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Dec 8

Experiments with Large Language Models on Retrieval-Augmented Generation for Closed-Source Simulation Software

Large Language Models (LLMs) are increasingly helpful in text generation, even writing code in programming languages based on user prompts written in natural language. They are even applied to generate simulation models for multibody systems from natural language. Research results suggest that LLMs surpass the mere replication of existing code examples, where some LLMs have been trained on an open-source multibody simulation code. However, for closed-source simulation software, such results are not to be expected as their ideas and concepts might differ from other publicly available ones. LLMs can hallucinate for knowledge-intensive tasks, such as model creation, which can lead to wrong responses. This is especially the case for the LLM unknown closed-source simulation software. The same applies to other internal knowledge kept private to protect intellectual property or data privacy. The Retrieval-Augmented Generation (RAG) approach might yield a solution for these knowledge-intensive tasks. This paper explores the application of RAG to closed-source simulation software and presents first experiments. After a brief introduction to LLMs, the RAG approach, and the simulation method applied by the close-source simulation software, several examples are provided to test LLMs' knowledge of the simulation software and the creation of simulation models using two RAG systems. The examples show promising results indicating the benefits of applying RAG systems to closed-source simulation software, helping to access their knowledge. Nevertheless, they also reveal gaps in the applied information and open questions for further research.

  • 2 authors
·
Feb 6

Revisiting Graph Neural Networks on Graph-level Tasks: Comprehensive Experiments, Analysis, and Improvements

Graphs are essential data structures for modeling complex interactions in domains such as social networks, molecular structures, and biological systems. Graph-level tasks, which predict properties or classes for the entire graph, are critical for applications, such as molecular property prediction and subgraph counting. Graph Neural Networks (GNNs) have shown promise in these tasks, but their evaluations are often limited to narrow datasets, tasks, and inconsistent experimental setups, restricting their generalizability. To address these limitations, we propose a unified evaluation framework for graph-level GNNs. This framework provides a standardized setting to evaluate GNNs across diverse datasets, various graph tasks (e.g., graph classification and regression), and challenging scenarios, including noisy, imbalanced, and few-shot graphs. Additionally, we propose a novel GNN model with enhanced expressivity and generalization capabilities. Specifically, we enhance the expressivity of GNNs through a k-path rooted subgraph approach, enabling the model to effectively count subgraphs (e.g., paths and cycles). Moreover, we introduce a unified graph contrastive learning algorithm for graphs across diverse domains, which adaptively removes unimportant edges to augment graphs, thereby significantly improving generalization performance. Extensive experiments demonstrate that our model achieves superior performance against fourteen effective baselines across twenty-seven graph datasets, establishing it as a robust and generalizable model for graph-level tasks.

  • 6 authors
·
Jan 1

Towards Enhancing Coherence in Extractive Summarization: Dataset and Experiments with LLMs

Extractive summarization plays a pivotal role in natural language processing due to its wide-range applications in summarizing diverse content efficiently, while also being faithful to the original content. Despite significant advancement achieved in extractive summarization by Large Language Models (LLMs), these summaries frequently exhibit incoherence. An important aspect of the coherent summary is its readability for intended users. Although there have been many datasets and benchmarks proposed for creating coherent extractive summaries, none of them currently incorporate user intent to improve coherence in extractive summarization. Motivated by this, we propose a systematically created human-annotated dataset consisting of coherent summaries for five publicly available datasets and natural language user feedback, offering valuable insights into how to improve coherence in extractive summaries. We utilize this dataset for aligning LLMs through supervised fine-tuning with natural language human feedback to enhance the coherence of their generated summaries. Preliminary experiments with Falcon-40B and Llama-2-13B show significant performance improvements (~10% Rouge-L) in terms of producing coherent summaries. We further utilize human feedback to benchmark results over instruction-tuned models such as FLAN-T5 which resulted in several interesting findings. Data and source code are available at https://github.com/Mihir3009/Extract-AI.

  • 6 authors
·
Jul 5, 2024

Comparing Machines and Children: Using Developmental Psychology Experiments to Assess the Strengths and Weaknesses of LaMDA Responses

Developmental psychologists have spent decades devising experiments to test the intelligence and knowledge of infants and children, tracing the origin of crucial concepts and capacities. Moreover, experimental techniques in developmental psychology have been carefully designed to discriminate the cognitive capacities that underlie particular behaviors. We propose that using classical experiments from child development is a particularly effective way to probe the computational abilities of AI models, in general, and LLMs in particular. First, the methodological techniques of developmental psychology, such as the use of novel stimuli to control for past experience or control conditions to determine whether children are using simple associations, can be equally helpful for assessing the capacities of LLMs. In parallel, testing LLMs in this way can tell us whether the information that is encoded in text is sufficient to enable particular responses, or whether those responses depend on other kinds of information, such as information from exploration of the physical world. In this work we adapt classical developmental experiments to evaluate the capabilities of LaMDA, a large language model from Google. We propose a novel LLM Response Score (LRS) metric which can be used to evaluate other language models, such as GPT. We find that LaMDA generates appropriate responses that are similar to those of children in experiments involving social understanding, perhaps providing evidence that knowledge of these domains is discovered through language. On the other hand, LaMDA's responses in early object and action understanding, theory of mind, and especially causal reasoning tasks are very different from those of young children, perhaps showing that these domains require more real-world, self-initiated exploration and cannot simply be learned from patterns in language input.

