pwc-archive/papers-with-abstracts huggingface dataset:
A theory of understanding for artificial intelligence: composability, catalysts, and learning
Authors: Zijian Zhang, Sara Aronowitz, Alán Aspuru-Guzik
Date: 2024-08-16 00:00:00

Understanding is a crucial yet elusive concept in artificial intelligence (AI). This work proposes a framework for analyzing understanding based on the notion of composability. Given any subject (e.g., a person or an AI), we suggest characterizing its understanding of an object in terms of its ability to process (compose) relevant inputs into satisfactory outputs from the perspective of a verifier. This highly universal framework can readily apply to non-human subjects, such as AIs, non-human animals, and institutions. Further, we propose methods for analyzing the inputs that enhance output quality in compositions, which we call catalysts. We show how the structure of a subject can be revealed by analyzing its components that act as catalysts and argue that a subject's learning ability can be regarded as its ability to compose inputs into its inner catalysts. Finally we examine the importance of learning ability for AIs to attain general intelligence. Our analysis indicates that models capable of generating outputs that can function as their own catalysts, such as language models, establish a foundation for potentially overcoming existing limitations in AI understanding.
Distributional Drift Detection in Medical Imaging with Sketching and Fine-Tuned Transformer
Authors: Yusen Wu, Phuong Nguyen, Rose Yesha, Yelena Yesha
Date: 2024-08-15 00:00:00
Tasks: Anomaly Detection, Diagnostic, Drift Detection

Distributional drift detection is important in medical applications as it helps ensure the accuracy and reliability of models by identifying changes in the underlying data distribution that could affect the prediction results of machine learning models. However, current methods have limitations in detecting drift, for example, the inclusion of abnormal datasets can lead to unfair comparisons. This paper presents an accurate and sensitive approach to detect distributional drift in CT-scan medical images by leveraging data-sketching and fine-tuning techniques. We developed a robust baseline library model for real-time anomaly detection, allowing for efficient comparison of incoming images and identification of anomalies. Additionally, we fine-tuned a pre-trained Vision Transformer model to extract relevant features, using mammography as a case study, significantly enhancing model accuracy to 99.11%. Combining with data-sketches and fine-tuning, our feature extraction evaluation demonstrated that cosine similarity scores between similar datasets provide greater improvements, from around 50% increased to 99.1%. Finally, the sensitivity evaluation shows that our solutions are highly sensitive to even 1% salt-and-pepper and speckle noise, and it is not sensitive to lighting noise (e.g., lighting conditions have no impact on data drift). The proposed methods offer a scalable and reliable solution for maintaining the accuracy of diagnostic models in dynamic clinical environments.
SpectralEarth: Training Hyperspectral Foundation Models at Scale
Authors: Nassim Ait Ali Braham, Conrad M Albrecht, Julien Mairal, Jocelyn Chanussot, Yi Wang, Xiao Xiang Zhu
Date: 2024-08-15 00:00:00
Tasks: Computational Efficiency, Crop Type Mapping, Self-Supervised Learning

Foundation models have triggered a paradigm shift in computer vision and are increasingly being adopted in remote sensing, particularly for multispectral imagery. Yet, their potential in hyperspectral imaging (HSI) remains untapped due to the absence of comprehensive and globally representative hyperspectral datasets. To close this gap, we introduce SpectralEarth, a large-scale multi-temporal dataset designed to pretrain hyperspectral foundation models leveraging data from the Environmental Mapping and Analysis Program (EnMAP). SpectralEarth comprises 538,974 image patches covering 415,153 unique locations from more than 11,636 globally distributed EnMAP scenes spanning two years of archive. Additionally, 17.5% of these locations include multiple timestamps, enabling multi-temporal HSI analysis. Utilizing state-of-the-art self-supervised learning (SSL) algorithms, we pretrain a series of foundation models on SpectralEarth. We integrate a spectral adapter into classical vision backbones to accommodate the unique characteristics of HSI. In tandem, we construct four downstream datasets for land-cover and crop-type mapping, providing benchmarks for model evaluation. Experimental results support the versatility of our models, showcasing their generalizability across different tasks and sensors. We also highlight computational efficiency during model fine-tuning. The dataset, models, and source code will be made publicly available.
W-RAG: Weakly Supervised Dense Retrieval in RAG for Open-domain Question Answering
Authors: Jinming Nian, Zhiyuan Peng, Qifan Wang, Yi Fang
Date: 2024-08-15 00:00:00
Tasks: Open-Domain Question Answering, Question Answering, RAG, Retrieval, Retrieval-augmented Generation

