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Dec 11

TrialPanorama: Database and Benchmark for Systematic Review and Design of Clinical Trials

Developing artificial intelligence (AI) for vertical domains requires a solid data foundation for both training and evaluation. In this work, we introduce TrialPanorama, a large-scale, structured database comprising 1,657,476 clinical trial records aggregated from 15 global sources. The database captures key aspects of trial design and execution, including trial setups, interventions, conditions, biomarkers, and outcomes, and links them to standard biomedical ontologies such as DrugBank and MedDRA. This structured and ontology-grounded design enables TrialPanorama to serve as a unified, extensible resource for a wide range of clinical trial tasks, including trial planning, design, and summarization. To demonstrate its utility, we derive a suite of benchmark tasks directly from the TrialPanorama database. The benchmark spans eight tasks across two categories: three for systematic review (study search, study screening, and evidence summarization) and five for trial design (arm design, eligibility criteria, endpoint selection, sample size estimation, and trial completion assessment). The experiments using five state-of-the-art large language models (LLMs) show that while general-purpose LLMs exhibit some zero-shot capability, their performance is still inadequate for high-stakes clinical trial workflows. We release TrialPanorama database and the benchmark to facilitate further research on AI for clinical trials.

  • 9 authors
·
May 21

The Alzheimer's Disease Prediction Of Longitudinal Evolution (TADPOLE) Challenge: Results after 1 Year Follow-up

We present the findings of "The Alzheimer's Disease Prediction Of Longitudinal Evolution" (TADPOLE) Challenge, which compared the performance of 92 algorithms from 33 international teams at predicting the future trajectory of 219 individuals at risk of Alzheimer's disease. Challenge participants were required to make a prediction, for each month of a 5-year future time period, of three key outcomes: clinical diagnosis, Alzheimer's Disease Assessment Scale Cognitive Subdomain (ADAS-Cog13), and total volume of the ventricles. The methods used by challenge participants included multivariate linear regression, machine learning methods such as support vector machines and deep neural networks, as well as disease progression models. No single submission was best at predicting all three outcomes. For clinical diagnosis and ventricle volume prediction, the best algorithms strongly outperform simple baselines in predictive ability. However, for ADAS-Cog13 no single submitted prediction method was significantly better than random guesswork. Two ensemble methods based on taking the mean and median over all predictions, obtained top scores on almost all tasks. Better than average performance at diagnosis prediction was generally associated with the additional inclusion of features from cerebrospinal fluid (CSF) samples and diffusion tensor imaging (DTI). On the other hand, better performance at ventricle volume prediction was associated with inclusion of summary statistics, such as the slope or maxima/minima of biomarkers. TADPOLE's unique results suggest that current prediction algorithms provide sufficient accuracy to exploit biomarkers related to clinical diagnosis and ventricle volume, for cohort refinement in clinical trials for Alzheimer's disease. However, results call into question the usage of cognitive test scores for patient selection and as a primary endpoint in clinical trials.

  • 96 authors
·
Feb 9, 2020

SEAGET: Seasonal and Active hours guided Graph Enhanced Transformer for the next POI recommendation

One of the most important challenges for improving personalized services in industries like tourism is predicting users' near-future movements based on prior behavior and current circumstances. Next POI (Point of Interest) recommendation is essential for helping users and service providers by providing personalized recommendations. The intricacy of this work, however, stems from the requirement to take into consideration several variables at once, such as user preferences, time contexts, and geographic locations. POI selection is also greatly influenced by elements like a POI's operational status during desired visit times, desirability for visiting during particular seasons, and its dynamic popularity over time. POI popularity is mostly determined by check-in frequency in recent studies, ignoring visitor volumes, operational constraints, and temporal dynamics. These restrictions result in recommendations that are less than ideal and do not take into account actual circumstances. We propose the Seasonal and Active hours-guided Graph-Enhanced Transformer (SEAGET) model as a solution to these problems. By integrating variations in the seasons, operational status, and temporal dynamics into a graph-enhanced transformer framework, SEAGET capitalizes on redefined POI popularity. This invention gives more accurate and context-aware next POI predictions, with potential applications for optimizing tourist experiences and enhancing location-based services in the tourism industry.

  • 2 authors
·
Mar 27

Automatically Extracting Web API Specifications from HTML Documentation

Web API specifications are machine-readable descriptions of APIs. These specifications, in combination with related tooling, simplify and support the consumption of APIs. However, despite the increased distribution of web APIs, specifications are rare and their creation and maintenance heavily relies on manual efforts by third parties. In this paper, we propose an automatic approach and an associated tool called D2Spec for extracting specifications from web API documentation pages. Given a seed online documentation page on an API, D2Spec first crawls all documentation pages on the API, and then uses a set of machine learning techniques to extract the base URL, path templates, and HTTP methods, which collectively describe the endpoints of an API. We evaluated whether D2Spec can accurately extract endpoints from documentation on 120 web APIs. The results showed that D2Spec achieved a precision of 87.5% in identifying base URLs, a precision of 81.3% and a recall of 80.6% in generating path templates, and a precision of 84.4% and a recall of 76.2% in extracting HTTP methods. In addition, we found that D2Spec was useful when applied to APIs with pre-existing API specifications: D2Spec revealed many inconsistencies between web API documentation and their corresponding publicly available specifications. Thus, D2Spec can be used by web API providers to keep documentation and specifications in synchronization.

  • 5 authors
·
Jan 26, 2018

GoalFlow: Goal-Driven Flow Matching for Multimodal Trajectories Generation in End-to-End Autonomous Driving

We propose GoalFlow, an end-to-end autonomous driving method for generating high-quality multimodal trajectories. In autonomous driving scenarios, there is rarely a single suitable trajectory. Recent methods have increasingly focused on modeling multimodal trajectory distributions. However, they suffer from trajectory selection complexity and reduced trajectory quality due to high trajectory divergence and inconsistencies between guidance and scene information. To address these issues, we introduce GoalFlow, a novel method that effectively constrains the generative process to produce high-quality, multimodal trajectories. To resolve the trajectory divergence problem inherent in diffusion-based methods, GoalFlow constrains the generated trajectories by introducing a goal point. GoalFlow establishes a novel scoring mechanism that selects the most appropriate goal point from the candidate points based on scene information. Furthermore, GoalFlow employs an efficient generative method, Flow Matching, to generate multimodal trajectories, and incorporates a refined scoring mechanism to select the optimal trajectory from the candidates. Our experimental results, validated on the NavsimDauner2024_navsim, demonstrate that GoalFlow achieves state-of-the-art performance, delivering robust multimodal trajectories for autonomous driving. GoalFlow achieved PDMS of 90.3, significantly surpassing other methods. Compared with other diffusion-policy-based methods, our approach requires only a single denoising step to obtain excellent performance. The code is available at https://github.com/YvanYin/GoalFlow.

