OpenRaiser/Intern-Atlas huggingface dataset:
Ontology-Driven and Weakly Supervised Rare Disease Identification from Clinical Notes
Venue: arXiv cs.CL 2023
Year: 2023

Computational text phenotyping is the practice of identifying patients with certain disorders and traits from clinical notes. Rare diseases are challenging to be identified due to few cases available for machine learning and the need for data annotation from domain experts. We propose a method using ontologies and weak supervision, with recent pre-trained contextual representations from Bi-directional Transformers (e.g. BERT). The ontology-based framework includes two steps: (i) Text-to-UMLS, extracting phenotypes by contextually linking mentions to concepts in Unified Medical Language System (UMLS), with a Named Entity Recognition and Linking (NER+L) tool, SemEHR, and weak supervision with customised rules and contextual mention representation; (ii) UMLS-to-ORDO, matching UMLS concepts to rare diseases in Orphanet Rare Disease Ontology (ORDO). The weakly supervised approach is proposed to learn a phenotype confirmation model to improve Text-to-UMLS linking, without annotated data from domain experts. We evaluated the approach on three clinical datasets, MIMIC-III discharge summaries, MIMIC-III radiology reports, and NHS Tayside brain imaging reports from two institutions in the US and the UK, with annotations. The improvements in the precision were pronounced (by over 30% to 50% absolute score for Text-to-UMLS linking), with almost no loss of recall compared to the existing NER+L tool, SemEHR. Results on radiology reports from MIMIC-III and NHS Tayside were consistent with the discharge summaries. The overall pipeline processing clinical notes can extract rare disease cases, mostly uncaptured in structured data (manually assigned ICD codes). We discuss the usefulness of the weak supervision approach and propose directions for future studies.
Process, Bias and Temperature Scalable CMOS Analog Computing Circuits for Machine Learning
Venue: arXiv cs.AR 2023
Year: 2023

Analog computing is attractive compared to digital computing due to its potential for achieving higher computational density and higher energy efficiency. However, unlike digital circuits, conventional analog computing circuits cannot be easily mapped across different process nodes due to differences in transistor biasing regimes, temperature variations and limited dynamic range. In this work, we generalize the previously reported margin-propagation-based analog computing framework for designing novel \textit{shape-based analog computing} (S-AC) circuits that can be easily cross-mapped across different process nodes. Similar to digital designs S-AC designs can also be scaled for precision, speed, and power. As a proof-of-concept, we show several examples of S-AC circuits implementing mathematical functions that are commonly used in machine learning (ML) architectures. Using circuit simulations we demonstrate that the circuit input/output characteristics remain robust when mapped from a planar CMOS 180nm process to a FinFET 7nm process. Also, using benchmark datasets we demonstrate that the classification accuracy of a S-AC based neural network remains robust when mapped across the two processes and to changes in temperature.
Ensemble Clustering via Co-association Matrix Self-enhancement
Venue: arXiv cs.LG 2023
Year: 2023

Ensemble clustering integrates a set of base clustering results to generate a stronger one. Existing methods usually rely on a co-association (CA) matrix that measures how many times two samples are grouped into the same cluster according to the base clusterings to achieve ensemble clustering. However, when the constructed CA matrix is of low quality, the performance will degrade. In this paper, we propose a simple yet effective CA matrix self-enhancement framework that can improve the CA matrix to achieve better clustering performance. Specifically, we first extract the high-confidence (HC) information from the base clusterings to form a sparse HC matrix. By propagating the highly-reliable information of the HC matrix to the CA matrix and complementing the HC matrix according to the CA matrix simultaneously, the proposed method generates an enhanced CA matrix for better clustering. Technically, the proposed model is formulated as a symmetric constrained convex optimization problem, which is efficiently solved by an alternating iterative algorithm with convergence and global optimum theoretically guaranteed. Extensive experimental comparisons with twelve state-of-the-art methods on eight benchmark datasets substantiate the effectiveness, flexibility and efficiency of the proposed model in ensemble clustering. The codes and datasets can be downloaded at https://github.com/Siritao/EC-CMS.
Strategic Latency Reduction in Blockchain Peer-to-Peer Networks
Venue: arXiv cs.CR 2023
Year: 2023