  • 5 authors
·
May 18, 2023

Train Once, Answer All: Many Pretraining Experiments for the Cost of One

Recent work has demonstrated that controlled pretraining experiments are a powerful tool for understanding learning, reasoning, and memorization in large language models (LLMs). However, the computational cost of pretraining presents a significant constraint. To overcome this constraint, we propose to conduct multiple pretraining experiments simultaneously during a single training run. We demonstrate the feasibility of this approach by conducting ten experiments during the training of a 1.5B parameter model on 210B tokens. Although we only train a single model, we can replicate the results from multiple previous works on data contamination, poisoning, and memorization. We also conduct novel investigations into knowledge acquisition, mathematical reasoning, and watermarking. For example, we dynamically update the training data until the model acquires a particular piece of knowledge. Remarkably, the influence of the ten experiments on the model's training dynamics and overall performance is minimal. However, interactions between different experiments may act as a potential confounder in our approach. We propose to test for interactions with continual pretraining experiments, finding them to be negligible in our setup. Overall, our findings suggest that performing multiple pretraining experiments in a single training run can enable rigorous scientific experimentation with large models on a compute budget.

  • 2 authors
·
Sep 27

Solar System Experiments in the Search for Dark Energy and Dark Matter

We reassess the realistic discovery reach of Solar-System experiments for dark energy (DE) and dark matter (DM), making explicit the bridge from cosmology-level linear responses to local, screened residuals. In scalar-tensor frameworks with a universal conformal coupling A(phi) and chameleon/Vainshtein screening, we map cosmological responses {mu(z,k),Sigma(z,k)} inferred by DESI and Euclid to thin-shell or Vainshtein residuals in deep Solar potentials Phi_N. We emphasize a two-branch strategy. In a detection-first branch, a verified local anomaly -- an Einstein equivalence principle (EEP) violation, a Shapiro-delay signal with |gamma-1|simfewtimes 10^{-6}, an AU-scale Yukawa tail, or a ultralight DM (ULDM) line in clocks/atom interferometers in space (AIS) -- triggers a joint refit of cosmology and Solar-System data under a common microphysical parameterization {V(phi),A(phi)}. In a guardrail branch, Solar-System tests enforce constraints (EEP; PPN parameters gamma,beta; and dot G/G) and close unscreened or weakly screened corners indicated by cosmology. We forecast, per conjunction, |gamma-1|lesssim (2-5)times 10^{-6} (Ka-/X-band or optical Shapiro), eta_{EEP}sim (1--10)times 10^{-17} (drag-free AIS), |dot G/G|sim(3-5)times10^{-15},yr^{-1} (sub-mm-class LLR), a uniform ~2x tightening of AU-scale Yukawa/DM-density bounds, and (3-10)times improved ULDM-coupling reach from clocks. For a conformal benchmark, mu_{ lin,0}=0.10 implies chisimeq mu_{lin,0/2} and a Sun thin shell Delta R/Rlesssim (1/3chi)|gamma-1|/2=2.4times 10^{-3} at |gamma-1|=5times 10^{-6}; Vainshtein screening at 1 AU yields |gamma-1|lesssim 10^{-11}, naturally below near-term reach. We recommend a cost-effective guardrail+discovery portfolio with explicit triggers for escalation to dedicated missions.

  • 1 authors
·
Sep 6

The Role of Language Imbalance in Cross-lingual Generalisation: Insights from Cloned Language Experiments

Multilinguality is crucial for extending recent advancements in language modelling to diverse linguistic communities. To maintain high performance while representing multiple languages, multilingual models ideally align representations, allowing what is learned in one language to generalise to others. Prior research has emphasised the importance of parallel data and shared vocabulary elements as key factors for such alignment. In this study, we investigate an unintuitive novel driver of cross-lingual generalisation: language imbalance. In controlled experiments on perfectly equivalent cloned languages, we observe that the existence of a predominant language during training boosts the performance of less frequent languages and leads to stronger alignment of model representations across languages. Furthermore, we find that this trend is amplified with scale: with large enough models or long enough training, we observe that bilingual training data with a 90/10 language split yields better performance on both languages than a balanced 50/50 split. Building on these insights, we design training schemes that can improve performance in all cloned languages, even without altering the training data. As we extend our analysis to real languages, we find that infrequent languages still benefit from frequent ones, yet whether language imbalance causes cross-lingual generalisation there is not conclusive.