  • 8 authors
·
Mar 7 2

A Survey on Data Selection for Language Models

A major factor in the recent success of large language models is the use of enormous and ever-growing text datasets for unsupervised pre-training. However, naively training a model on all available data may not be optimal (or feasible), as the quality of available text data can vary. Filtering out data can also decrease the carbon footprint and financial costs of training models by reducing the amount of training required. Data selection methods aim to determine which candidate data points to include in the training dataset and how to appropriately sample from the selected data points. The promise of improved data selection methods has caused the volume of research in the area to rapidly expand. However, because deep learning is mostly driven by empirical evidence and experimentation on large-scale data is expensive, few organizations have the resources for extensive data selection research. Consequently, knowledge of effective data selection practices has become concentrated within a few organizations, many of which do not openly share their findings and methodologies. To narrow this gap in knowledge, we present a comprehensive review of existing literature on data selection methods and related research areas, providing a taxonomy of existing approaches. By describing the current landscape of research, this work aims to accelerate progress in data selection by establishing an entry point for new and established researchers. Additionally, throughout this review we draw attention to noticeable holes in the literature and conclude the paper by proposing promising avenues for future research.

  • 14 authors
·
Feb 26, 2024

Illuminating search spaces by mapping elites

Many fields use search algorithms, which automatically explore a search space to find high-performing solutions: chemists search through the space of molecules to discover new drugs; engineers search for stronger, cheaper, safer designs, scientists search for models that best explain data, etc. The goal of search algorithms has traditionally been to return the single highest-performing solution in a search space. Here we describe a new, fundamentally different type of algorithm that is more useful because it provides a holistic view of how high-performing solutions are distributed throughout a search space. It creates a map of high-performing solutions at each point in a space defined by dimensions of variation that a user gets to choose. This Multi-dimensional Archive of Phenotypic Elites (MAP-Elites) algorithm illuminates search spaces, allowing researchers to understand how interesting attributes of solutions combine to affect performance, either positively or, equally of interest, negatively. For example, a drug company may wish to understand how performance changes as the size of molecules and their cost-to-produce vary. MAP-Elites produces a large diversity of high-performing, yet qualitatively different solutions, which can be more helpful than a single, high-performing solution. Interestingly, because MAP-Elites explores more of the search space, it also tends to find a better overall solution than state-of-the-art search algorithms. We demonstrate the benefits of this new algorithm in three different problem domains ranging from producing modular neural networks to designing simulated and real soft robots. Because MAP- Elites (1) illuminates the relationship between performance and dimensions of interest in solutions, (2) returns a set of high-performing, yet diverse solutions, and (3) improves finding a single, best solution, it will advance science and engineering.

  • 2 authors
·
Apr 19, 2015

Selection of Prompt Engineering Techniques for Code Generation through Predicting Code Complexity

Large Language Models (LLMs) have demonstrated impressive performance in software engineering tasks. However, improving their accuracy in generating correct and reliable code remains challenging. Numerous prompt engineering techniques (PETs) have been developed to address this, but no single approach is universally optimal. Selecting the right PET for each query is difficult for two primary reasons: (1) interactive prompting techniques may not consistently deliver the expected benefits, especially for simpler queries, and (2) current automated prompt engineering methods lack adaptability and fail to fully utilize multi-stage responses. To overcome these challenges, we propose PET-Select, a PET-agnostic selection model that uses code complexity as a proxy to classify queries and select the most appropriate PET. By incorporating contrastive learning, PET-Select effectively distinguishes between simple and complex problems, allowing it to choose PETs that are best suited for each query's complexity level. Our evaluations on the MBPP and HumanEval benchmarks using GPT-3.5 Turbo and GPT-4o show up to a 1.9% improvement in pass@1 accuracy, along with a 74.8% reduction in token usage. Additionally, we provide both quantitative and qualitative results to demonstrate how PET-Select effectively selects the most appropriate techniques for each code generation query, further showcasing its efficiency in optimizing PET selection.

  • 3 authors
·
Sep 24, 2024

ERASE: Benchmarking Feature Selection Methods for Deep Recommender Systems

Deep Recommender Systems (DRS) are increasingly dependent on a large number of feature fields for more precise recommendations. Effective feature selection methods are consequently becoming critical for further enhancing the accuracy and optimizing storage efficiencies to align with the deployment demands. This research area, particularly in the context of DRS, is nascent and faces three core challenges. Firstly, variant experimental setups across research papers often yield unfair comparisons, obscuring practical insights. Secondly, the existing literature's lack of detailed analysis on selection attributes, based on large-scale datasets and a thorough comparison among selection techniques and DRS backbones, restricts the generalizability of findings and impedes deployment on DRS. Lastly, research often focuses on comparing the peak performance achievable by feature selection methods, an approach that is typically computationally infeasible for identifying the optimal hyperparameters and overlooks evaluating the robustness and stability of these methods. To bridge these gaps, this paper presents ERASE, a comprehensive bEnchmaRk for feAture SElection for DRS. ERASE comprises a thorough evaluation of eleven feature selection methods, covering both traditional and deep learning approaches, across four public datasets, private industrial datasets, and a real-world commercial platform, achieving significant enhancement. Our code is available online for ease of reproduction.

  • 9 authors
·
Mar 19, 2024

What are the Desired Characteristics of Calibration Sets? Identifying Correlates on Long Form Scientific Summarization

Summarization models often generate text that is poorly calibrated to quality metrics because they are trained to maximize the likelihood of a single reference (MLE). To address this, recent work has added a calibration step, which exposes a model to its own ranked outputs to improve relevance or, in a separate line of work, contrasts positive and negative sets to improve faithfulness. While effective, much of this work has focused on how to generate and optimize these sets. Less is known about why one setup is more effective than another. In this work, we uncover the underlying characteristics of effective sets. For each training instance, we form a large, diverse pool of candidates and systematically vary the subsets used for calibration fine-tuning. Each selection strategy targets distinct aspects of the sets, such as lexical diversity or the size of the gap between positive and negatives. On three diverse scientific long-form summarization datasets (spanning biomedical, clinical, and chemical domains), we find, among others, that faithfulness calibration is optimal when the negative sets are extractive and more likely to be generated, whereas for relevance calibration, the metric margin between candidates should be maximized and surprise--the disagreement between model and metric defined candidate rankings--minimized. Code to create, select, and optimize calibration sets is available at https://github.com/griff4692/calibrating-summaries

  • 10 authors
·
May 12, 2023 1

Generalized Trajectory Scoring for End-to-end Multimodal Planning

End-to-end multi-modal planning is a promising paradigm in autonomous driving, enabling decision-making with diverse trajectory candidates. A key component is a robust trajectory scorer capable of selecting the optimal trajectory from these candidates. While recent trajectory scorers focus on scoring either large sets of static trajectories or small sets of dynamically generated ones, both approaches face significant limitations in generalization. Static vocabularies provide effective coarse discretization but struggle to make fine-grained adaptation, while dynamic proposals offer detailed precision but fail to capture broader trajectory distributions. To overcome these challenges, we propose GTRS (Generalized Trajectory Scoring), a unified framework for end-to-end multi-modal planning that combines coarse and fine-grained trajectory evaluation. GTRS consists of three complementary innovations: (1) a diffusion-based trajectory generator that produces diverse fine-grained proposals; (2) a vocabulary generalization technique that trains a scorer on super-dense trajectory sets with dropout regularization, enabling its robust inference on smaller subsets; and (3) a sensor augmentation strategy that enhances out-of-domain generalization while incorporating refinement training for critical trajectory discrimination. As the winning solution of the Navsim v2 Challenge, GTRS demonstrates superior performance even with sub-optimal sensor inputs, approaching privileged methods that rely on ground-truth perception. Code will be available at https://github.com/NVlabs/GTRS.

