OpenRaiser/Intern-Atlas huggingface dataset:
Fully transformer-based biomarker prediction from colorectal cancer histology: a large-scale multicentric study
Venue: arXiv cs.CV 2023
Year: 2023

Background: Deep learning (DL) can extract predictive and prognostic biomarkers from routine pathology slides in colorectal cancer. For example, a DL test for the diagnosis of microsatellite instability (MSI) in CRC has been approved in 2022. Current approaches rely on convolutional neural networks (CNNs). Transformer networks are outperforming CNNs and are replacing them in many applications, but have not been used for biomarker prediction in cancer at a large scale. In addition, most DL approaches have been trained on small patient cohorts, which limits their clinical utility. Methods: In this study, we developed a new fully transformer-based pipeline for end-to-end biomarker prediction from pathology slides. We combine a pre-trained transformer encoder and a transformer network for patch aggregation, capable of yielding single and multi-target prediction at patient level. We train our pipeline on over 9,000 patients from 10 colorectal cancer cohorts. Results: A fully transformer-based approach massively improves the performance, generalizability, data efficiency, and interpretability as compared with current state-of-the-art algorithms. After training on a large multicenter cohort, we achieve a sensitivity of 0.97 with a negative predictive value of 0.99 for MSI prediction on surgical resection specimens. We demonstrate for the first time that resection specimen-only training reaches clinical-grade performance on endoscopic biopsy tissue, solving a long-standing diagnostic problem. Interpretation: A fully transformer-based end-to-end pipeline trained on thousands of pathology slides yields clinical-grade performance for biomarker prediction on surgical resections and biopsies. Our new methods are freely available under an open source license.
Feature construction using explanations of individual predictions
Venue: arXiv cs.LG 2023
Year: 2023

Feature construction can contribute to comprehensibility and performance of machine learning models. Unfortunately, it usually requires exhaustive search in the attribute space or time-consuming human involvement to generate meaningful features. We propose a novel heuristic approach for reducing the search space based on aggregation of instance-based explanations of predictive models. The proposed Explainable Feature Construction (EFC) methodology identifies groups of co-occurring attributes exposed by popular explanation methods, such as IME and SHAP. We empirically show that reducing the search to these groups significantly reduces the time of feature construction using logical, relational, Cartesian, numerical, and threshold num-of-N and X-of-N constructive operators. An analysis on 10 transparent synthetic datasets shows that EFC effectively identifies informative groups of attributes and constructs relevant features. Using 30 real-world classification datasets, we show significant improvements in classification accuracy for several classifiers and demonstrate the feasibility of the proposed feature construction even for large datasets. Finally, EFC generated interpretable features on a real-world problem from the financial industry, which were confirmed by a domain expert.
Architectural Support for Efficient Data Movement in Disaggregated Systems
Venue: arXiv cs.AR 2023
Year: 2023

Resource disaggregation offers a cost effective solution to resource scaling, utilization, and failure-handling in data centers by physically separating hardware devices in a server. Servers are architected as pools of processor, memory, and storage devices, organized as independent failure-isolated components interconnected by a high-bandwidth network. A critical challenge, however, is the high performance penalty of accessing data from a remote memory module over the network. Addressing this challenge is difficult as disaggregated systems have high runtime variability in network latencies/bandwidth, and page migration can significantly delay critical path cache line accesses in other pages. This paper introduces DaeMon, the first software-transparent and robust mechanism to significantly alleviate data movement overheads in fully disaggregated systems. First, to enable scalability to multiple hardware components in the system, we enhance each compute and memory unit with specialized engines that transparently handle data migrations. Second, to achieve high performance and provide robustness across various network, architecture and application characteristics, we implement a synergistic approach of bandwidth partitioning, link compression, decoupled data movement of multiple granularities, and adaptive granularity selection in data movements. We evaluate DaeMon in a wide variety of workloads at different network and architecture configurations using a state-of-the-art accurate simulator and demonstrate that DaeMon significantly improves system performance and data access costs over the widely-adopted approach of moving data at page granularity.
Using I4.0 digital twins in agriculture
Venue: arXiv cs.OH 2023
Year: 2023

Agriculture is a huge domain where an enormous landscape of systems interact to support agricultural processes, which are becoming increasingly digital. From the perspective of agricultural service providers, a prominent challenge is interoperability. In the Fraunhofer lighthouse project Cognitive Agriculture (COGNAC), we investigated how the usage of Industry 4.0 digital twins (I4.0 DTs) can help overcome this challenge. This paper contributes architecture drivers and a solution concept using I4.0 DTs in the agricultural domain. Furthermore, we discuss the opportunities and limitations offered by I4.0 DTs for the agricultural domain.
Noisy Parallel Data Alignment
Venue: arXiv cs.CL 2023
Year: 2023