  • 5 authors
·
Apr 11, 2024

FineBio: A Fine-Grained Video Dataset of Biological Experiments with Hierarchical Annotation

In the development of science, accurate and reproducible documentation of the experimental process is crucial. Automatic recognition of the actions in experiments from videos would help experimenters by complementing the recording of experiments. Towards this goal, we propose FineBio, a new fine-grained video dataset of people performing biological experiments. The dataset consists of multi-view videos of 32 participants performing mock biological experiments with a total duration of 14.5 hours. One experiment forms a hierarchical structure, where a protocol consists of several steps, each further decomposed into a set of atomic operations. The uniqueness of biological experiments is that while they require strict adherence to steps described in each protocol, there is freedom in the order of atomic operations. We provide hierarchical annotation on protocols, steps, atomic operations, object locations, and their manipulation states, providing new challenges for structured activity understanding and hand-object interaction recognition. To find out challenges on activity understanding in biological experiments, we introduce baseline models and results on four different tasks, including (i) step segmentation, (ii) atomic operation detection (iii) object detection, and (iv) manipulated/affected object detection. Dataset and code are available from https://github.com/aistairc/FineBio.

  • 7 authors
·
Jan 31, 2024

Balancing Computational Efficiency and Forecast Error in Machine Learning-based Time-Series Forecasting: Insights from Live Experiments on Meteorological Nowcasting

Machine learning for time-series forecasting remains a key area of research. Despite successful application of many machine learning techniques, relating computational efficiency to forecast error remains an under-explored domain. This paper addresses this topic through a series of real-time experiments to quantify the relationship between computational cost and forecast error using meteorological nowcasting as an example use-case. We employ a variety of popular regression techniques (XGBoost, FC-MLP, Transformer, and LSTM) for multi-horizon, short-term forecasting of three variables (temperature, wind speed, and cloud cover) for multiple locations. During a 5-day live experiment, 4000 data sources were streamed for training and inferencing 144 models per hour. These models were parameterized to explore forecast error for two computational cost minimization methods: a novel auto-adaptive data reduction technique (Variance Horizon) and a performance-based concept drift-detection mechanism. Forecast error of all model variations were benchmarked in real-time against a state-of-the-art numerical weather prediction model. Performance was assessed using classical and novel evaluation metrics. Results indicate that using the Variance Horizon reduced computational usage by more than 50\%, while increasing between 0-15\% in error. Meanwhile, performance-based retraining reduced computational usage by up to 90\% while also improving forecast error by up to 10\%. Finally, the combination of both the Variance Horizon and performance-based retraining outperformed other model configurations by up to 99.7\% when considering error normalized to computational usage.

  • 5 authors
·
Sep 26, 2023

EXP-Bench: Can AI Conduct AI Research Experiments?

Automating AI research holds immense potential for accelerating scientific progress, yet current AI agents struggle with the complexities of rigorous, end-to-end experimentation. We introduce EXP-Bench, a novel benchmark designed to systematically evaluate AI agents on complete research experiments sourced from influential AI publications. Given a research question and incomplete starter code, EXP-Bench challenges AI agents to formulate hypotheses, design and implement experimental procedures, execute them, and analyze results. To enable the creation of such intricate and authentic tasks with high-fidelity, we design a semi-autonomous pipeline to extract and structure crucial experimental details from these research papers and their associated open-source code. With the pipeline, EXP-Bench curated 461 AI research tasks from 51 top-tier AI research papers. Evaluations of leading LLM-based agents, such as OpenHands and IterativeAgent on EXP-Bench demonstrate partial capabilities: while scores on individual experimental aspects such as design or implementation correctness occasionally reach 20-35%, the success rate for complete, executable experiments was a mere 0.5%. By identifying these bottlenecks and providing realistic step-by-step experiment procedures, EXP-Bench serves as a vital tool for future AI agents to improve their ability to conduct AI research experiments. EXP-Bench is open-sourced at https://github.com/Just-Curieous/Curie/tree/main/benchmark/exp_bench.

  • 13 authors
·
May 30 3

Tiny LVLM-eHub: Early Multimodal Experiments with Bard

Recent advancements in Large Vision-Language Models (LVLMs) have demonstrated significant progress in tackling complex multimodal tasks. Among these cutting-edge developments, Google's Bard stands out for its remarkable multimodal capabilities, promoting comprehensive comprehension and reasoning across various domains. This work presents an early and holistic evaluation of LVLMs' multimodal abilities, with a particular focus on Bard, by proposing a lightweight variant of LVLM-eHub, named Tiny LVLM-eHub. In comparison to the vanilla version, Tiny LVLM-eHub possesses several appealing properties. Firstly, it provides a systematic assessment of six categories of multimodal capabilities, including visual perception, visual knowledge acquisition, visual reasoning, visual commonsense, object hallucination, and embodied intelligence, through quantitative evaluation of 42 standard text-related visual benchmarks. Secondly, it conducts an in-depth analysis of LVLMs' predictions using the ChatGPT Ensemble Evaluation (CEE), which leads to a robust and accurate evaluation and exhibits improved alignment with human evaluation compared to the word matching approach. Thirdly, it comprises a mere 2.1K image-text pairs, facilitating ease of use for practitioners to evaluate their own offline LVLMs. Through extensive experimental analysis, this study demonstrates that Bard outperforms previous LVLMs in most multimodal capabilities except object hallucination, to which Bard is still susceptible. Tiny LVLM-eHub serves as a baseline evaluation for various LVLMs and encourages innovative strategies aimed at advancing multimodal techniques. Our project is publicly available at https://github.com/OpenGVLab/Multi-Modality-Arena.