  • 10 authors
·
Jun 7

Geography-Aware Large Language Models for Next POI Recommendation

The next Point-of-Interest (POI) recommendation task aims to predict users' next destinations based on their historical movement data and plays a key role in location-based services and personalized applications. Accurate next POI recommendation depends on effectively modeling geographic information and POI transition relations, which are crucial for capturing spatial dependencies and user movement patterns. While Large Language Models (LLMs) exhibit strong capabilities in semantic understanding and contextual reasoning, applying them to spatial tasks like next POI recommendation remains challenging. First, the infrequent nature of specific GPS coordinates makes it difficult for LLMs to model precise spatial contexts. Second, the lack of knowledge about POI transitions limits their ability to capture potential POI-POI relationships. To address these issues, we propose GA-LLM (Geography-Aware Large Language Model), a novel framework that enhances LLMs with two specialized components. The Geographic Coordinate Injection Module (GCIM) transforms GPS coordinates into spatial representations using hierarchical and Fourier-based positional encoding, enabling the model to understand geographic features from multiple perspectives. The POI Alignment Module (PAM) incorporates POI transition relations into the LLM's semantic space, allowing it to infer global POI relationships and generalize to unseen POIs. Experiments on three real-world datasets demonstrate the state-of-the-art performance of GA-LLM.

  • 7 authors
·
May 17

kNN-Embed: Locally Smoothed Embedding Mixtures For Multi-interest Candidate Retrieval

Candidate generation is the first stage in recommendation systems, where a light-weight system is used to retrieve potentially relevant items for an input user. These candidate items are then ranked and pruned in later stages of recommender systems using a more complex ranking model. Since candidate generation is the top of the recommendation funnel, it is important to retrieve a high-recall candidate set to feed into downstream ranking models. A common approach for candidate generation is to leverage approximate nearest neighbor (ANN) search from a single dense query embedding; however, this approach this can yield a low-diversity result set with many near duplicates. As users often have multiple interests, candidate retrieval should ideally return a diverse set of candidates reflective of the user's multiple interests. To this end, we introduce kNN-Embed, a general approach to improving diversity in dense ANN-based retrieval. kNN-Embed represents each user as a smoothed mixture over learned item clusters that represent distinct `interests' of the user. By querying each of a user's mixture component in proportion to their mixture weights, we retrieve a high-diversity set of candidates reflecting elements from each of a user's interests. We experimentally compare kNN-Embed to standard ANN candidate retrieval, and show significant improvements in overall recall and improved diversity across three datasets. Accompanying this work, we open source a large Twitter follow-graph dataset, to spur further research in graph-mining and representation learning for recommender systems.

  • 6 authors
·
May 12, 2022

ToolCoder: Teach Code Generation Models to use API search tools

Automatically generating source code from natural language descriptions has been a growing field of research in recent years. However, current large-scale code generation models often encounter difficulties when selecting appropriate APIs for specific contexts. These models may generate APIs that do not meet requirements or refer to non-existent APIs in third-party libraries, especially for lesser-known or private libraries. Inspired by the process of human developers using tools to search APIs, we propose ToolCoder, a novel approach that integrates API search tools with existing models to assist in code generation and API selection. To teach our model to use tools, we introduce an automated data annotation method using ChatGPT to add tool usage information into the source code data and fine-tune code generation models. During inference, we integrate API search tools into the generation process so that our model can automatically use the search tool to get suggestions when selecting an API. Our experimental results demonstrate that ToolCoder exhibits excellent performance and generalization across five public and private library code generation benchmarks, with at least 6.21\% improvement on average pass@1 metrics and 9.64\% improvement on average pass@10 metrics compared to state-of-the-art methods. Furthermore, we show that our relatively small ToolCoder model is comparable to one of the current best models, GPT-3.5, highlighting the potential of incorporating programming tools into the code generation process.

  • 6 authors
·
May 6, 2023

Performance Scaling via Optimal Transport: Enabling Data Selection from Partially Revealed Sources

Traditionally, data selection has been studied in settings where all samples from prospective sources are fully revealed to a machine learning developer. However, in practical data exchange scenarios, data providers often reveal only a limited subset of samples before an acquisition decision is made. Recently, there have been efforts to fit scaling laws that predict model performance at any size and data source composition using the limited available samples. However, these scaling functions are black-box, computationally expensive to fit, highly susceptible to overfitting, or/and difficult to optimize for data selection. This paper proposes a framework called <projektor>, which predicts model performance and supports data selection decisions based on partial samples of prospective data sources. Our approach distinguishes itself from existing work by introducing a novel *two-stage* performance inference process. In the first stage, we leverage the Optimal Transport distance to predict the model's performance for any data mixture ratio within the range of disclosed data sizes. In the second stage, we extrapolate the performance to larger undisclosed data sizes based on a novel parameter-free mapping technique inspired by neural scaling laws. We further derive an efficient gradient-based method to select data sources based on the projected model performance. Evaluation over a diverse range of applications demonstrates that <projektor> significantly improves existing performance scaling approaches in terms of both the accuracy of performance inference and the computation costs associated with constructing the performance predictor. Also, <projektor> outperforms by a wide margin in data selection effectiveness compared to a range of other off-the-shelf solutions.

  • 4 authors
·
Jul 5, 2023

ShortcutsBench: A Large-Scale Real-world Benchmark for API-based Agents

Recent advancements in integrating large language models (LLMs) with application programming interfaces (APIs) have gained significant interest in both academia and industry. These API-based agents, leveraging the strong autonomy and planning capabilities of LLMs, can efficiently solve problems requiring multi-step actions. However, their ability to handle multi-dimensional difficulty levels, diverse task types, and real-world demands through APIs remains unknown. In this paper, we introduce ShortcutsBench, a large-scale benchmark for the comprehensive evaluation of API-based agents in solving tasks with varying levels of difficulty, diverse task types, and real-world demands. ShortcutsBench includes a wealth of real APIs from Apple Inc.'s operating systems, refined user queries from shortcuts, human-annotated high-quality action sequences from shortcut developers, and accurate parameter filling values about primitive parameter types, enum parameter types, outputs from previous actions, and parameters that need to request necessary information from the system or user. Our extensive evaluation of agents built with 5 leading open-source (size >= 57B) and 4 closed-source LLMs (e.g. Gemini-1.5-Pro and GPT-3.5) reveals significant limitations in handling complex queries related to API selection, parameter filling, and requesting necessary information from systems and users. These findings highlight the challenges that API-based agents face in effectively fulfilling real and complex user queries. All datasets, code, and experimental results will be available at https://github.com/eachsheep/shortcutsbench.