An ongoing challenge in current natural language processing is how its major advancements tend to disproportionately favor resource-rich languages, leaving a significant number of under-resourced languages behind. Due to the lack of resources required to train and evaluate models, most modern language technologies are either nonexistent or unreliable to process endangered, local, and non-standardized languages. Optical character recognition (OCR) is often used to convert endangered language documents into machine-readable data. However, such OCR output is typically noisy, and most word alignment models are not built to work under such noisy conditions. In this work, we study the existing word-level alignment models under noisy settings and aim to make them more robust to noisy data. Our noise simulation and structural biasing method, tested on multiple language pairs, manages to reduce the alignment error rate on a state-of-the-art neural-based alignment model up to 59.6%.
Graph Neural Networks for Decentralized Multi-Agent Perimeter Defense
Venue: arXiv cs.MA 2023
Year: 2023

In this work, we study the problem of decentralized multi-agent perimeter defense that asks for computing actions for defenders with local perceptions and communications to maximize the capture of intruders. One major challenge for practical implementations is to make perimeter defense strategies scalable for large-scale problem instances. To this end, we leverage graph neural networks (GNNs) to develop an imitation learning framework that learns a mapping from defenders' local perceptions and their communication graph to their actions. The proposed GNN-based learning network is trained by imitating a centralized expert algorithm such that the learned actions are close to that generated by the expert algorithm. We demonstrate that our proposed network performs closer to the expert algorithm and is superior to other baseline algorithms by capturing more intruders. Our GNN-based network is trained at a small scale and can be generalized to large-scale cases. We run perimeter defense games in scenarios with different team sizes and configurations to demonstrate the performance of the learned network.
Mathematics, word problems, common sense, and artificial intelligence
Venue: arXiv cs.AI 2023
Year: 2023

The paper discusses the capacities and limitations of current artificial intelligence (AI) technology to solve word problems that combine elementary knowledge with commonsense reasoning. No existing AI systems can solve these reliably. We review three approaches that have been developed, using AI natural language technology: outputting the answer directly, outputting a computer program that solves the problem, and outputting a formalized representation that can be input to an automated theorem verifier. We review some benchmarks that have been developed to evaluate these systems and some experimental studies. We discuss the limitations of the existing technology at solving these kinds of problems. We argue that it is not clear whether these kinds of limitations will be important in developing AI technology for pure mathematical research, but that they will be important in applications of mathematics, and may well be important in developing programs capable of reading and understanding mathematical content written by humans.
Long-term stable Electromyography classification using Canonical Correlation Analysis
Venue: arXiv cs.LG 2023
Year: 2023

Discrimination of hand gestures based on the decoding of surface electromyography (sEMG) signals is a well-establish approach for controlling prosthetic devices and for Human-Machine Interfaces (HMI). However, despite the promising results achieved by this approach in well-controlled experimental conditions, its deployment in long-term real-world application scenarios is still hindered by several challenges. One of the most critical challenges is maintaining high EMG data classification performance across multiple days without retraining the decoding system. The drop in performance is mostly due to the high EMG variability caused by electrodes shift, muscle artifacts, fatigue, user adaptation, or skin-electrode interfacing issues. Here we propose a novel statistical method based on canonical correlation analysis (CCA) that stabilizes EMG classification performance across multiple days for long-term control of prosthetic devices. We show how CCA can dramatically decrease the performance drop of standard classifiers observed across days, by maximizing the correlation among multiple-day acquisition data sets. Our results show how the performance of a classifier trained on EMG data acquired only of the first day of the experiment maintains 90% relative accuracy across multiple days, compensating for the EMG data variability that occurs over long-term periods, using the CCA transformation on data obtained from a small number of gestures. This approach eliminates the need for large data sets and multiple or periodic training sessions, which currently hamper the usability of conventional pattern recognition based approaches
Security of Electrical, Optical and Wireless On-Chip Interconnects: A Survey
Venue: arXiv cs.CR 2023
Year: 2023

The advancement of manufacturing technologies has enabled the integration of more intellectual property (IP) cores on the same system-on-chip (SoC). Scalable and high throughput on-chip communication architecture has become a vital component in today's SoCs. Diverse technologies such as electrical, wireless, optical, and hybrid are available for on-chip communication with different architectures supporting them. Security of the on-chip communication is crucial because exploiting any vulnerability would be a goldmine for an attacker. In this survey, we provide a comprehensive review of threat models, attacks, and countermeasures over diverse on-chip communication technologies as well as sophisticated architectures.
SONIA: an immersive customizable virtual reality system for the education and exploration of brain networks
Venue: arXiv cs.HC 2023
Year: 2023