  • 11 authors
·
Aug 7, 2023

Open RL Benchmark: Comprehensive Tracked Experiments for Reinforcement Learning

In many Reinforcement Learning (RL) papers, learning curves are useful indicators to measure the effectiveness of RL algorithms. However, the complete raw data of the learning curves are rarely available. As a result, it is usually necessary to reproduce the experiments from scratch, which can be time-consuming and error-prone. We present Open RL Benchmark, a set of fully tracked RL experiments, including not only the usual data such as episodic return, but also all algorithm-specific and system metrics. Open RL Benchmark is community-driven: anyone can download, use, and contribute to the data. At the time of writing, more than 25,000 runs have been tracked, for a cumulative duration of more than 8 years. Open RL Benchmark covers a wide range of RL libraries and reference implementations. Special care is taken to ensure that each experiment is precisely reproducible by providing not only the full parameters, but also the versions of the dependencies used to generate it. In addition, Open RL Benchmark comes with a command-line interface (CLI) for easy fetching and generating figures to present the results. In this document, we include two case studies to demonstrate the usefulness of Open RL Benchmark in practice. To the best of our knowledge, Open RL Benchmark is the first RL benchmark of its kind, and the authors hope that it will improve and facilitate the work of researchers in the field.

  • 33 authors
·
Feb 5, 2024

Sparks of Artificial General Intelligence: Early experiments with GPT-4

Artificial intelligence (AI) researchers have been developing and refining large language models (LLMs) that exhibit remarkable capabilities across a variety of domains and tasks, challenging our understanding of learning and cognition. The latest model developed by OpenAI, GPT-4, was trained using an unprecedented scale of compute and data. In this paper, we report on our investigation of an early version of GPT-4, when it was still in active development by OpenAI. We contend that (this early version of) GPT-4 is part of a new cohort of LLMs (along with ChatGPT and Google's PaLM for example) that exhibit more general intelligence than previous AI models. We discuss the rising capabilities and implications of these models. We demonstrate that, beyond its mastery of language, GPT-4 can solve novel and difficult tasks that span mathematics, coding, vision, medicine, law, psychology and more, without needing any special prompting. Moreover, in all of these tasks, GPT-4's performance is strikingly close to human-level performance, and often vastly surpasses prior models such as ChatGPT. Given the breadth and depth of GPT-4's capabilities, we believe that it could reasonably be viewed as an early (yet still incomplete) version of an artificial general intelligence (AGI) system. In our exploration of GPT-4, we put special emphasis on discovering its limitations, and we discuss the challenges ahead for advancing towards deeper and more comprehensive versions of AGI, including the possible need for pursuing a new paradigm that moves beyond next-word prediction. We conclude with reflections on societal influences of the recent technological leap and future research directions.

  • 14 authors
·
Mar 22, 2023

CRISPR-GPT: An LLM Agent for Automated Design of Gene-Editing Experiments

The introduction of genome engineering technology has transformed biomedical research, making it possible to make precise changes to genetic information. However, creating an efficient gene-editing system requires a deep understanding of CRISPR technology, and the complex experimental systems under investigation. While Large Language Models (LLMs) have shown promise in various tasks, they often lack specific knowledge and struggle to accurately solve biological design problems. In this work, we introduce CRISPR-GPT, an LLM agent augmented with domain knowledge and external tools to automate and enhance the design process of CRISPR-based gene-editing experiments. CRISPR-GPT leverages the reasoning ability of LLMs to facilitate the process of selecting CRISPR systems, designing guide RNAs, recommending cellular delivery methods, drafting protocols, and designing validation experiments to confirm editing outcomes. We showcase the potential of CRISPR-GPT for assisting non-expert researchers with gene-editing experiments from scratch and validate the agent's effectiveness in a real-world use case. Furthermore, we explore the ethical and regulatory considerations associated with automated gene-editing design, highlighting the need for responsible and transparent use of these tools. Our work aims to bridge the gap between beginner biological researchers and CRISPR genome engineering techniques, and demonstrate the potential of LLM agents in facilitating complex biological discovery tasks.