  • 8 authors
·
Jun 28, 2024

Avoiding tipping points in fisheries management through Gaussian Process Dynamic Programming

Model uncertainty and limited data are fundamental challenges to robust management of human intervention in a natural system. These challenges are acutely highlighted by concerns that many ecological systems may contain tipping points, such as Allee population sizes. Before a collapse, we do not know where the tipping points lie, if they exist at all. Hence, we know neither a complete model of the system dynamics nor do we have access to data in some large region of state-space where such a tipping point might exist. We illustrate how a Bayesian Non-Parametric (BNP) approach using a Gaussian Process (GP) prior provides a flexible representation of this inherent uncertainty. We embed GPs in a Stochastic Dynamic Programming (SDP) framework in order to make robust management predictions with both model uncertainty and limited data. We use simulations to evaluate this approach as compared with the standard approach of using model selection to choose from a set of candidate models. We find that model selection erroneously favors models without tipping points -- leading to harvest policies that guarantee extinction. The GPDP performs nearly as well as the true model and significantly outperforms standard approaches. We illustrate this using examples of simulated single-species dynamics, where the standard model selection approach should be most effective, and find that it still fails to account for uncertainty appropriately and leads to population crashes, while management based on the GPDP does not, since it does not underestimate the uncertainty outside of the observed data.

  • 3 authors
·
Dec 27, 2014

MeSH Suggester: A Library and System for MeSH Term Suggestion for Systematic Review Boolean Query Construction

Boolean query construction is often critical for medical systematic review literature search. To create an effective Boolean query, systematic review researchers typically spend weeks coming up with effective query terms and combinations. One challenge to creating an effective systematic review Boolean query is the selection of effective MeSH Terms to include in the query. In our previous work, we created neural MeSH term suggestion methods and compared them to state-of-the-art MeSH term suggestion methods. We found neural MeSH term suggestion methods to be highly effective. In this demonstration, we build upon our previous work by creating (1) a Web-based MeSH term suggestion prototype system that allows users to obtain suggestions from a number of underlying methods and (2) a Python library that implements ours and others' MeSH term suggestion methods and that is aimed at researchers who want to further investigate, create or deploy such type of methods. We describe the architecture of the web-based system and how to use it for the MeSH term suggestion task. For the Python library, we describe how the library can be used for advancing further research and experimentation, and we validate the results of the methods contained in the library on standard datasets. Our web-based prototype system is available at http://ielab-mesh-suggest.uqcloud.net, while our Python library is at https://github.com/ielab/meshsuggestlib.

  • 3 authors
·
Dec 18, 2022

Optimized Conformal Selection: Powerful Selective Inference After Conformity Score Optimization

Model selection/optimization in conformal inference is challenging, since it may break the exchangeability between labeled and unlabeled data. We study this problem in the context of conformal selection, which uses conformal p-values to select ``interesting'' instances with large unobserved labels from a pool of unlabeled data, while controlling the FDR in finite sample. For validity, existing solutions require the model choice to be independent of the data used to construct the p-values and calibrate the selection set. However, when presented with many model choices and limited labeled data, it is desirable to (i) select the best model in a data-driven manner, and (ii) mitigate power loss due to sample splitting. This paper presents OptCS, a general framework that allows valid statistical testing (selection) after flexible data-driven model optimization. We introduce general conditions under which OptCS constructs valid conformal p-values despite substantial data reuse and handles complex p-value dependencies to maintain finite-sample FDR control via a novel multiple testing procedure. We instantiate this general recipe to propose three FDR-controlling procedures, each optimizing the models differently: (i) selecting the most powerful one among multiple pre-trained candidate models, (ii) using all data for model fitting without sample splitting, and (iii) combining full-sample model fitting and selection. We demonstrate the efficacy of our methods via simulation studies and real applications in drug discovery and alignment of large language models in radiology report generation.

  • 2 authors
·
Nov 26, 2024

LLM+Reasoning+Planning for supporting incomplete user queries in presence of APIs

Recent availability of Large Language Models (LLMs) has led to the development of numerous LLM-based approaches aimed at providing natural language interfaces for various end-user tasks. These end-user tasks in turn can typically be accomplished by orchestrating a given set of APIs. In practice, natural language task requests (user queries) are often incomplete, i.e., they may not contain all the information required by the APIs. While LLMs excel at natural language processing (NLP) tasks, they frequently hallucinate on missing information or struggle with orchestrating the APIs. The key idea behind our proposed approach is to leverage logical reasoning and classical AI planning along with an LLM for accurately answering user queries including identification and gathering of any missing information in these queries. Our approach uses an LLM and ASP (Answer Set Programming) solver to translate a user query to a representation in Planning Domain Definition Language (PDDL) via an intermediate representation in ASP. We introduce a special API "get_info_api" for gathering missing information. We model all the APIs as PDDL actions in a way that supports dataflow between the APIs. Our approach then uses a classical AI planner to generate an orchestration of API calls (including calls to get_info_api) to answer the user query. Our evaluation results show that our approach significantly outperforms a pure LLM based approach by achieving over 95\% success rate in most cases on a dataset containing complete and incomplete single goal and multi-goal queries where the multi-goal queries may or may not require dataflow among the APIs.

  • 4 authors
·
May 20, 2024

Online Matching with Stochastic Rewards: Advanced Analyses Using Configuration Linear Programs

Mehta and Panigrahi (2012) proposed Online Matching with Stochastic Rewards, which generalizes the Online Bipartite Matching problem of Karp, Vazirani, and Vazirani (1990) by associating the edges with success probabilities. This new feature captures the pay-per-click model in online advertising. Recently, Huang and Zhang (2020) studied this problem under the online primal dual framework using the Configuration Linear Program (LP), and got the best known competitive ratios of the Stochastic Balance algorithm. Their work suggests that the more expressive Configuration LP is more suitable for this problem than the Matching LP. This paper advances the theory of Configuration LP in two directions. Our technical contribution includes a characterization of the joint matching outcome of an offline vertex and all its neighbors. This characterization may be of independent interest, and is aligned with the spirit of Configuration LP. By contrast, previous analyses of Ranking generally focus on only one neighbor. Second, we designed a Stochastic Configuration LP that captures a stochastic benchmark proposed by Goyal and Udwani (2020), who used a Path-based LP. The Stochastic Configuration LP is smaller and simpler than the Path-based LP. Moreover, using the new LP we improved the competitive ratio of Stochastic Balance from 0.596 to 0.611 when the success probabilities are infinitesimal, and to 0.613 when the success probabilities are further equal.

  • 6 authors
·
Sep 18, 2023

ERank: Fusing Supervised Fine-Tuning and Reinforcement Learning for Effective and Efficient Text Reranking

Text reranking models are a crucial component in modern systems like Retrieval-Augmented Generation, tasked with selecting the most relevant documents prior to generation. However, current Large Language Models (LLMs) powered rerankers often face a fundamental trade-off. On one hand, Supervised Fine-Tuning based pointwise methods that frame relevance as a binary classification task lack the necessary scoring discrimination, particularly for those built on reasoning LLMs. On the other hand, approaches designed for complex reasoning often employ powerful yet inefficient listwise formulations, rendering them impractical for low latency applications. To resolve this dilemma, we introduce ERank, a highly effective and efficient pointwise reranker built from a reasoning LLM that excels across diverse relevance scenarios. We propose a novel two-stage training pipeline that begins with Supervised Fine-Tuning (SFT). In this stage, we move beyond binary labels and train the model generatively to output fine grained integer scores, which significantly enhances relevance discrimination. The model is then further refined using Reinforcement Learning (RL) with a novel, listwise derived reward. This technique instills global ranking awareness into the efficient pointwise architecture. We evaluate the ERank reranker on the BRIGHT, FollowIR, TREC DL, and BEIR benchmarks, demonstrating superior effectiveness and robustness compared to existing approaches. On the reasoning-intensive BRIGHT benchmark, our ERank-4B achieves an nDCG@10 of 38.7, while a larger 32B variant reaches a state of the art nDCG@10 of 40.2.

