, Árpi Vezér, Craig A Glastonbury, Páidí Creed, Sam Abujudeh, Aaron Sim

Learning meaningful representations of data that can address challenges such as batch effect correction, data integration and counterfactual inference is a central problem in many domains including computational biology. Adopting a Conditional VAE framework, we identify the mathematical principle that unites these challenges: learning a representation that is marginally independent of a condition variable. We therefore propose the Contrastive Mixtures of Posteriors (CoMP) method that uses a novel misalignment penalty to enforce this independence. This penalty is defined in terms of mixtures of the variational posteriors themselves, unlike prior work which uses external discrepancy measures such as MMD to ensure independence in latent space. We show that CoMP has attractive theoretical properties compared to previous approaches, especially when there is complex global structure in latent space. We further demonstrate state of the art performance on a number of real-world problems, including the challenging tasks of aligning human tumour samples with cancer cell-lines and performing counterfactual inference on single-cell RNA sequencing data. Incidentally, we find parallels with the fair representation learning literature, and demonstrate CoMP has competitive performance in learning fair yet expressive latent representations.
SOSP: Efficiently Capturing Global Correlations by Second-Order Structured Pruning
Authors: Manuel Nonnenmacher, Thomas Pfeil, Ingo Steinwart, David Reeb

Pruning neural networks reduces inference time and memory cost, as well as accelerates training when done at initialization. On standard hardware, these benefits will be especially prominent if coarse-grained structures, like feature maps, are pruned. We devise global saliency-based methods for second-order structured pruning (SOSP) which include correlations among structures, whereas highest efficiency is achieved by saliency approximations using fast Hessian-vector products. We achieve state-of-the-art results for various object classification benchmarks, especially for large pruning rates highly relevant for resource-constrained applications. We showcase that our approach scales to large-scale vision tasks, even though it captures correlations across all layers of the network. Further, we highlight two outstanding features of our methods. First, to reduce training costs our pruning objectives can also be applied at initialization with no or only minor degradation in accuracy compared to pruning after pre-training. Second, our structured pruning methods allow to reveal architectural bottlenecks, which we remove to further increase the accuracy of the networks.
Scheduling jobs with stochastic holding costs
Authors: Dabeen Lee, Milan Vojnovic

This paper proposes a learning and scheduling algorithm to minimize the expected cumulative holding cost incurred by jobs, where statistical parameters defining their individual holding costs are unknown a priori. In each time slot, the server can process a job while receiving the realized random holding costs of the jobs remaining in the system. Our algorithm is a learning-based variant of the $c\mu$ rule for scheduling: it starts with a preemption period of fixed length which serves as a learning phase, and after accumulating enough data about individual jobs, it switches to nonpreemptive scheduling mode. The algorithm is designed to handle instances with large or small gaps in jobs' parameters and achieves near-optimal performance guarantees. The performance of our algorithm is captured by its regret, where the benchmark is the minimum possible cost attained when the statistical parameters of jobs are fully known.  We prove upper bounds on the regret of our algorithm, and we derive a regret lower bound that is almost matching the proposed upper bounds. Our numerical results demonstrate the effectiveness of our algorithm and show that our theoretical regret analysis is nearly tight.
Quantifying and Learning Linear Symmetry-Based Disentanglement
Authors: Loek Tonnaer, Luis Armando Pérez Rey, Vlado Menkovski, Mike Holenderski, Jacobus Willem Portegies

The definition of Linear Symmetry-Based Disentanglement (LSBD) formalizes the notion of linearly disentangled representations, but there is currently no metric to quantify LSBD. Such a metric is crucial to evaluate LSBD methods and to compare to previous understandings of disentanglement. We propose $\mathcal{D}_{\mathrm{LSBD}}$, a mathematically sound metric to quantify LSBD, and provide a practical implementation. Furthermore, from this metric we derive LSBD-VAE, a semi-supervised method to learn LSBD representations. We demonstrate the utility of our metric by showing that (1) common VAE-based disentanglement methods don't learn LSBD representations, (2) LSBD-VAE as well as other recent methods \emph{can} learn LSBD representations, needing only limited supervision on transformations, and (3) various desirable properties expressed by existing disentanglement metrics are also achieved by LSBD representations.
Black-Box Dissector: Towards Erasing-based Hard-Label Model Stealing Attack
Authors: Yixu Wang, Jie Li, Hong Liu, Yan Wang, YONGJIAN WU, Feiyue Huang, Rongrong Ji

Previous studies have verified that the functionality of black-box models can be stolen with the full probability outputs. However, under the more practical hard-label setting, we observe that existing methods suffer from catastrophic performance degradation. We argue this is due to the lack of rich information in the probability prediction and the over-fitting caused by hard labels. To this end, we propose a novel hard-label model stealing method termed black-box dissector, which consists of two erasing-based modules. One is a CAM-driven erasing strategy that is designed to increase the information capacity hidden in hard labels from the victim model. The other is a random-erasing-based self-knowledge distillation module that utilizes soft labels from the substitute model to mitigate over-fitting. Extensive experiments on four widely-used datasets consistently demonstrate that our method outperforms state-of-the-art methods, with an improvement of at most $8.27\%$. We also validate the effectiveness and practical potential of our method on real-world APIs and defense methods. Furthermore, our method promotes other downstream tasks, i.e.,  transfer adversarial attacks.