  • 10 authors
·
Apr 27, 2024

First observation of the Josephson-Anderson relation in experiments on hydrodynamic drag

We verify a recent prediction (Eq. 3.50 in G. L. Eyink, Phys. Rev. X 11, 031054 (2021)) for the drag on an object moving through a fluid. In this prediction the velocity field is decomposed into a nonvortical (potential) and vortical contribution, and so is the associated drag force. In the Josephson-Anderson relation the vortical contribution of the drag force follows from the flux of vorticity traversing the streamlines of the corresponding potential flow. The potential component is directly determined by the plate acceleration and its added mass. The Josephson-Anderson relation is derived from the quantum description of superfluids, but remarkably applies to the classical fluid in our experiment. In our experiment a flat plate is accelerated through water using a robotic arm. This geometry is simple enough to allow analytic potential flow streamlines. The monitored plate position shows an oscillatory component of the acceleration, which adds an additional test of the Josephson-Anderson relation. The instantaneous velocity field is measured using particle image velocimetry. It enables us to evaluate Eq. 3.50 from [1] and compare its prediction to the measured drag force. We find excellent agreement, and, most remarkably find that the added mass contribution to the drag force still stands out after the flow has turned vortical. We finally comment on the requirements on the experimental techniques for evaluating the Josephson-Anderson relation.

  • 5 authors
·
Aug 27

BioMARS: A Multi-Agent Robotic System for Autonomous Biological Experiments

Large language models (LLMs) and vision-language models (VLMs) have the potential to transform biological research by enabling autonomous experimentation. Yet, their application remains constrained by rigid protocol design, limited adaptability to dynamic lab conditions, inadequate error handling, and high operational complexity. Here we introduce BioMARS (Biological Multi-Agent Robotic System), an intelligent platform that integrates LLMs, VLMs, and modular robotics to autonomously design, plan, and execute biological experiments. BioMARS uses a hierarchical architecture: the Biologist Agent synthesizes protocols via retrieval-augmented generation; the Technician Agent translates them into executable robotic pseudo-code; and the Inspector Agent ensures procedural integrity through multimodal perception and anomaly detection. The system autonomously conducts cell passaging and culture tasks, matching or exceeding manual performance in viability, consistency, and morphological integrity. It also supports context-aware optimization, outperforming conventional strategies in differentiating retinal pigment epithelial cells. A web interface enables real-time human-AI collaboration, while a modular backend allows scalable integration with laboratory hardware. These results highlight the feasibility of generalizable, AI-driven laboratory automation and the transformative role of language-based reasoning in biological research.

  • 10 authors
·
Jul 2

Exploring Next Token Prediction in Theory of Mind (ToM) Tasks: Comparative Experiments with GPT-2 and LLaMA-2 AI Models

Language models have made significant progress in generating coherent text and predicting next tokens based on input prompts. This study compares the next-token prediction performance of two well-known models: OpenAI's GPT-2 and Meta's Llama-2-7b-chat-hf on Theory of Mind (ToM) tasks. To evaluate their capabilities, we built a dataset from 10 short stories sourced from the Explore ToM Dataset. We enhanced these stories by programmatically inserting additional sentences (infills) using GPT-4, creating variations that introduce different levels of contextual complexity. This setup enables analysis of how increasing context affects model performance. We tested both models under four temperature settings (0.01, 0.5, 1.0, 2.0) and evaluated their ability to predict the next token across three reasoning levels. Zero-order reasoning involves tracking the state, either current (ground truth) or past (memory). First-order reasoning concerns understanding another's mental state (e.g., "Does Anne know the apple is salted?"). Second-order reasoning adds recursion (e.g., "Does Anne think that Charles knows the apple is salted?"). Our results show that adding more infill sentences slightly reduces prediction accuracy, as added context increases complexity and ambiguity. Llama-2 consistently outperforms GPT-2 in prediction accuracy, especially at lower temperatures, demonstrating greater confidence in selecting the most probable token. As reasoning complexity rises, model responses diverge more. Notably, GPT-2 and Llama-2 display greater variability in predictions during first- and second-order reasoning tasks. These findings illustrate how model architecture, temperature, and contextual complexity influence next-token prediction, contributing to a better understanding of the strengths and limitations of current language models.

  • 5 authors
·
Apr 22

BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments

Agents based on large language models have shown great potential in accelerating scientific discovery by leveraging their rich background knowledge and reasoning capabilities. In this paper, we introduce BioDiscoveryAgent, an agent that designs new experiments, reasons about their outcomes, and efficiently navigates the hypothesis space to reach desired solutions. We demonstrate our agent on the problem of designing genetic perturbation experiments, where the aim is to find a small subset out of many possible genes that, when perturbed, result in a specific phenotype (e.g., cell growth). Utilizing its biological knowledge, BioDiscoveryAgent can uniquely design new experiments without the need to train a machine learning model or explicitly design an acquisition function as in Bayesian optimization. Moreover, BioDiscoveryAgent, using Claude 3.5 Sonnet, achieves an average of 21% improvement in predicting relevant genetic perturbations across six datasets, and a 46% improvement in the harder task of non-essential gene perturbation, compared to existing Bayesian optimization baselines specifically trained for this task. Our evaluation includes one dataset that is unpublished, ensuring it is not part of the language model's training data. Additionally, BioDiscoveryAgent predicts gene combinations to perturb more than twice as accurately as a random baseline, a task so far not explored in the context of closed-loop experiment design. The agent also has access to tools for searching the biomedical literature, executing code to analyze biological datasets, and prompting another agent to critically evaluate its predictions. Overall, BioDiscoveryAgent is interpretable at every stage, representing an accessible new paradigm in the computational design of biological experiments with the potential to augment scientists' efficacy.