Most permissionless blockchain networks run on peer-to-peer (P2P) networks, which offer flexibility and decentralization at the expense of performance (e.g., network latency). Historically, this tradeoff has not been a bottleneck for most blockchains. However, an emerging host of blockchain-based applications (e.g., decentralized finance) are increasingly sensitive to latency; users who can reduce their network latency relative to other users can accrue (sometimes significant) financial gains. In this work, we initiate the study of strategic latency reduction in blockchain P2P networks. We first define two classes of latency that are of interest in blockchain applications. We then show empirically that a strategic agent who controls only their local peering decisions can manipulate both types of latency, achieving 60\% of the global latency gains provided by the centralized, paid service bloXroute, or, in targeted scenarios, comparable gains. Finally, we show that our results are not due to the poor design of existing P2P networks. Under a simple network model, we theoretically prove that an adversary can always manipulate the P2P network's latency to their advantage, provided the network experiences sufficient peer churn and transaction activity.
Exploring How Machine Learning Practitioners (Try To) Use Fairness Toolkits
Venue: arXiv cs.HC 2023
Year: 2023

Recent years have seen the development of many open-source ML fairness toolkits aimed at helping ML practitioners assess and address unfairness in their systems. However, there has been little research investigating how ML practitioners actually use these toolkits in practice. In this paper, we conducted the first in-depth empirical exploration of how industry practitioners (try to) work with existing fairness toolkits. In particular, we conducted think-aloud interviews to understand how participants learn about and use fairness toolkits, and explored the generality of our findings through an anonymous online survey. We identified several opportunities for fairness toolkits to better address practitioner needs and scaffold them in using toolkits effectively and responsibly. Based on these findings, we highlight implications for the design of future open-source fairness toolkits that can support practitioners in better contextualizing, communicating, and collaborating around ML fairness efforts.
Realistic Defocus Blur for Multiplane Computer-Generated Holography
Venue: arXiv cs.CV 2023
Year: 2023

This paper introduces a new multiplane CGH computation method to reconstruct artefact-free high-quality holograms with natural-looking defocus blur. Our method introduces a new targeting scheme and a new loss function. While the targeting scheme accounts for defocused parts of the scene at each depth plane, the new loss function analyzes focused and defocused parts separately in reconstructed images. Our method support phase-only CGH calculations using various iterative (e.g., Gerchberg-Saxton, Gradient Descent) and non-iterative (e.g., Double Phase) CGH techniques. We achieve our best image quality using a modified gradient descent-based optimization recipe where we introduce a constraint inspired by the double phase method. We validate our method experimentally using our proof-of-concept holographic display, comparing various algorithms, including multi-depth scenes with sparse and dense contents.
RoMFAC: A robust mean-field actor-critic reinforcement learning against adversarial perturbations on states
Venue: arXiv cs.LG 2023
Year: 2023

Multi-agent deep reinforcement learning makes optimal decisions dependent on system states observed by agents, but any uncertainty on the observations may mislead agents to take wrong actions. The Mean-Field Actor-Critic reinforcement learning (MFAC) is well-known in the multi-agent field since it can effectively handle a scalability problem. However, it is sensitive to state perturbations that can significantly degrade the team rewards. This work proposes a Robust Mean-field Actor-Critic reinforcement learning (RoMFAC) that has two innovations: 1) a new objective function of training actors, composed of a \emph{policy gradient function} that is related to the expected cumulative discount reward on sampled clean states and an \emph{action loss function} that represents the difference between actions taken on clean and adversarial states; and 2) a repetitive regularization of the action loss, ensuring the trained actors to obtain excellent performance. Furthermore, this work proposes a game model named a State-Adversarial Stochastic Game (SASG). Despite the Nash equilibrium of SASG may not exist, adversarial perturbations to states in the RoMFAC are proven to be defensible based on SASG. Experimental results show that RoMFAC is robust against adversarial perturbations while maintaining its competitive performance in environments without perturbations.
Sibyl: Adaptive and Extensible Data Placement in Hybrid Storage Systems Using Online Reinforcement Learning
Venue: arXiv cs.AR 2023
Year: 2023