In knowledge-intensive tasks such as open-domain question answering (OpenQA), large language models (LLMs) often struggle to generate factual answers, relying solely on their internal (parametric) knowledge. To address this limitation, Retrieval-Augmented Generation (RAG) systems enhance LLMs by retrieving relevant information from external sources, thereby positioning the retriever as a pivotal component. Although dense retrieval demonstrates state-of-the-art performance, its training poses challenges due to the scarcity of ground-truth evidence, largely attributed to the high costs of human annotation. In this paper, we propose W-RAG, a method that draws weak training signals from the downstream task (such as OpenQA) of an LLM, and fine-tunes the retriever to prioritize passages that most benefit the task. Specifically, we rerank the top-$k$ passages retrieved via BM25 by assessing the probability that the LLM will generate the correct answer for a question given each passage. The highest-ranking passages are then used as positive fine-tuning examples for dense retrieval. We conduct comprehensive experiments across four publicly available OpenQA datasets to demonstrate that our approach enhances both retrieval and OpenQA performance compared to baseline models, achieving results comparable to models fine-tuned with human-labeled data.
PQV-Mobile: A Combined Pruning and Quantization Toolkit to Optimize Vision Transformers for Mobile Applications
Authors: Kshitij Bhardwaj
Date: 2024-08-15 00:00:00
Tasks: Quantization

While Vision Transformers (ViTs) are extremely effective at computer vision tasks and are replacing convolutional neural networks as the new state-of-the-art, they are complex and memory-intensive models. In order to effectively run these models on resource-constrained mobile/edge systems, there is a need to not only compress these models but also to optimize them and convert them into deployment-friendly formats. To this end, this paper presents a combined pruning and quantization tool, called PQV-Mobile, to optimize vision transformers for mobile applications. The tool is able to support different types of structured pruning based on magnitude importance, Taylor importance, and Hessian importance. It also supports quantization from FP32 to FP16 and int8, targeting different mobile hardware backends. We demonstrate the capabilities of our tool and show important latency-memory-accuracy trade-offs for different amounts of pruning and int8 quantization with Facebook Data Efficient Image Transformer (DeiT) models. Our results show that even pruning a DeiT model by 9.375% and quantizing it to int8 from FP32 followed by optimizing for mobile applications, we find a latency reduction by 7.18X with a small accuracy loss of 2.24%. The tool is open source.
Automated Design of Agentic Systems
Authors: Shengran Hu, Cong Lu, Jeff Clune
Date: 2024-08-15 00:00:00

Researchers are investing substantial effort in developing powerful general-purpose agents, wherein Foundation Models are used as modules within agentic systems (e.g. Chain-of-Thought, Self-Reflection, Toolformer). However, the history of machine learning teaches us that hand-designed solutions are eventually replaced by learned solutions. We formulate a new research area, Automated Design of Agentic Systems (ADAS), which aims to automatically create powerful agentic system designs, including inventing novel building blocks and/or combining them in new ways. We further demonstrate that there is an unexplored yet promising approach within ADAS where agents can be defined in code and new agents can be automatically discovered by a meta agent programming ever better ones in code. Given that programming languages are Turing Complete, this approach theoretically enables the learning of any possible agentic system: including novel prompts, tool use, control flows, and combinations thereof. We present a simple yet effective algorithm named Meta Agent Search to demonstrate this idea, where a meta agent iteratively programs interesting new agents based on an ever-growing archive of previous discoveries. Through extensive experiments across multiple domains including coding, science, and math, we show that our algorithm can progressively invent agents with novel designs that greatly outperform state-of-the-art hand-designed agents. Importantly, we consistently observe the surprising result that agents invented by Meta Agent Search maintain superior performance even when transferred across domains and models, demonstrating their robustness and generality. Provided we develop it safely, our work illustrates the potential of an exciting new research direction toward automatically designing ever-more powerful agentic systems to benefit humanity.
Predictive uncertainty estimation in deep learning for lung carcinoma classification in digital pathology under real dataset shifts
Authors: Abdur R. Fayjie, Jutika Borah, Florencia Carbone, Jan Tack, Patrick Vandewalle
Date: 2024-08-15 00:00:00
Tasks: Decision Making, Diagnostic, Few-Shot Learning, image-classification, Image Classification, Medical Image Classification, whole slide images