  • 9 authors
·
May 27, 2024

A review of path following control strategies for autonomous robotic vehicles: theory, simulations, and experiments

This article presents an in-depth review of the topic of path following for autonomous robotic vehicles, with a specific focus on vehicle motion in two dimensional space (2D). From a control system standpoint, path following can be formulated as the problem of stabilizing a path following error system that describes the dynamics of position and possibly orientation errors of a vehicle with respect to a path, with the errors defined in an appropriate reference frame. In spite of the large variety of path following methods described in the literature we show that, in principle, most of them can be categorized in two groups: stabilization of the path following error system expressed either in the vehicle's body frame or in a frame attached to a "reference point" moving along the path, such as a Frenet-Serret (F-S) frame or a Parallel Transport (P-T) frame. With this observation, we provide a unified formulation that is simple but general enough to cover many methods available in the literature. We then discuss the advantages and disadvantages of each method, comparing them from the design and implementation standpoint. We further show experimental results of the path following methods obtained from field trials testing with under-actuated and fully-actuated autonomous marine vehicles. In addition, we introduce open-source Matlab and Gazebo/ROS simulation toolboxes that are helpful in testing path following methods prior to their integration in the combined guidance, navigation, and control systems of autonomous vehicles.

  • 9 authors
·
Apr 14, 2022

Transformer in Transformer

Transformer is a new kind of neural architecture which encodes the input data as powerful features via the attention mechanism. Basically, the visual transformers first divide the input images into several local patches and then calculate both representations and their relationship. Since natural images are of high complexity with abundant detail and color information, the granularity of the patch dividing is not fine enough for excavating features of objects in different scales and locations. In this paper, we point out that the attention inside these local patches are also essential for building visual transformers with high performance and we explore a new architecture, namely, Transformer iN Transformer (TNT). Specifically, we regard the local patches (e.g., 16times16) as "visual sentences" and present to further divide them into smaller patches (e.g., 4times4) as "visual words". The attention of each word will be calculated with other words in the given visual sentence with negligible computational costs. Features of both words and sentences will be aggregated to enhance the representation ability. Experiments on several benchmarks demonstrate the effectiveness of the proposed TNT architecture, e.g., we achieve an 81.5% top-1 accuracy on the ImageNet, which is about 1.7% higher than that of the state-of-the-art visual transformer with similar computational cost. The PyTorch code is available at https://github.com/huawei-noah/CV-Backbones, and the MindSpore code is available at https://gitee.com/mindspore/models/tree/master/research/cv/TNT.

  • 6 authors
·
Feb 26, 2021 1

Learning to Mine Aligned Code and Natural Language Pairs from Stack Overflow

For tasks like code synthesis from natural language, code retrieval, and code summarization, data-driven models have shown great promise. However, creating these models require parallel data between natural language (NL) and code with fine-grained alignments. Stack Overflow (SO) is a promising source to create such a data set: the questions are diverse and most of them have corresponding answers with high-quality code snippets. However, existing heuristic methods (e.g., pairing the title of a post with the code in the accepted answer) are limited both in their coverage and the correctness of the NL-code pairs obtained. In this paper, we propose a novel method to mine high-quality aligned data from SO using two sets of features: hand-crafted features considering the structure of the extracted snippets, and correspondence features obtained by training a probabilistic model to capture the correlation between NL and code using neural networks. These features are fed into a classifier that determines the quality of mined NL-code pairs. Experiments using Python and Java as test beds show that the proposed method greatly expands coverage and accuracy over existing mining methods, even when using only a small number of labeled examples. Further, we find that reasonable results are achieved even when training the classifier on one language and testing on another, showing promise for scaling NL-code mining to a wide variety of programming languages beyond those for which we are able to annotate data.

  • 5 authors
·
May 22, 2018

PMC-Patients: A Large-scale Dataset of Patient Notes and Relations Extracted from Case Reports in PubMed Central

Objective: Data unavailability has been one of the biggest barriers in clinical natural language processing. This paper is aimed at providing a large-scale and publicly available patient note dataset, named PMC-Patients, with relevant articles and similar patients annotations. The ultimate goal of PMC-Patients is to facilitate the development of retrieval-based clinical decision support systems. Materials and Methods: To collect PMC-Patients, we extract patient notes from case reports in PubMed Central by recognizing certain section patterns. Patient-article relevance and patient-patient similarity are annotated by citation relationships in PubMed. In addition, we perform three tasks with PMC-Patients to demonstrate its utility in providing clinical decision support for a given patient, including (1) classifying whether another patient is similar, (2) retrieving similar patients in PMC-Patients, and (3) retrieving relevant articles in PubMed. Results: We collect and release PMC-Patients under the CC BY-NC-SA license, which becomes the largest publicly available patient note dataset so far. PMC-Patients contains 167k patient notes that are annotated with 3.1M relevant articles and 293k similar patients. Qualitative and quantitative analyses reveal the high quality and richness of our dataset. Experiments show that classifying the similarity of patient pairs is relatively easy, but it is hard to retrieve similar patients or relevant articles for a given patient from a large set of candidates. Conclusion: We present PMC-Patients, a large-scale dataset of patient notes with high quality, easy access, diverse conditions, and rich annotations. The proposed dataset can also serve as a hard benchmark for evaluating retrieval-based clinical decision support systems.