  • 6 authors
·
Aug 30

Out-of-Town Recommendation with Travel Intention Modeling

Out-of-town recommendation is designed for those users who leave their home-town areas and visit the areas they have never been to before. It is challenging to recommend Point-of-Interests (POIs) for out-of-town users since the out-of-town check-in behavior is determined by not only the user's home-town preference but also the user's travel intention. Besides, the user's travel intentions are complex and dynamic, which leads to big difficulties in understanding such intentions precisely. In this paper, we propose a TRAvel-INtention-aware Out-of-town Recommendation framework, named TRAINOR. The proposed TRAINOR framework distinguishes itself from existing out-of-town recommenders in three aspects. First, graph neural networks are explored to represent users' home-town check-in preference and geographical constraints in out-of-town check-in behaviors. Second, a user-specific travel intention is formulated as an aggregation combining home-town preference and generic travel intention together, where the generic travel intention is regarded as a mixture of inherent intentions that can be learned by Neural Topic Model (NTM). Third, a non-linear mapping function, as well as a matrix factorization method, are employed to transfer users' home-town preference and estimate out-of-town POI's representation, respectively. Extensive experiments on real-world data sets validate the effectiveness of the TRAINOR framework. Moreover, the learned travel intention can deliver meaningful explanations for understanding a user's travel purposes.

  • 7 authors
·
Jan 29, 2021

GenUP: Generative User Profilers as In-Context Learners for Next POI Recommender Systems

Traditional POI recommendation systems often lack transparency, interpretability, and scrutability due to their reliance on dense vector-based user embeddings. Furthermore, the cold-start problem -- where systems have insufficient data for new users -- limits their ability to generate accurate recommendations. Existing methods often address this by leveraging similar trajectories from other users, but this approach can be computationally expensive and increases the context length for LLM-based methods, making them difficult to scale. To address these limitations, we propose a method that generates natural language (NL) user profiles from large-scale, location-based social network (LBSN) check-ins, utilizing robust personality assessments and behavioral theories. These NL profiles capture user preferences, routines, and behaviors, improving POI prediction accuracy while offering enhanced transparency. By incorporating NL profiles as system prompts to LLMs, our approach reduces reliance on extensive historical data, while remaining flexible, easily updated, and computationally efficient. Our method is not only competitive with other LLM-based and complex agentic frameworks but is also more scalable for real-world scenarios and on-device POI recommendations. Results demonstrate that our approach consistently outperforms baseline methods, offering a more interpretable and resource-efficient solution for POI recommendation systems. Our source code is available at: https://github.com/w11wo/GenUP.

  • 3 authors
·
Oct 27, 2024

Patherea: Cell Detection and Classification for the 2020s

This paper presents a Patherea, a framework for point-based cell detection and classification that provides a complete solution for developing and evaluating state-of-the-art approaches. We introduce a large-scale dataset collected to directly replicate a clinical workflow for Ki-67 proliferation index estimation and use it to develop an efficient point-based approach that directly predicts point-based predictions, without the need for intermediate representations. The proposed approach effectively utilizes point proposal candidates with the hybrid Hungarian matching strategy and a flexible architecture that enables the usage of various backbones and (pre)training strategies. We report state-of-the-art results on existing public datasets - Lizard, BRCA-M2C, BCData, and the newly proposed Patherea dataset. We show that the performance on existing public datasets is saturated and that the newly proposed Patherea dataset represents a significantly harder challenge for the recently proposed approaches. We also demonstrate the effectiveness of recently proposed pathology foundational models that our proposed approach can natively utilize and benefit from. We also revisit the evaluation protocol that is used in the broader field of cell detection and classification and identify the erroneous calculation of performance metrics. Patherea provides a benchmarking utility that addresses the identified issues and enables a fair comparison of different approaches. The dataset and the code will be publicly released upon acceptance.

  • 6 authors
·
Dec 20, 2024

NOTE: Notable generation Of patient Text summaries through Efficient approach based on direct preference optimization

The discharge summary is a one of critical documents in the patient journey, encompassing all events experienced during hospitalization, including multiple visits, medications, tests, surgery/procedures, and admissions/discharge. Providing a summary of the patient's progress is crucial, as it significantly influences future care and planning. Consequently, clinicians face the laborious and resource-intensive task of manually collecting, organizing, and combining all the necessary data for a discharge summary. Therefore, we propose "NOTE", which stands for "Notable generation Of patient Text summaries through an Efficient approach based on direct preference optimization". NOTE is based on Medical Information Mart for Intensive Care- III dataset and summarizes a single hospitalization of a patient. Patient events are sequentially combined and used to generate a discharge summary for each hospitalization. In the present circumstances, large language models' application programming interfaces (LLMs' APIs) are widely available, but importing and exporting medical data presents significant challenges due to privacy protection policies in healthcare institutions. Moreover, to ensure optimal performance, it is essential to implement a lightweight model for internal server or program within the hospital. Therefore, we utilized DPO and parameter efficient fine tuning (PEFT) techniques to apply a fine-tuning method that guarantees superior performance. To demonstrate the practical application of the developed NOTE, we provide a webpage-based demonstration software. In the future, we will aim to deploy the software available for actual use by clinicians in hospital. NOTE can be utilized to generate various summaries not only discharge summaries but also throughout a patient's journey, thereby alleviating the labor-intensive workload of clinicians and aiming for increased efficiency.

  • 5 authors
·
Feb 19, 2024

A Comprehensive Survey of Evaluation Techniques for Recommendation Systems

The effectiveness of recommendation systems is pivotal to user engagement and satisfaction in online platforms. As these recommendation systems increasingly influence user choices, their evaluation transcends mere technical performance and becomes central to business success. This paper addresses the multifaceted nature of recommendations system evaluation by introducing a comprehensive suite of metrics, each tailored to capture a distinct aspect of system performance. We discuss * Similarity Metrics: to quantify the precision of content-based filtering mechanisms and assess the accuracy of collaborative filtering techniques. * Candidate Generation Metrics: to evaluate how effectively the system identifies a broad yet relevant range of items. * Predictive Metrics: to assess the accuracy of forecasted user preferences. * Ranking Metrics: to evaluate the effectiveness of the order in which recommendations are presented. * Business Metrics: to align the performance of the recommendation system with economic objectives. Our approach emphasizes the contextual application of these metrics and their interdependencies. In this paper, we identify the strengths and limitations of current evaluation practices and highlight the nuanced trade-offs that emerge when optimizing recommendation systems across different metrics. The paper concludes by proposing a framework for selecting and interpreting these metrics to not only improve system performance but also to advance business goals. This work is to aid researchers and practitioners in critically assessing recommendation systems and fosters the development of more nuanced, effective, and economically viable personalization strategies. Our code is available at GitHub - https://github.com/aryan-jadon/Evaluation-Metrics-for-Recommendation-Systems.