Hybrid storage systems (HSS) use multiple different storage devices to provide high and scalable storage capacity at high performance. Recent research proposes various techniques that aim to accurately identify performance-critical data to place it in a "best-fit" storage device. Unfortunately, most of these techniques are rigid, which (1) limits their adaptivity to perform well for a wide range of workloads and storage device configurations, and (2) makes it difficult for designers to extend these techniques to different storage system configurations (e.g., with a different number or different types of storage devices) than the configuration they are designed for. We introduce Sibyl, the first technique that uses reinforcement learning for data placement in hybrid storage systems. Sibyl observes different features of the running workload as well as the storage devices to make system-aware data placement decisions. For every decision it makes, Sibyl receives a reward from the system that it uses to evaluate the long-term performance impact of its decision and continuously optimizes its data placement policy online. We implement Sibyl on real systems with various HSS configurations. Our results show that Sibyl provides 21.6%/19.9% performance improvement in a performance-oriented/cost-oriented HSS configuration compared to the best previous data placement technique. Our evaluation using an HSS configuration with three different storage devices shows that Sibyl outperforms the state-of-the-art data placement policy by 23.9%-48.2%, while significantly reducing the system architect's burden in designing a data placement mechanism that can simultaneously incorporate three storage devices. We show that Sibyl achieves 80% of the performance of an oracle policy that has complete knowledge of future access patterns while incurring a very modest storage overhead of only 124.4 KiB.
Estimating Patch Propagation Times across (Blockchain) Forks
Venue: arXiv cs.CR 2023
Year: 2023

The wide success of Bitcoin has led to a huge surge of alternative cryptocurrencies (altcoins). Most altcoins essentially fork Bitcoin's code with minor modifications, such as the number of coins to be minted, the block size, and the block generation time. As such, they are often deemed identical to Bitcoin in terms of security, robustness, and maturity. In this paper, we show that this common conception is misleading. By mining data retrieved from the GitHub repositories of various altcoin projects, we estimate the time it took to propagate relevant patches from Bitcoin to the altcoins. We find that, while the Bitcoin development community is quite active in fixing security flaws of Bitcoin's code base, forked cryptocurrencies are not as rigorous in patching the same vulnerabilities (inherited from Bitcoin). In some cases, we observe that even critical vulnerabilities, discovered and fixed within the Bitcoin community, have been addressed by the altcoins tens of months after disclosure. Besides raising awareness of this problem, our work aims to motivate the need for a proper responsible disclosure of vulnerabilities to all forked chains prior to reporting them publicly.
Fundamental Laws of Binary Classification
Venue: arXiv cs.LG 2023
Year: 2023

Finding discriminant functions of minimum risk binary classification systems is a novel geometric locus problem -- which requires solving a system of fundamental locus equations of binary classification -- subject to deep-seated statistical laws. We show that a discriminant function of a minimum risk binary classification system is the solution of a locus equation that represents the geometric locus of the decision boundary of the system, wherein the discriminant function is connected to the decision boundary by an exclusive principal eigen-coordinate system -- at which point the discriminant function is represented by a geometric locus of a novel principal eigenaxis -- structured as a dual locus of likelihood components and principal eigenaxis components. We demonstrate that a minimum risk binary classification system acts to jointly minimize its eigenenergy and risk by locating a point of equilibrium, at which point critical minimum eigenenergies exhibited by the system are symmetrically concentrated in such a manner that the novel principal eigenaxis of the system exhibits symmetrical dimensions and densities, so that counteracting and opposing forces and influences of the system are symmetrically balanced with each other -- about the geometric center of the locus of the novel principal eigenaxis -- whereon the statistical fulcrum of the system is located. Thereby, a minimum risk binary classification system satisfies a state of statistical equilibrium -- so that the total allowed eigenenergy and the expected risk exhibited by the system are jointly minimized within the decision space of the system -- at which point the system exhibits the minimum probability of classification error.
Addressable Superconductor Integrated Circuit Memory from Delay Lines
Venue: arXiv cs.ET 2023
Year: 2023