  • 4 authors
·
Feb 28, 2022

VOLO: Vision Outlooker for Visual Recognition

Visual recognition has been dominated by convolutional neural networks (CNNs) for years. Though recently the prevailing vision transformers (ViTs) have shown great potential of self-attention based models in ImageNet classification, their performance is still inferior to that of the latest SOTA CNNs if no extra data are provided. In this work, we try to close the performance gap and demonstrate that attention-based models are indeed able to outperform CNNs. We find a major factor limiting the performance of ViTs for ImageNet classification is their low efficacy in encoding fine-level features into the token representations. To resolve this, we introduce a novel outlook attention and present a simple and general architecture, termed Vision Outlooker (VOLO). Unlike self-attention that focuses on global dependency modeling at a coarse level, the outlook attention efficiently encodes finer-level features and contexts into tokens, which is shown to be critically beneficial to recognition performance but largely ignored by the self-attention. Experiments show that our VOLO achieves 87.1% top-1 accuracy on ImageNet-1K classification, which is the first model exceeding 87% accuracy on this competitive benchmark, without using any extra training data In addition, the pre-trained VOLO transfers well to downstream tasks, such as semantic segmentation. We achieve 84.3% mIoU score on the cityscapes validation set and 54.3% on the ADE20K validation set. Code is available at https://github.com/sail-sg/volo.

  • 5 authors
·
Jun 24, 2021

Melanoma Detection using Adversarial Training and Deep Transfer Learning

Skin lesion datasets consist predominantly of normal samples with only a small percentage of abnormal ones, giving rise to the class imbalance problem. Also, skin lesion images are largely similar in overall appearance owing to the low inter-class variability. In this paper, we propose a two-stage framework for automatic classification of skin lesion images using adversarial training and transfer learning toward melanoma detection. In the first stage, we leverage the inter-class variation of the data distribution for the task of conditional image synthesis by learning the inter-class mapping and synthesizing under-represented class samples from the over-represented ones using unpaired image-to-image translation. In the second stage, we train a deep convolutional neural network for skin lesion classification using the original training set combined with the newly synthesized under-represented class samples. The training of this classifier is carried out by minimizing the focal loss function, which assists the model in learning from hard examples, while down-weighting the easy ones. Experiments conducted on a dermatology image benchmark demonstrate the superiority of our proposed approach over several standard baseline methods, achieving significant performance improvements. Interestingly, we show through feature visualization and analysis that our method leads to context based lesion assessment that can reach an expert dermatologist level.

  • 2 authors
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Apr 14, 2020

Classification Benchmarks for Under-resourced Bengali Language based on Multichannel Convolutional-LSTM Network

Exponential growths of social media and micro-blogging sites not only provide platforms for empowering freedom of expressions and individual voices but also enables people to express anti-social behaviour like online harassment, cyberbullying, and hate speech. Numerous works have been proposed to utilize these data for social and anti-social behaviours analysis, document characterization, and sentiment analysis by predicting the contexts mostly for highly resourced languages such as English. However, there are languages that are under-resources, e.g., South Asian languages like Bengali, Tamil, Assamese, Telugu that lack of computational resources for the NLP tasks. In this paper, we provide several classification benchmarks for Bengali, an under-resourced language. We prepared three datasets of expressing hate, commonly used topics, and opinions for hate speech detection, document classification, and sentiment analysis, respectively. We built the largest Bengali word embedding models to date based on 250 million articles, which we call BengFastText. We perform three different experiments, covering document classification, sentiment analysis, and hate speech detection. We incorporate word embeddings into a Multichannel Convolutional-LSTM (MConv-LSTM) network for predicting different types of hate speech, document classification, and sentiment analysis. Experiments demonstrate that BengFastText can capture the semantics of words from respective contexts correctly. Evaluations against several baseline embedding models, e.g., Word2Vec and GloVe yield up to 92.30%, 82.25%, and 90.45% F1-scores in case of document classification, sentiment analysis, and hate speech detection, respectively during 5-fold cross-validation tests.