Deep learning has shown tremendous progress in a wide range of digital pathology and medical image classification tasks. Its integration into safe clinical decision-making support requires robust and reliable models. However, real-world data comes with diversities that often lie outside the intended source distribution. Moreover, when test samples are dramatically different, clinical decision-making is greatly affected. Quantifying predictive uncertainty in models is crucial for well-calibrated predictions and determining when (or not) to trust a model. Unfortunately, many works have overlooked the importance of predictive uncertainty estimation. This paper evaluates whether predictive uncertainty estimation adds robustness to deep learning-based diagnostic decision-making systems. We investigate the effect of various carcinoma distribution shift scenarios on predictive performance and calibration. We first systematically investigate three popular methods for improving predictive uncertainty: Monte Carlo dropout, deep ensemble, and few-shot learning on lung adenocarcinoma classification as a primary disease in whole slide images. Secondly, we compare the effectiveness of the methods in terms of performance and calibration under clinically relevant distribution shifts such as in-distribution shifts comprising primary disease sub-types and other characterization analysis data; out-of-distribution shifts comprising well-differentiated cases, different organ origin, and imaging modality shifts. While studies on uncertainty estimation exist, to our best knowledge, no rigorous large-scale benchmark compares predictive uncertainty estimation including these dataset shifts for lung carcinoma classification.
Multi-Modal Dialogue State Tracking for Playing GuessWhich Game
Authors: Wei Pang, Ruixue Duan, Jinfu Yang, Ning li
Date: 2024-08-15 00:00:00
Tasks: Dialogue State Tracking, Visual Reasoning

GuessWhich is an engaging visual dialogue game that involves interaction between a Questioner Bot (QBot) and an Answer Bot (ABot) in the context of image-guessing. In this game, QBot's objective is to locate a concealed image solely through a series of visually related questions posed to ABot. However, effectively modeling visually related reasoning in QBot's decision-making process poses a significant challenge. Current approaches either lack visual information or rely on a single real image sampled at each round as decoding context, both of which are inadequate for visual reasoning. To address this limitation, we propose a novel approach that focuses on visually related reasoning through the use of a mental model of the undisclosed image. Within this framework, QBot learns to represent mental imagery, enabling robust visual reasoning by tracking the dialogue state. The dialogue state comprises a collection of representations of mental imagery, as well as representations of the entities involved in the conversation. At each round, QBot engages in visually related reasoning using the dialogue state to construct an internal representation, generate relevant questions, and update both the dialogue state and internal representation upon receiving an answer. Our experimental results on the VisDial datasets (v0.5, 0.9, and 1.0) demonstrate the effectiveness of our proposed model, as it achieves new state-of-the-art performance across all metrics and datasets, surpassing previous state-of-the-art models. Codes and datasets from our experiments are freely available at \href{https://github.com/xubuvd/GuessWhich}.
Assessing and Enhancing Large Language Models in Rare Disease Question-answering
Authors: Guanchu Wang, Junhao Ran, Ruixiang Tang, Chia-Yuan Chang, Yu-Neng Chuang, Zirui Liu, Vladimir Braverman, Zhandong Liu, Xia Hu
Date: 2024-08-15 00:00:00
Tasks: Diagnostic, Question Answering