Recent advances in logic schemes and fabrication processes have renewed interest in using superconductor electronics for energy-efficient computing and quantum control processors. However, scalable superconducting memory still poses a challenge. To address this issue, we present an alternative to approaches that solely emphasize storage cell miniaturization by exploiting the minimal attenuation and dispersion properties of superconducting passive transmission lines to develop a delay-line memory system. This fully superconducting design operates at speeds between 20 GHz and 100 GHz, with $\pm$24\% and $\pm$13\% bias margins, respectively, and demonstrates data densities in the 10s of Mbit/cm$^2$ with the MIT Lincoln Laboratory SC2 fabrication process. Additionally, the circulating nature of this design allows for minimal control circuitry, eliminates the need for data splitting and merging, and enables inexpensive implementations of sequential access and content-addressable memories. Further advances in fabrication processes suggest data densities of 100s of Mbit/cm$^2$ and beyond
DynPL-SVO: A Robust Stereo Visual Odometry for Dynamic Scenes
Venue: arXiv cs.CV 2023
Year: 2023

Most feature-based stereo visual odometry (SVO) approaches estimate the motion of mobile robots by matching and tracking point features along a sequence of stereo images. However, in dynamic scenes mainly comprising moving pedestrians, vehicles, etc., there are insufficient robust static point features to enable accurate motion estimation, causing failures when reconstructing robotic motion. In this paper, we proposed DynPL-SVO, a complete dynamic SVO method that integrated united cost functions containing information between matched point features and re-projection errors perpendicular and parallel to the direction of the line features. Additionally, we introduced a \textit{dynamic} \textit{grid} algorithm to enhance its performance in dynamic scenes. The stereo camera motion was estimated through Levenberg-Marquard minimization of the re-projection errors of both point and line features. Comprehensive experimental results on KITTI and EuRoC MAV datasets showed that accuracy of the DynPL-SVO was improved by over 20\% on average compared to other state-of-the-art SVO systems, especially in dynamic scenes.
Momentum-Based Policy Gradient with Second-Order Information
Venue: arXiv cs.LG 2023
Year: 2023

Variance-reduced gradient estimators for policy gradient methods have been one of the main focus of research in the reinforcement learning in recent years as they allow acceleration of the estimation process. We propose a variance-reduced policy-gradient method, called SHARP, which incorporates second-order information into stochastic gradient descent (SGD) using momentum with a time-varying learning rate. SHARP algorithm is parameter-free, achieving $ε$-approximate first-order stationary point with $O(ε^{-3})$ number of trajectories, while using a batch size of $O(1)$ at each iteration. Unlike most previous work, our proposed algorithm does not require importance sampling which can compromise the advantage of variance reduction process. Moreover, the variance of estimation error decays with the fast rate of $O(1/t^{2/3})$ where $t$ is the number of iterations. Our extensive experimental evaluations show the effectiveness of the proposed algorithm on various control tasks and its advantage over the state of the art in practice.
Robust Losses for Learning Value Functions
Venue: arXiv cs.LG 2023
Year: 2023