  • 2 authors
·
Dec 26, 2023

EndoBench: A Comprehensive Evaluation of Multi-Modal Large Language Models for Endoscopy Analysis

Endoscopic procedures are essential for diagnosing and treating internal diseases, and multi-modal large language models (MLLMs) are increasingly applied to assist in endoscopy analysis. However, current benchmarks are limited, as they typically cover specific endoscopic scenarios and a small set of clinical tasks, failing to capture the real-world diversity of endoscopic scenarios and the full range of skills needed in clinical workflows. To address these issues, we introduce EndoBench, the first comprehensive benchmark specifically designed to assess MLLMs across the full spectrum of endoscopic practice with multi-dimensional capacities. EndoBench encompasses 4 distinct endoscopic scenarios, 12 specialized clinical tasks with 12 secondary subtasks, and 5 levels of visual prompting granularities, resulting in 6,832 rigorously validated VQA pairs from 21 diverse datasets. Our multi-dimensional evaluation framework mirrors the clinical workflow--spanning anatomical recognition, lesion analysis, spatial localization, and surgical operations--to holistically gauge the perceptual and diagnostic abilities of MLLMs in realistic scenarios. We benchmark 23 state-of-the-art models, including general-purpose, medical-specialized, and proprietary MLLMs, and establish human clinician performance as a reference standard. Our extensive experiments reveal: (1) proprietary MLLMs outperform open-source and medical-specialized models overall, but still trail human experts; (2) medical-domain supervised fine-tuning substantially boosts task-specific accuracy; and (3) model performance remains sensitive to prompt format and clinical task complexity. EndoBench establishes a new standard for evaluating and advancing MLLMs in endoscopy, highlighting both progress and persistent gaps between current models and expert clinical reasoning. We publicly release our benchmark and code.

  • 8 authors
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May 29

Paired Open-Ended Trailblazer (POET): Endlessly Generating Increasingly Complex and Diverse Learning Environments and Their Solutions

While the history of machine learning so far largely encompasses a series of problems posed by researchers and algorithms that learn their solutions, an important question is whether the problems themselves can be generated by the algorithm at the same time as they are being solved. Such a process would in effect build its own diverse and expanding curricula, and the solutions to problems at various stages would become stepping stones towards solving even more challenging problems later in the process. The Paired Open-Ended Trailblazer (POET) algorithm introduced in this paper does just that: it pairs the generation of environmental challenges and the optimization of agents to solve those challenges. It simultaneously explores many different paths through the space of possible problems and solutions and, critically, allows these stepping-stone solutions to transfer between problems if better, catalyzing innovation. The term open-ended signifies the intriguing potential for algorithms like POET to continue to create novel and increasingly complex capabilities without bound. Our results show that POET produces a diverse range of sophisticated behaviors that solve a wide range of environmental challenges, many of which cannot be solved by direct optimization alone, or even through a direct-path curriculum-building control algorithm introduced to highlight the critical role of open-endedness in solving ambitious challenges. The ability to transfer solutions from one environment to another proves essential to unlocking the full potential of the system as a whole, demonstrating the unpredictable nature of fortuitous stepping stones. We hope that POET will inspire a new push towards open-ended discovery across many domains, where algorithms like POET can blaze a trail through their interesting possible manifestations and solutions.

  • 4 authors
·
Jan 7, 2019

The Hitchhiker's Guide to Human Alignment with *PO

With the growing utilization of large language models (LLMs) across domains, alignment towards human preferences has become one of the most critical aspects of training models. At the forefront of state-of-the-art human alignment methods are preference optimization methods (*PO). However, prior research has often concentrated on identifying the best-performing method, typically involving a grid search over hyperparameters, which can be impractical for general practitioners. In this paper, we aim to identify the algorithm that, while being performant, is simultaneously more robust to varying hyperparameters, thereby increasing the likelihood of achieving better results. We focus on a realistic out-of-distribution (OOD) scenario that mirrors real-world applications of human alignment, offering practical insights into the strengths and weaknesses of these methods. Furthermore, to better understand the shortcomings of generations from the different methods, we analyze the model generations through the lens of KL divergence of the SFT model and the response length statistics. Our analysis reveals that the widely adopted DPO method consistently produces lengthy responses of inferior quality that are very close to the SFT responses. Motivated by these findings, we propose an embarrassingly simple extension to the DPO algorithm, LN-DPO, resulting in more concise responses without sacrificing quality compared to the policy obtained by vanilla DPO.

  • 7 authors
·
Jul 21, 2024

MetaTool Benchmark for Large Language Models: Deciding Whether to Use Tools and Which to Use

Large language models (LLMs) have garnered significant attention due to their impressive natural language processing (NLP) capabilities. Recently, many studies have focused on the tool utilization ability of LLMs. They primarily investigated how LLMs effectively collaborate with given specific tools. However, in scenarios where LLMs serve as intelligent agents, as seen in applications like AutoGPT and MetaGPT, LLMs are expected to engage in intricate decision-making processes that involve deciding whether to employ a tool and selecting the most suitable tool(s) from a collection of available tools to fulfill user requests. Therefore, in this paper, we introduce MetaTool, a benchmark designed to evaluate whether LLMs have tool usage awareness and can correctly choose tools. Specifically, we create a dataset called ToolE within the benchmark. This dataset contains various types of user queries in the form of prompts that trigger LLMs to use tools, including both single-tool and multi-tool scenarios. Subsequently, we set the tasks for both tool usage awareness and tool selection. We define four subtasks from different perspectives in tool selection, including tool selection with similar choices, tool selection in specific scenarios, tool selection with possible reliability issues, and multi-tool selection. We conduct experiments involving nine popular LLMs and find that the majority of them still struggle to effectively select tools, highlighting the existing gaps between LLMs and genuine intelligent agents. However, through the error analysis, we found there is still significant room for improvement. Finally, we conclude with insights for tool developers that follow ChatGPT to provide detailed descriptions that can enhance the tool selection performance of LLMs.

  • 11 authors
·
Oct 4, 2023

Unleashing the Power of Data Tsunami: A Comprehensive Survey on Data Assessment and Selection for Instruction Tuning of Language Models

Instruction tuning plays a critical role in aligning large language models (LLMs) with human preference. Despite the vast amount of open instruction datasets, naively training a LLM on all existing instructions may not be optimal and practical. To pinpoint the most beneficial datapoints, data assessment and selection methods have been proposed in the fields of natural language processing (NLP) and deep learning. However, under the context of instruction tuning, there still exists a gap in knowledge on what kind of data evaluation metrics can be employed and how they can be integrated into the selection mechanism. To bridge this gap, we present a comprehensive review on existing literature of data assessment and selection especially for instruction tuning of LLMs. We systematically categorize all applicable methods into quality-based, diversity-based, and importance-based ones where a unified, fine-grained taxonomy is structured. For each category, representative methods are elaborated to describe the landscape of relevant research. In addition, comparison between latest methods is conducted on their officially reported results to provide in-depth discussions on their limitations. Finally, we summarize the open challenges and propose the promosing avenues for future studies. All related contents are available at https://github.com/yuleiqin/fantastic-data-engineering.