Despite the impressive capabilities of Large Language Models (LLMs) in general medical domains, questions remain about their performance in diagnosing rare diseases. To answer this question, we aim to assess the diagnostic performance of LLMs in rare diseases, and explore methods to enhance their effectiveness in this area. In this work, we introduce a rare disease question-answering (ReDis-QA) dataset to evaluate the performance of LLMs in diagnosing rare diseases. Specifically, we collected 1360 high-quality question-answer pairs within the ReDis-QA dataset, covering 205 rare diseases. Additionally, we annotated meta-data for each question, facilitating the extraction of subsets specific to any given disease and its property. Based on the ReDis-QA dataset, we benchmarked several open-source LLMs, revealing that diagnosing rare diseases remains a significant challenge for these models. To facilitate retrieval augmentation generation for rare disease diagnosis, we collect the first rare diseases corpus (ReCOP), sourced from the National Organization for Rare Disorders (NORD) database. Specifically, we split the report of each rare disease into multiple chunks, each representing a different property of the disease, including their overview, symptoms, causes, effects, related disorders, diagnosis, and standard therapies. This structure ensures that the information within each chunk aligns consistently with a question. Experiment results demonstrate that ReCOP can effectively improve the accuracy of LLMs on the ReDis-QA dataset by an average of 8%. Moreover, it significantly guides LLMs to generate trustworthy answers and explanations that can be traced back to existing literature.
Understanding Help-Seeking Behavior of Students Using LLMs vs. Web Search for Writing SQL Queries
Authors: Harsh Kumar, Mohi Reza, Jeb Mitchell, Ilya Musabirov, Lisa Zhang, Michael Liut
Date: 2024-08-15 00:00:00

Growth in the use of large language models (LLMs) in programming education is altering how students write SQL queries. Traditionally, students relied heavily on web search for coding assistance, but this has shifted with the adoption of LLMs like ChatGPT. However, the comparative process and outcomes of using web search versus LLMs for coding help remain underexplored. To address this, we conducted a randomized interview study in a database classroom to compare web search and LLMs, including a publicly available LLM (ChatGPT) and an instructor-tuned LLM, for writing SQL queries. Our findings indicate that using an instructor-tuned LLM required significantly more interactions than both ChatGPT and web search, but resulted in a similar number of edits to the final SQL query. No significant differences were found in the quality of the final SQL queries between conditions, although the LLM conditions directionally showed higher query quality. Furthermore, students using instructor-tuned LLM reported a lower mental demand. These results have implications for learning and productivity in programming education.
Decoding the human brain tissue response to radiofrequency excitation using a biophysical-model-free deep MRI on a chip framework
Authors: Dinor Nagar, Moritz Zaiss, Or Perlman
Date: 2024-08-15 00:00:00

Magnetic resonance imaging (MRI) relies on radiofrequency (RF) excitation of proton spin. Clinical diagnosis requires a comprehensive collation of biophysical data via multiple MRI contrasts, acquired using a series of RF sequences that lead to lengthy examinations. Here, we developed a vision transformer-based framework that captures the spatiotemporal magnetic signal evolution and decodes the brain tissue response to RF excitation, constituting an MRI on a chip. Following a per-subject rapid calibration scan (28.2 s), a wide variety of image contrasts including fully quantitative molecular, water relaxation, and magnetic field maps can be generated automatically. The method was validated across healthy subjects and a cancer patient in two different imaging sites, and proved to be 94% faster than alternative protocols. The deep MRI on a chip (DeepMonC) framework may reveal the molecular composition of the human brain tissue in a wide range of pathologies, while offering clinically attractive scan times.
API-guided Dataset Synthesis to Finetune Large Code Models
Authors: Zongjie Li, Daoyuan Wu, Shuai Wang, Zhendong Su
Date: 2024-08-15 00:00:00