Most value function learning algorithms in reinforcement learning are based on the mean squared (projected) Bellman error. However, squared errors are known to be sensitive to outliers, both skewing the solution of the objective and resulting in high-magnitude and high-variance gradients. To control these high-magnitude updates, typical strategies in RL involve clipping gradients, clipping rewards, rescaling rewards, or clipping errors. While these strategies appear to be related to robust losses -- like the Huber loss -- they are built on semi-gradient update rules which do not minimize a known loss. In this work, we build on recent insights reformulating squared Bellman errors as a saddlepoint optimization problem and propose a saddlepoint reformulation for a Huber Bellman error and Absolute Bellman error. We start from a formalization of robust losses, then derive sound gradient-based approaches to minimize these losses in both the online off-policy prediction and control settings. We characterize the solutions of the robust losses, providing insight into the problem settings where the robust losses define notably better solutions than the mean squared Bellman error. Finally, we show that the resulting gradient-based algorithms are more stable, for both prediction and control, with less sensitivity to meta-parameters.
The Solvability of Interpretability Evaluation Metrics
Venue: arXiv cs.LG 2023
Year: 2023

Feature attribution methods are popular for explaining neural network predictions, and they are often evaluated on metrics such as comprehensiveness and sufficiency. In this paper, we highlight an intriguing property of these metrics: their solvability. Concretely, we can define the problem of optimizing an explanation for a metric, which can be solved by beam search. This observation leads to the obvious yet unaddressed question: why do we use explainers (e.g., LIME) not based on solving the target metric, if the metric value represents explanation quality? We present a series of investigations showing strong performance of this beam search explainer and discuss its broader implication: a definition-evaluation duality of interpretability concepts. We implement the explainer and release the Python solvex package for models of text, image and tabular domains.
CALIPSO: A Differentiable Solver for Trajectory Optimization with Conic and Complementarity Constraints
Venue: arXiv cs.RO 2023
Year: 2023

We present a new solver for non-convex trajectory optimization problems that is specialized for robotics applications. CALIPSO, or the Conic Augmented Lagrangian Interior-Point SOlver, combines several strategies for constrained numerical optimization to natively handle second-order cones and complementarity constraints. It reliably solves challenging motion-planning problems that include contact-implicit formulations of impacts and Coulomb friction and state-triggered constraints where general-purpose non-convex solvers like SNOPT and Ipopt fail to converge. Additionally, CALIPSO supports efficient differentiation of solutions with respect to problem data, enabling bi-level optimization applications like auto-tuning of feedback policies. Reliable convergence of the solver is demonstrated on a range of problems from manipulation, locomotion, and aerospace domains. An open-source implementation of this solver is available.
Minority Stress Experienced by LGBTQ Online Communities during the COVID-19 Pandemic
Venue: arXiv cs.SI 2023
Year: 2023

The COVID-19 pandemic has disproportionately impacted the lives of minorities, such as members of the LGBTQ community (lesbian, gay, bisexual, transgender, and queer) due to pre-existing social disadvantages and health disparities. Although extensive research has been carried out on the impact of the COVID-19 pandemic on different aspects of the general population's lives, few studies are focused on the LGBTQ population. In this paper, we develop and evaluate two sets of machine learning classifiers using a pre-pandemic and a during-pandemic dataset to identify Twitter posts exhibiting minority stress, which is a unique pressure faced by the members of the LGBTQ population due to their sexual and gender identities. We demonstrate that our best pre- and during-pandemic models show strong and stable performance for detecting posts that contain minority stress. We investigate the linguistic differences in minority stress posts across pre- and during-pandemic periods. We find that anger words are strongly associated with minority stress during the COVID-19 pandemic. We explore the impact of the pandemic on the emotional states of the LGBTQ population by adopting propensity score-based matching to perform a causal analysis. The results show that the LGBTQ population have a greater increase in the usage of cognitive words and worsened observable attribute in the usage of positive emotion words than the group of the general population with similar pre-pandemic behavioral attributes. Our findings have implications for the public health domain and policy-makers to provide adequate support, especially with respect to mental health, to the LGBTQ population during future crises.