  • 10 authors
·
Aug 4, 2024 4

Selection Function of Clusters in Dark Energy Survey Year 3 Data from Cross-Matching with South Pole Telescope Detections

Galaxy clusters selected based on overdensities of galaxies in photometric surveys provide the largest cluster samples. Yet modeling the selection function of such samples is complicated by non-cluster members projected along the line of sight (projection effects) and the potential detection of unvirialized objects (contamination). We empirically constrain the magnitude of these effects by cross-matching galaxy clusters selected in the Dark Energy survey data with the \rdmpr, algorithm with significant detections in three South Pole Telescope surveys (SZ, pol-ECS, pol-500d). For matched clusters, we augment the \rdmpr,catalog by the SPT detection significance. For unmatched objects we use the SPT detection threshold as an upper limit on the SZe signature. Using a Bayesian population model applied to the collected multi-wavelength data, we explore various physically motivated models to describe the relationship between observed richness and halo mass. Our analysis reveals the limitations of a simple lognormal scatter model in describing the data. We rule out significant contamination by unvirialized objects at the high-richness end of the sample. While dedicated simulations offer a well-fitting calibration of projection effects, our findings suggest the presence of redshift-dependent trends that these simulations may not have captured. Our findings highlight that modeling the selection function of optically detected clusters remains a complicated challenge, requiring a combination of simulation and data-driven approaches.

  • 55 authors
·
Feb 18

carps: A Framework for Comparing N Hyperparameter Optimizers on M Benchmarks

Hyperparameter Optimization (HPO) is crucial to develop well-performing machine learning models. In order to ease prototyping and benchmarking of HPO methods, we propose carps, a benchmark framework for Comprehensive Automated Research Performance Studies allowing to evaluate N optimizers on M benchmark tasks. In this first release of carps, we focus on the four most important types of HPO task types: blackbox, multi-fidelity, multi-objective and multi-fidelity-multi-objective. With 3 336 tasks from 5 community benchmark collections and 28 variants of 9 optimizer families, we offer the biggest go-to library to date to evaluate and compare HPO methods. The carps framework relies on a purpose-built, lightweight interface, gluing together optimizers and benchmark tasks. It also features an analysis pipeline, facilitating the evaluation of optimizers on benchmarks. However, navigating a huge number of tasks while developing and comparing methods can be computationally infeasible. To address this, we obtain a subset of representative tasks by minimizing the star discrepancy of the subset, in the space spanned by the full set. As a result, we propose an initial subset of 10 to 30 diverse tasks for each task type, and include functionality to re-compute subsets as more benchmarks become available, enabling efficient evaluations. We also establish a first set of baseline results on these tasks as a measure for future comparisons. With carps (https://www.github.com/automl/CARP-S), we make an important step in the standardization of HPO evaluation.

  • 17 authors
·
Jun 6

Model Evaluation, Model Selection, and Algorithm Selection in Machine Learning

The correct use of model evaluation, model selection, and algorithm selection techniques is vital in academic machine learning research as well as in many industrial settings. This article reviews different techniques that can be used for each of these three subtasks and discusses the main advantages and disadvantages of each technique with references to theoretical and empirical studies. Further, recommendations are given to encourage best yet feasible practices in research and applications of machine learning. Common methods such as the holdout method for model evaluation and selection are covered, which are not recommended when working with small datasets. Different flavors of the bootstrap technique are introduced for estimating the uncertainty of performance estimates, as an alternative to confidence intervals via normal approximation if bootstrapping is computationally feasible. Common cross-validation techniques such as leave-one-out cross-validation and k-fold cross-validation are reviewed, the bias-variance trade-off for choosing k is discussed, and practical tips for the optimal choice of k are given based on empirical evidence. Different statistical tests for algorithm comparisons are presented, and strategies for dealing with multiple comparisons such as omnibus tests and multiple-comparison corrections are discussed. Finally, alternative methods for algorithm selection, such as the combined F-test 5x2 cross-validation and nested cross-validation, are recommended for comparing machine learning algorithms when datasets are small.

  • 1 authors
·
Nov 13, 2018

APIGen: Generative API Method Recommendation

Automatic API method recommendation is an essential task of code intelligence, which aims to suggest suitable APIs for programming queries. Existing approaches can be categorized into two primary groups: retrieval-based and learning-based approaches. Although these approaches have achieved remarkable success, they still come with notable limitations. The retrieval-based approaches rely on the text representation capabilities of embedding models, while the learning-based approaches require extensive task-specific labeled data for training. To mitigate the limitations, we propose APIGen, a generative API recommendation approach through enhanced in-context learning (ICL). APIGen involves two main components: (1) Diverse Examples Selection. APIGen searches for similar posts to the programming queries from the lexical, syntactical, and semantic perspectives, providing more informative examples for ICL. (2) Guided API Recommendation. APIGen enables large language models (LLMs) to perform reasoning before generating API recommendations, where the reasoning involves fine-grained matching between the task intent behind the queries and the factual knowledge of the APIs. With the reasoning process, APIGen makes recommended APIs better meet the programming requirement of queries and also enhances the interpretability of results. We compare APIGen with four existing approaches on two publicly available benchmarks. Experiments show that APIGen outperforms the best baseline CLEAR by 105.8% in method-level API recommendation and 54.3% in class-level API recommendation in terms of SuccessRate@1. Besides, APIGen achieves an average 49.87% increase compared to the zero-shot performance of popular LLMs such as GPT-4 in method-level API recommendation regarding the SuccessRate@3 metric.

  • 6 authors
·
Jan 28, 2024

TPTU-v2: Boosting Task Planning and Tool Usage of Large Language Model-based Agents in Real-world Systems

Large Language Models (LLMs) have demonstrated proficiency in addressing tasks that necessitate a combination of task planning and the usage of external tools that require a blend of task planning and the utilization of external tools, such as APIs. However, real-world complex systems present three prevalent challenges concerning task planning and tool usage: (1) The real system usually has a vast array of APIs, so it is impossible to feed the descriptions of all APIs to the prompt of LLMs as the token length is limited; (2) the real system is designed for handling complex tasks, and the base LLMs can hardly plan a correct sub-task order and API-calling order for such tasks; (3) Similar semantics and functionalities among APIs in real systems create challenges for both LLMs and even humans in distinguishing between them. In response, this paper introduces a comprehensive framework aimed at enhancing the Task Planning and Tool Usage (TPTU) abilities of LLM-based agents operating within real-world systems. Our framework comprises three key components designed to address these challenges: (1) the API Retriever selects the most pertinent APIs for the user task among the extensive array available; (2) LLM Finetuner tunes a base LLM so that the finetuned LLM can be more capable for task planning and API calling; (3) the Demo Selector adaptively retrieves different demonstrations related to hard-to-distinguish APIs, which is further used for in-context learning to boost the final performance. We validate our methods using a real-world commercial system as well as an open-sourced academic dataset, and the outcomes clearly showcase the efficacy of each individual component as well as the integrated framework.