While mastery of neuroanatomy is important for the investigation of the brain, there is an increasing interest in exploring the neural pathways to better understand the roles of neural circuitry in brain functions. To tackle the limitations of traditional 2D-display-based neuronavigation software in intuitively visualizing complex 3D anatomies, several virtual reality (VR) and augmented reality (AR) solutions have been proposed to facilitate neuroanatomical education. However, with the increasing knowledge on brain connectivity and the functioning of the sub-systems, there is still a lack of similar software solutions for the education and exploration of these topics, which demand more elaborate visualization and interaction strategies. To address this gap, we designed the immerSive custOmizable Neuro learnIng plAform (SONIA), a novel user-friendly VR software system with a multi-scale interaction paradigm that allows flexible customization of learning materials. With both quantitative and qualitative evaluations through user studies, the proposed system is shown to have high usability, attractive visual design, and good educational value. As the first immersive system that integrates customizable design and detailed narratives of the brain sub-systems for the education of neuroanatomy and brain connectivity, SONIA showcases new potential directions and provides valuable insights regarding medical learning and exploration in VR.
Reverse Logistics Network Design to Estimate the Economic and Environmental Impacts of Take-back Legislation: A Case Study for E-waste Management System in Washington State
Venue: arXiv cs.CY 2023
Year: 2023

In recent years, recycling and disposal of end-of-life (EOL) electronic products has attracted considerable attention in response to concerns over resource recovery and environmental impacts of electronic waste (e-waste). In many countries, legislation to make manufacturers responsible for taking e-waste at the end of their useful lives either has been adopted or is being considered. In this paper, by capturing different stages in the life-cycle of EOL electronic products (or, e-waste) generated from private or small-entity users, we develop two different formulations of a reverse logistics network, i.e. system-optimum model and user-optimum model, to estimate both economic and environmental effects of take-back legislation. In this system, e-waste is collected through user drop-off at designated collection sites. While we study the whole reverse logistics network associated with recycling and remanufacturing of e-waste in the system-optimum model and obtain an optimum solution from the policy maker's perspective, we split the logistics network into two distinct parts in the user-optimum model in order to derive an optimum solution from the users' standpoint. Implementing the proposed models on an illustrative example shows how they are capable of estimating the economic and environmental impacts of take-back legislation in various stages of e-waste's life-cycle.
Inductive Reasoning for Coinductive Types
Venue: arXiv cs.LO 2023
Year: 2023

We present AlgCo (Algebraic Coinductives), a practical framework for inductive reasoning over commonly used coinductive types such as conats, streams, and infinitary trees with finite branching factor. The key idea is to exploit the notion of algebraic complete partial order from domain theory to define continuous operations over coinductive types via primitive recursion on ``dense'' collections of their elements, enabling a convenient strategy for reasoning about algebraic coinductives by straightforward proofs by induction. We implement the AlgCo framework in Coq and demonstrate its power by verifying a stream variant of the sieve of Eratosthenes, a regular expression library based on coinductive trie encodings of formal languages, and expected value semantics for coinductive sampling processes over discrete probability distributions in the random bit model.
Model Agnostic Sample Reweighting for Out-of-Distribution Learning
Venue: arXiv cs.LG 2023
Year: 2023

Distributionally robust optimization (DRO) and invariant risk minimization (IRM) are two popular methods proposed to improve out-of-distribution (OOD) generalization performance of machine learning models. While effective for small models, it has been observed that these methods can be vulnerable to overfitting with large overparameterized models. This work proposes a principled method, \textbf{M}odel \textbf{A}gnostic sam\textbf{PL}e r\textbf{E}weighting (\textbf{MAPLE}), to effectively address OOD problem, especially in overparameterized scenarios. Our key idea is to find an effective reweighting of the training samples so that the standard empirical risk minimization training of a large model on the weighted training data leads to superior OOD generalization performance. The overfitting issue is addressed by considering a bilevel formulation to search for the sample reweighting, in which the generalization complexity depends on the search space of sample weights instead of the model size. We present theoretical analysis in linear case to prove the insensitivity of MAPLE to model size, and empirically verify its superiority in surpassing state-of-the-art methods by a large margin. Code is available at \url{https://github.com/x-zho14/MAPLE}.
A Stability Analysis of Fine-Tuning a Pre-Trained Model
Venue: arXiv cs.LG 2023
Year: 2023