  • 4 authors
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Apr 11, 2020

FastSpeech: Fast, Robust and Controllable Text to Speech

Neural network based end-to-end text to speech (TTS) has significantly improved the quality of synthesized speech. Prominent methods (e.g., Tacotron 2) usually first generate mel-spectrogram from text, and then synthesize speech from the mel-spectrogram using vocoder such as WaveNet. Compared with traditional concatenative and statistical parametric approaches, neural network based end-to-end models suffer from slow inference speed, and the synthesized speech is usually not robust (i.e., some words are skipped or repeated) and lack of controllability (voice speed or prosody control). In this work, we propose a novel feed-forward network based on Transformer to generate mel-spectrogram in parallel for TTS. Specifically, we extract attention alignments from an encoder-decoder based teacher model for phoneme duration prediction, which is used by a length regulator to expand the source phoneme sequence to match the length of the target mel-spectrogram sequence for parallel mel-spectrogram generation. Experiments on the LJSpeech dataset show that our parallel model matches autoregressive models in terms of speech quality, nearly eliminates the problem of word skipping and repeating in particularly hard cases, and can adjust voice speed smoothly. Most importantly, compared with autoregressive Transformer TTS, our model speeds up mel-spectrogram generation by 270x and the end-to-end speech synthesis by 38x. Therefore, we call our model FastSpeech.

  • 7 authors
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May 22, 2019 1

Med3D: Transfer Learning for 3D Medical Image Analysis

The performance on deep learning is significantly affected by volume of training data. Models pre-trained from massive dataset such as ImageNet become a powerful weapon for speeding up training convergence and improving accuracy. Similarly, models based on large dataset are important for the development of deep learning in 3D medical images. However, it is extremely challenging to build a sufficiently large dataset due to difficulty of data acquisition and annotation in 3D medical imaging. We aggregate the dataset from several medical challenges to build 3DSeg-8 dataset with diverse modalities, target organs, and pathologies. To extract general medical three-dimension (3D) features, we design a heterogeneous 3D network called Med3D to co-train multi-domain 3DSeg-8 so as to make a series of pre-trained models. We transfer Med3D pre-trained models to lung segmentation in LIDC dataset, pulmonary nodule classification in LIDC dataset and liver segmentation on LiTS challenge. Experiments show that the Med3D can accelerate the training convergence speed of target 3D medical tasks 2 times compared with model pre-trained on Kinetics dataset, and 10 times compared with training from scratch as well as improve accuracy ranging from 3% to 20%. Transferring our Med3D model on state-the-of-art DenseASPP segmentation network, in case of single model, we achieve 94.6\% Dice coefficient which approaches the result of top-ranged algorithms on the LiTS challenge.

  • 3 authors
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Apr 1, 2019

Personalized Dialogue Generation with Diversified Traits

Endowing a dialogue system with particular personality traits is essential to deliver more human-like conversations. However, due to the challenge of embodying personality via language expression and the lack of large-scale persona-labeled dialogue data, this research problem is still far from well-studied. In this paper, we investigate the problem of incorporating explicit personality traits in dialogue generation to deliver personalized dialogues. To this end, firstly, we construct PersonalDialog, a large-scale multi-turn dialogue dataset containing various traits from a large number of speakers. The dataset consists of 20.83M sessions and 56.25M utterances from 8.47M speakers. Each utterance is associated with a speaker who is marked with traits like Age, Gender, Location, Interest Tags, etc. Several anonymization schemes are designed to protect the privacy of each speaker. This large-scale dataset will facilitate not only the study of personalized dialogue generation, but also other researches on sociolinguistics or social science. Secondly, to study how personality traits can be captured and addressed in dialogue generation, we propose persona-aware dialogue generation models within the sequence to sequence learning framework. Explicit personality traits (structured by key-value pairs) are embedded using a trait fusion module. During the decoding process, two techniques, namely persona-aware attention and persona-aware bias, are devised to capture and address trait-related information. Experiments demonstrate that our model is able to address proper traits in different contexts. Case studies also show interesting results for this challenging research problem.

  • 5 authors
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Jan 28, 2019

Neural Speech Synthesis with Transformer Network

Although end-to-end neural text-to-speech (TTS) methods (such as Tacotron2) are proposed and achieve state-of-the-art performance, they still suffer from two problems: 1) low efficiency during training and inference; 2) hard to model long dependency using current recurrent neural networks (RNNs). Inspired by the success of Transformer network in neural machine translation (NMT), in this paper, we introduce and adapt the multi-head attention mechanism to replace the RNN structures and also the original attention mechanism in Tacotron2. With the help of multi-head self-attention, the hidden states in the encoder and decoder are constructed in parallel, which improves the training efficiency. Meanwhile, any two inputs at different times are connected directly by self-attention mechanism, which solves the long range dependency problem effectively. Using phoneme sequences as input, our Transformer TTS network generates mel spectrograms, followed by a WaveNet vocoder to output the final audio results. Experiments are conducted to test the efficiency and performance of our new network. For the efficiency, our Transformer TTS network can speed up the training about 4.25 times faster compared with Tacotron2. For the performance, rigorous human tests show that our proposed model achieves state-of-the-art performance (outperforms Tacotron2 with a gap of 0.048) and is very close to human quality (4.39 vs 4.44 in MOS).

  • 6 authors
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Sep 19, 2018