  • 12 authors
·
Nov 19, 2023 2

Doing More with Less -- Implementing Routing Strategies in Large Language Model-Based Systems: An Extended Survey

Large Language Models (LLM)-based systems, i.e. interconnected elements that include an LLM as a central component (e.g., conversational agents), are typically monolithic static architectures that rely on a single LLM for all user queries. However, they often require different preprocessing strategies, levels of reasoning, or knowledge. Generalist LLMs (i.e. GPT-4), trained on very large multi-topic corpora, can perform well in a variety of tasks. However, they require significant financial, energy, and hardware resources that may not be justified for basic tasks. This implies potentially investing in unnecessary costs for a given query. To overcome this problem, a routing mechanism routes user queries to the most suitable components, such as smaller LLMs or experts in specific topics. This approach may improve response quality while minimising costs. Routing can be expanded to other components of the conversational agent architecture, such as the selection of optimal embedding strategies. This paper explores key considerations for integrating routing into LLM-based systems, focusing on resource management, cost definition, and strategy selection. Our main contributions include a formalisation of the problem, a novel taxonomy of existing approaches emphasising relevance and resource efficiency, and a comparative analysis of these strategies in relation to industry practices. Finally, we identify critical challenges and directions for future research.

  • 6 authors
·
Feb 1

UniSite: The First Cross-Structure Dataset and Learning Framework for End-to-End Ligand Binding Site Detection

The detection of ligand binding sites for proteins is a fundamental step in Structure-Based Drug Design. Despite notable advances in recent years, existing methods, datasets, and evaluation metrics are confronted with several key challenges: (1) current datasets and methods are centered on individual protein-ligand complexes and neglect that diverse binding sites may exist across multiple complexes of the same protein, introducing significant statistical bias; (2) ligand binding site detection is typically modeled as a discontinuous workflow, employing binary segmentation and subsequent clustering algorithms; (3) traditional evaluation metrics do not adequately reflect the actual performance of different binding site prediction methods. To address these issues, we first introduce UniSite-DS, the first UniProt (Unique Protein)-centric ligand binding site dataset, which contains 4.81 times more multi-site data and 2.08 times more overall data compared to the previously most widely used datasets. We then propose UniSite, the first end-to-end ligand binding site detection framework supervised by set prediction loss with bijective matching. In addition, we introduce Average Precision based on Intersection over Union (IoU) as a more accurate evaluation metric for ligand binding site prediction. Extensive experiments on UniSite-DS and several representative benchmark datasets demonstrate that IoU-based Average Precision provides a more accurate reflection of prediction quality, and that UniSite outperforms current state-of-the-art methods in ligand binding site detection. The dataset and codes will be made publicly available at https://github.com/quanlin-wu/unisite.

  • 4 authors
·
Jun 3

EndoNet: A Deep Architecture for Recognition Tasks on Laparoscopic Videos

Surgical workflow recognition has numerous potential medical applications, such as the automatic indexing of surgical video databases and the optimization of real-time operating room scheduling, among others. As a result, phase recognition has been studied in the context of several kinds of surgeries, such as cataract, neurological, and laparoscopic surgeries. In the literature, two types of features are typically used to perform this task: visual features and tool usage signals. However, the visual features used are mostly handcrafted. Furthermore, the tool usage signals are usually collected via a manual annotation process or by using additional equipment. In this paper, we propose a novel method for phase recognition that uses a convolutional neural network (CNN) to automatically learn features from cholecystectomy videos and that relies uniquely on visual information. In previous studies, it has been shown that the tool signals can provide valuable information in performing the phase recognition task. Thus, we present a novel CNN architecture, called EndoNet, that is designed to carry out the phase recognition and tool presence detection tasks in a multi-task manner. To the best of our knowledge, this is the first work proposing to use a CNN for multiple recognition tasks on laparoscopic videos. Extensive experimental comparisons to other methods show that EndoNet yields state-of-the-art results for both tasks.

  • 6 authors
·
Feb 9, 2016

MeSH Term Suggestion for Systematic Review Literature Search

High-quality medical systematic reviews require comprehensive literature searches to ensure the recommendations and outcomes are sufficiently reliable. Indeed, searching for relevant medical literature is a key phase in constructing systematic reviews and often involves domain (medical researchers) and search (information specialists) experts in developing the search queries. Queries in this context are highly complex, based on Boolean logic, include free-text terms and index terms from standardised terminologies (e.g., MeSH), and are difficult and time-consuming to build. The use of MeSH terms, in particular, has been shown to improve the quality of the search results. However, identifying the correct MeSH terms to include in a query is difficult: information experts are often unfamiliar with the MeSH database and unsure about the appropriateness of MeSH terms for a query. Naturally, the full value of the MeSH terminology is often not fully exploited. This paper investigates methods to suggest MeSH terms based on an initial Boolean query that includes only free-text terms. These methods promise to automatically identify highly effective MeSH terms for inclusion in a systematic review query. Our study contributes an empirical evaluation of several MeSH term suggestion methods. We perform an extensive analysis of the retrieval, ranking, and refinement of MeSH term suggestions for each method and how these suggestions impact the effectiveness of Boolean queries.

  • 5 authors
·
Dec 1, 2021

EasyTPP: Towards Open Benchmarking Temporal Point Processes

Continuous-time event sequences play a vital role in real-world domains such as healthcare, finance, online shopping, social networks, and so on. To model such data, temporal point processes (TPPs) have emerged as the most natural and competitive models, making a significant impact in both academic and application communities. Despite the emergence of many powerful models in recent years, there hasn't been a central benchmark for these models and future research endeavors. This lack of standardization impedes researchers and practitioners from comparing methods and reproducing results, potentially slowing down progress in this field. In this paper, we present EasyTPP, the first central repository of research assets (e.g., data, models, evaluation programs, documentations) in the area of event sequence modeling. Our EasyTPP makes several unique contributions to this area: a unified interface of using existing datasets and adding new datasets; a wide range of evaluation programs that are easy to use and extend as well as facilitate reproducible research; implementations of popular neural TPPs, together with a rich library of modules by composing which one could quickly build complex models. All the data and implementation can be found at https://github.com/ant-research/EasyTemporalPointProcess. We will actively maintain this benchmark and welcome contributions from other researchers and practitioners. Our benchmark will help promote reproducible research in this field, thus accelerating research progress as well as making more significant real-world impacts.

  • 12 authors
·
Jul 16, 2023

Using clarification questions to improve software developers' Web search

Context: Recent research indicates that Web queries written by software developers are not very successful in retrieving relevant results, performing measurably worse compared to general purpose Web queries. Most approaches up to this point have addressed this problem with software engineering-specific automated query reformulation techniques, which work without developer involvement but are limited by the content of the original query. In other words, these techniques automatically improve the existing query but can not contribute new, previously unmentioned, concepts. Objective: In this paper, we propose a technique to guide software developers in manually improving their own Web search queries. We examine a conversational approach that follows unsuccessful queries with a clarification question aimed at eliciting additional query terms, thus providing to the developer a clear dimension along which the query could be improved. Methods: We describe a set of clarification questions derived from a corpus of software developer queries and a neural approach to recommending them for a newly issued query. Results: Our evaluation indicates that the recommendation technique is accurate, predicting a valid clarification question 80% of the time and outperforms simple baselines, as well as, state-of-the-art Learning To Rank (LTR) baselines. Conclusion: As shown in the experimental results, the described approach is capable at recommending appropriate clarification questions to software developers and considered useful by a sample of developers ranging from novices to experienced professionals.

  • 2 authors
·
Jul 26, 2022