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Phenotype-driven gene prioritization is a critical process in the diagnosis of rare genetic disorders for identifying and ranking potential disease-causing genes based on observed physical traits or phenotypes. While traditional approaches…

Quantitative Methods · Quantitative Biology 2024-04-04 Junyoung Kim , Jingye Yang , Kai Wang , Chunhua Weng , Cong Liu

The extraction of sequence patterns from a collection of functionally linked unlabeled DNA sequences is known as DNA motif discovery, and it is a key task in computational biology. Several deep learning-based techniques have recently been…

Machine Learning · Computer Science 2022-10-03 Wen Wang , Jianzong Wang , Shijing Si , Zhangcheng Huang , Jing Xiao

The goal of unbiased learning to rank (ULTR) is to leverage implicit user feedback for optimizing learning-to-rank systems. Among existing solutions, automatic ULTR algorithms that jointly learn user bias models (i.e., propensity models)…

Information Retrieval · Computer Science 2023-07-11 Dan Luo , Lixin Zou , Qingyao Ai , Zhiyu Chen , Chenliang Li , Dawei Yin , Brian D. Davison

Dynamic treatment regimes (DTRs) consist of a sequence of decision rules, one per stage of intervention, that finds effective treatments for individual patients according to patient information history. DTRs can be estimated from models…

Methodology · Statistics 2021-12-07 Zeyu Bian , Erica EM Moodie , Susan M Shortreed , Sahir Bhatnagar

We propose a meta-learning method for positive and unlabeled (PU) classification, which improves the performance of binary classifiers obtained from only PU data in unseen target tasks. PU learning is an important problem since PU data…

Machine Learning · Computer Science 2024-06-07 Atsutoshi Kumagai , Tomoharu Iwata , Yasuhiro Fujiwara

Supervised fine-tuning (SFT) has become a crucial step for aligning pretrained large language models (LLMs) using supervised datasets of input-output pairs. However, despite being supervised, SFT is inherently limited by its generative…

Computation and Language · Computer Science 2025-07-25 Siqi Guo , Ilgee Hong , Vicente Balmaseda , Changlong Yu , Liang Qiu , Xin Liu , Haoming Jiang , Tuo Zhao , Tianbao Yang

This work proposes `PET', a novel pessimistic reward fine-tuning method, to learn a pessimistic reward model robust against reward hacking in offline reinforcement learning from human feedback (RLHF). Traditional reward modeling techniques…

Machine Learning · Computer Science 2025-05-28 Yinglun Xu , Hangoo Kang , Tarun Suresh , Yuxuan Wan , Gagandeep Singh

Many real-world applications have to tackle the Positive-Unlabeled (PU) learning problem, i.e., learning binary classifiers from a large amount of unlabeled data and a few labeled positive examples. While current state-of-the-art methods…

Machine Learning · Computer Science 2020-06-23 Xuxi Chen , Wuyang Chen , Tianlong Chen , Ye Yuan , Chen Gong , Kewei Chen , Zhangyang Wang

Deep neural networks (DNNs) achieve state-of-the-art results in a variety of domains. Unfortunately, DNNs are notorious for their non-interpretability, and thus limit their applicability in hypothesis-driven domains such as biology and…

Machine Learning · Computer Science 2018-03-12 Chun-Hao Chang , Ladislav Rampasek , Anna Goldenberg

In reinforcement learning (RL), temporal difference (TD) error is known to be related to the firing rate of dopamine neurons. It has been observed that each dopamine neuron does not behave uniformly, but each responds to the TD error in an…

Machine Learning · Computer Science 2026-04-09 Taisuke Kobayashi

Recent advances in dynamic treatment regimes (DTRs) facilitate the search for optimal treatments, which are tailored to individuals' specific needs and able to maximize their expected clinical benefits. However, existing algorithms relying…

Machine Learning · Statistics 2024-10-18 Hanwen Ye , Wenzhuo Zhou , Ruoqing Zhu , Annie Qu

Aligning generative diffusion models with human preferences via reinforcement learning (RL) is critical yet challenging. Most existing algorithms are often vulnerable to reward hacking, such as quality degradation, over-stylization, or…

Bias is a common problem inherent in recommender systems, which is entangled with users' preferences and poses a great challenge to unbiased learning. For debiasing tasks, the doubly robust (DR) method and its variants show superior…

Information Retrieval · Computer Science 2023-03-03 Haoxuan Li , Yan Lyu , Chunyuan Zheng , Peng Wu

With the prevalence of Diabetes, the Diabetes Mellitus Retinopathy (DR) is becoming a major health problem across the world. The long-term medical complications arising due to DR have a significant impact on the patient as well as the…

Computer Vision and Pattern Recognition · Computer Science 2022-01-04 Shreyas Rajesh Labhsetwar , Raj Sunil Salvi , Piyush Arvind Kolte , Veerasai Subramaniam venkatesh , Alistair Michael Baretto

Food recommendation system has proven as an effective technology to provide guidance on dietary choices, and this is especially important for patients suffering from chronic diseases. Unlike other multimedia recommendations, such as books…

Information Retrieval · Computer Science 2022-10-18 Xinwei Ju , Frank Po Wen Lo , Jianing Qiu , Peilun Shi , Jiachuan Peng , Benny Lo

Diabetic Retinopathy (DR) is a significant cause of blindness globally, highlighting the urgent need for early detection and effective treatment. Recent advancements in Machine Learning (ML) techniques have shown promise in DR detection,…

Computer Vision and Pattern Recognition · Computer Science 2023-09-06 D. Dhinakaran , L. Srinivasan , D. Selvaraj , S. M. Udhaya Sankar

With surge of available but unlabeled data, Positive Unlabeled (PU) learning is becoming a thriving challenge. This work deals with this demanding task for which recent GAN-based PU approaches have demonstrated promising results. Generative…

Computer Vision and Pattern Recognition · Computer Science 2019-10-07 Florent Chiaroni , Ghazaleh Khodabandelou , Mohamed-Cherif Rahal , Nicolas Hueber , Frederic Dufaux

Reward models are crucial for aligning large language models (LLMs) with human values and intentions. Existing approaches follow either Generative (GRMs) or Discriminative (DRMs) paradigms, yet both suffer from limitations: GRMs typically…

Computation and Language · Computer Science 2026-03-03 Longze Chen , Lu Wang , Renke Shan , Ze Gong , Run Luo , Jiaming Li , Jing Luo , Qiyao Wang , Min Yang

Developing new drugs is laborious and costly, demanding extensive time investment. In this paper, we introduce a de-novo drug design strategy, which harnesses the capabilities of language models to devise targeted drugs for specific…

Biomolecules · Quantitative Biology 2025-05-20 Salma J. Ahmed , Emad A. Mohammed

Reinforcement learning (RL) is pivotal for enhancing the reasoning capabilities of diffusion large language models (dLLMs). However, existing dLLM policy optimization methods suffer from two critical reliability bottlenecks: (1) reward…

Computation and Language · Computer Science 2026-05-14 Leyi Pan , Shuchang Tao , Yunpeng Zhai , Zheyu Fu , Liancheng Fang , Minghua He , Lingzhe Zhang , Zhaoyang Liu , Bolin Ding , Aiwei Liu , Lijie Wen
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