Large code models (LCMs), pre-trained on vast code corpora, have demonstrated remarkable performance across a wide array of code-related tasks. Supervised fine-tuning (SFT) plays a vital role in aligning these models with specific requirements and enhancing their performance in particular domains. However, synthesizing high-quality SFT datasets poses a significant challenge due to the uneven quality of datasets and the scarcity of domain-specific datasets. Inspired by APIs as high-level abstractions of code that encapsulate rich semantic information in a concise structure, we propose DataScope, an API-guided dataset synthesis framework designed to enhance the SFT process for LCMs in both general and domain-specific scenarios. DataScope comprises two main components: Dsel and Dgen. On one hand, Dsel employs API coverage as a core metric, enabling efficient dataset synthesis in general scenarios by selecting subsets of existing (uneven-quality) datasets with higher API coverage. On the other hand, Dgen recasts domain dataset synthesis as a process of using API-specified high-level functionality and deliberately-constituted code skeletons to synthesize concrete code. Extensive experiments demonstrate DataScope's effectiveness, with models fine-tuned on its synthesized datasets outperforming those tuned on unoptimized datasets five times larger. Furthermore, a series of analyses on model internals, relevant hyperparameters, and case studies provide additional evidence for the efficacy of our proposed methods. These findings underscore the significance of dataset quality in SFT and advance the field of LCMs by providing an efficient, cost-effective framework for constructing high-quality datasets. This contribution enhances performance across both general and domain-specific scenarios, paving the way for more powerful and tailored LCMs.
Exploring Latent Space for Generating Peptide Analogs Using Protein Language Models
Authors: Po-Yu Liang, Xueting Huang, Tibo Duran, Andrew J. Wiemer, Jun Bai
Date: 2024-08-15 00:00:00
Tasks: Drug Discovery

Generating peptides with desired properties is crucial for drug discovery and biotechnology. Traditional sequence-based and structure-based methods often require extensive datasets, which limits their effectiveness. In this study, we proposed a novel method that utilized autoencoder shaped models to explore the protein embedding space, and generate novel peptide analogs by leveraging protein language models. The proposed method requires only a single sequence of interest, avoiding the need for large datasets. Our results show significant improvements over baseline models in similarity indicators of peptide structures, descriptors and bioactivities. The proposed method validated through Molecular Dynamics simulations on TIGIT inhibitors, demonstrates that our method produces peptide analogs with similar yet distinct properties, highlighting its potential to enhance peptide screening processes.
Graph representations of 3D data for machine learning
Authors: Tomasz Prytuła
Date: 2024-08-15 00:00:00

We give an overview of combinatorial methods to represent 3D data, such as graphs and meshes, from the viewpoint of their amenability to analysis using machine learning algorithms. We highlight pros and cons of various representations and we discuss some methods of generating/switching between the representations. We finally present two concrete applications in life science and industry. Despite its theoretical nature, our discussion is in general motivated by, and biased towards real-world challenges.
Plan with Code: Comparing approaches for robust NL to DSL generation
Authors: Nastaran Bassamzadeh, Chhaya Methani
Date: 2024-08-15 00:00:00
Tasks: Code Generation, Hallucination, RAG, Retrieval-augmented Generation, Task Planning

Planning in code is considered a more reliable approach for many orchestration tasks. This is because code is more tractable than steps generated via Natural Language and make it easy to support more complex sequences by abstracting deterministic logic into functions. It also allows spotting issues with incorrect function names with the help of parsing checks that can be run on code. Progress in Code Generation methodologies, however, remains limited to general-purpose languages like C, C++, and Python. LLMs continue to face challenges with custom function names in Domain Specific Languages or DSLs, leading to higher hallucination rates and syntax errors. This is more common for custom function names, that are typically part of the plan. Moreover, keeping LLMs up-to-date with newer function names is an issue. This poses a challenge for scenarios like task planning over a large number of APIs, since the plan is represented as a DSL having custom API names. In this paper, we focus on workflow automation in RPA (Robotic Process Automation) domain as a special case of task planning. We present optimizations for using Retrieval Augmented Generation (or RAG) with LLMs for DSL generation along with an ablation study comparing these strategies with a fine-tuned model. Our results showed that the fine-tuned model scored the best on code similarity metric. However, with our optimizations, RAG approach is able to match the quality for in-domain API names in the test set. Additionally, it offers significant advantage for out-of-domain or unseen API names, outperforming Fine-Tuned model on similarity metric by 7 pts.