Fine-tuning a pre-trained model (such as BERT, ALBERT, RoBERTa, T5, GPT, etc.) has proven to be one of the most promising paradigms in recent NLP research. However, numerous recent works indicate that fine-tuning suffers from the instability problem, i.e., tuning the same model under the same setting results in significantly different performance. Many recent works have proposed different methods to solve this problem, but there is no theoretical understanding of why and how these methods work. In this paper, we propose a novel theoretical stability analysis of fine-tuning that focuses on two commonly used settings, namely, full fine-tuning and head tuning. We define the stability under each setting and prove the corresponding stability bounds. The theoretical bounds explain why and how several existing methods can stabilize the fine-tuning procedure. In addition to being able to explain most of the observed empirical discoveries, our proposed theoretical analysis framework can also help in the design of effective and provable methods. Based on our theory, we propose three novel strategies to stabilize the fine-tuning procedure, namely, Maximal Margin Regularizer (MMR), Multi-Head Loss (MHLoss), and Self Unsupervised Re-Training (SURT). We extensively evaluate our proposed approaches on 11 widely used real-world benchmark datasets, as well as hundreds of synthetic classification datasets. The experiment results show that our proposed methods significantly stabilize the fine-tuning procedure and also corroborate our theoretical analysis.
FUSEE: A Fully Memory-Disaggregated Key-Value Store (Extended Version)
Venue: arXiv cs.DC 2023
Year: 2023

Distributed in-memory key-value (KV) stores are embracing the disaggregated memory (DM) architecture for higher resource utilization. However, existing KV stores on DM employ a semi-disaggregated design that stores KV pairs on DM but manages metadata with monolithic metadata servers, hence still suffering from low resource efficiency on metadata servers. To address this issue, this paper proposes FUSEE, a FUlly memory-diSaggrEgated KV StorE that brings disaggregation to metadata management. FUSEE replicates metadata, i.e., the index and memory management information, on memory nodes, manages them directly on the client side, and handles complex failures under the DM architecture. To scalably replicate the index on clients, FUSEE proposes a client-centric replication protocol that allows clients to concurrently access and modify the replicated index. To efficiently manage disaggregated memory, FUSEE adopts a two-level memory management scheme that splits the memory management duty among clients and memory nodes. Finally, to handle the metadata corruption under client failures, FUSEE leverages an embedded operation log scheme to repair metadata with low log maintenance overhead. We evaluate FUSEE with both micro and YCSB hybrid benchmarks. The experimental results show that FUSEE outperforms the state-of-the-art KV stores on DM by up to 4.5 times with less resource consumption.
Effective Baselines for Multiple Object Rearrangement Planning in Partially Observable Mapped Environments
Venue: arXiv cs.RO 2023
Year: 2023

Many real-world tasks, from house-cleaning to cooking, can be formulated as multi-object rearrangement problems -- where an agent needs to get specific objects into appropriate goal states. For such problems, we focus on the setting that assumes a pre-specified goal state, availability of perfect manipulation and object recognition capabilities, and a static map of the environment but unknown initial location of objects to be rearranged. Our goal is to enable home-assistive intelligent agents to efficiently plan for rearrangement under such partial observability. This requires efficient trade-offs between exploration of the environment and planning for rearrangement, which is challenging because of long-horizon nature of the problem. To make progress on this problem, we first analyze the effects of various factors such as number of objects and receptacles, agent carrying capacity, environment layouts etc. on exploration and planning for rearrangement using classical methods. We then investigate both monolithic and modular deep reinforcement learning (DRL) methods for planning in our setting. We find that monolithic DRL methods do not succeed at long-horizon planning needed for multi-object rearrangement. Instead, modular greedy approaches surprisingly perform reasonably well and emerge as competitive baselines for planning with partial observability in multi-object rearrangement problems. We also show that our greedy modular agents are empirically optimal when the objects that need to be rearranged are uniformly distributed in the environment -- thereby contributing baselines with strong performance for future work on multi-object rearrangement planning in partially observable settings.
Probabilistic Bilevel Coreset Selection
Venue: arXiv cs.LG 2023
Year: 2023

The goal of coreset selection in supervised learning is to produce a weighted subset of data, so that training only on the subset achieves similar performance as training on the entire dataset. Existing methods achieved promising results in resource-constrained scenarios such as continual learning and streaming. However, most of the existing algorithms are limited to traditional machine learning models. A few algorithms that can handle large models adopt greedy search approaches due to the difficulty in solving the discrete subset selection problem, which is computationally costly when coreset becomes larger and often produces suboptimal results. In this work, for the first time we propose a continuous probabilistic bilevel formulation of coreset selection by learning a probablistic weight for each training sample. The overall objective is posed as a bilevel optimization problem, where 1) the inner loop samples coresets and train the model to convergence and 2) the outer loop updates the sample probability progressively according to the model's performance. Importantly, we develop an efficient solver to the bilevel optimization problem via unbiased policy gradient without trouble of implicit differentiation. We provide the convergence property of our training procedure and demonstrate the superiority of our algorithm against various coreset selection methods in various tasks, especially in more challenging label-noise and class-imbalance scenarios.
Transfer Learning for Olfactory Object Detection
Venue: arXiv cs.CV 2023
Year: 2023

We investigate the effect of style and category similarity in multiple datasets used for object detection pretraining. We find that including an additional stage of object-detection pretraining can increase the detection performance considerably. While our experiments suggest that style similarities between pre-training and target datasets are less important than matching categories, further experiments are needed to verify this hypothesis.