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Efficient Chromosome Parallelization for Precision Medicine Genomic Workflows
Montserrat, Daniel Mas, Verma, Ray, Barrabés, Míriam, de la Vega, Francisco M., Bustamante, Carlos D., Ioannidis, Alexander G.
Large-scale genomic workflows used in precision medicine can process datasets spanning tens to hundreds of gigabytes per sample, leading to high memory spikes, intensive disk I/O, and task failures due to out-of-memory errors. Simple static resource allocation methods struggle to handle the variability in per-chromosome RAM demands, resulting in poor resource utilization and long runtimes. In this work, we propose multiple mechanisms for adaptive, RAM-efficient par-allelization of chromosome-level bioinformatics workflows. First, we develop a symbolic regression model that estimates per-chromosome memory consumption for a given task and introduces an interpolating bias to conservatively minimize over-allocation. Second, we present a dynamic scheduler that adaptively predicts RAM usage with a polynomial regression model, treating task packing as a Knapsack problem to optimally batch jobs based on predicted memory requirements. Additionally, we present a static scheduler that optimizes chromosome processing order to minimize peak memory while preserving throughput. Our proposed methods, evaluated on simulations and real-world genomic pipelines, provide new mechanisms to reduce memory overruns and balance load across threads. We thereby achieve faster end-to-end execution, showcasing the potential to optimize large-scale genomic workflows.
TOD-ProcBench: Benchmarking Complex Instruction-Following in Task-Oriented Dialogues
Ghazarian, Sarik, Gullapalli, Abhinav, Shah, Swair, Beniwal, Anurag, Peng, Nanyun, Sadagopan, Narayanan, Yu, Zhou
In real-world task-oriented dialogue (TOD) settings, agents are required to strictly adhere to complex instructions while conducting multi-turn conversations with customers. These instructions are typically presented in natural language format and include general guidelines and step-by-step procedures with complex constraints. Existing TOD benchmarks often oversimplify the complex nature of these instructions by reducing them to simple schemas composed of intents, slots, and API call configurations. To address this gap and systematically benchmark LLMs' instruction-following capabilities, we propose TOD-ProcBench, a challenging benchmark featuring complex process instructions with intricate, fine-grained constraints that evaluates various LLMs' abilities to understand and follow instructions in multi-turn TODs. Our benchmark dataset comprises instruction documents derived from the high-quality ABCD dataset with corresponding conversations under human quality control. We formulate fine-grained constraints and action procedures as multi-level condition-action instruction statements. We design three tasks to comprehensively benchmark LLMs' complex instruction-following capabilities in multi-turn TODs. Task 1 evaluates how LLMs retrieve the most relevant statement from a complex instruction and predict the corresponding next action. In Task 2, we synthesize instruction-violating responses by injecting inconsistencies and manipulating the original instructions, and then we analyze how effectively LLMs can identify instruction-violating responses. Task 3 investigates LLMs' abilities in conditional generation of instruction-following responses based on the original complex instructions. Additionally, we conduct studies on the impact of multilingual settings and different instruction text formats on compliance performance. We release our benchmark under the Llama 3.3 Community License Agreement.
Externally Validated Multi-Task Learning via Consistency Regularization Using Differentiable BI-RADS Features for Breast Ultrasound Tumor Segmentation
Zhang, Jingru, Moradi, Saed, Saha, Ashirbani
Multi-task learning can suffer from destructive task interference, where jointly trained models underperform single-task baselines and limit generalization. To improve generalization performance in breast ultrasound-based tumor segmentation via multi-task learning, we propose a novel consistency regularization approach that mitigates destructive interference between segmentation and classification. The consistency regularization approach is composed of differentiable BI-RADS-inspired morphological features. We validated this approach by training all models on the BrEaST dataset (Poland) and evaluating them on three external datasets: UDIAT (Spain), BUSI (Egypt), and BUS-UCLM (Spain). Our comprehensive analysis demonstrates statistically significant (p<0.001) improvements in generalization for segmentation task of the proposed multi-task approach vs. the baseline one: UDIAT, BUSI, BUS-UCLM (Dice coefficient=0.81 vs 0.59, 0.66 vs 0.56, 0.69 vs 0.49, resp.). The proposed approach also achieves state-of-the-art segmentation performance under rigorous external validation on the UDIAT dataset.
Self-supervised and Multi-fidelity Learning for Extended Predictive Soil Spectroscopy
Sun, Luning, Safanelli, José L., Sanderman, Jonathan, Georgiou, Katerina, Brungard, Colby, Grover, Kanchan, Hopkins, Bryan G., Liu, Shusen, Bremer, Timo
We propose a self-supervised machine learning (SSML) framework for multi-fidelity learning and extended predictive soil spectroscopy based on latent space embeddings. A self-supervised representation was pretrained with the large MIR spectral library and the Variational Autoencoder algorithm to obtain a compressed latent space for generating spectral embeddings. At this stage, only unlabeled spectral data were used, allowing us to leverage the full spectral database and the availability of scan repeats for augmented training. We also leveraged and froze the trained MIR decoder for a spectrum conversion task by plugging it into a NIR encoder to learn the mapping between NIR and MIR spectra in an attempt to leverage the predictive capabilities contained in the large MIR library with a low cost portable NIR scanner. This was achieved by using a smaller subset of the KSSL library with paired NIR and MIR spectra. Downstream machine learning models were then trained to map between original spectra, predicted spectra, and latent space embeddings for nine soil properties. The performance of was evaluated independently of the KSSL training data using a gold-standard test set, along with regression goodness-of-fit metrics. Compared to baseline models, the proposed SSML and its embeddings yielded similar or better accuracy in all soil properties prediction tasks. Predictions derived from the spectrum conversion (NIR to MIR) task did not match the performance of the original MIR spectra but were similar or superior to predictive performance of NIR-only models, suggesting the unified spectral latent space can effectively leverage the larger and more diverse MIR dataset for prediction of soil properties not well represented in current NIR libraries.
Machine Learning vs. Randomness: Challenges in Predicting Binary Options Movements
Arantes, Gabriel M., Pinto, Richard F., Dalmazo, Bruno L., Borges, Eduardo N., Lucca, Giancarlo, de Mattos, Viviane L. D., Cardoso, Fabian C., Berri, Rafael A.
Binary options trading is often marketed as a field where predictive models can generate consistent profits. However, the inherent randomness and stochastic nature of binary options make price movements highly unpredictable, posing significant challenges for any forecasting approach. This study demonstrates that machine learning algorithms struggle to outperform a simple baseline in predicting binary options movements. Using a dataset of EUR/USD currency pairs from 2021 to 2023, we tested multiple models, including Random Forest, Logistic Regression, Gradient Boosting, and k-Nearest Neighbors (kNN), both before and after hyperparameter optimization. Furthermore, several neural network architectures, including Multi-Layer Perceptrons (MLP) and a Long Short-Term Memory (LSTM) network, were evaluated under different training conditions. Despite these exhaustive efforts, none of the models surpassed the ZeroR baseline accuracy, highlighting the inherent randomness of binary options. These findings reinforce the notion that binary options lack predictable patterns, making them unsuitable for machine learning-based forecasting.
JudgeBoard: Benchmarking and Enhancing Small Language Models for Reasoning Evaluation
Bi, Zhenyu, Srivastava, Gaurav, Li, Yang, Lu, Meng, Roy, Swastik, Ziyadi, Morteza, Wang, Xuan
While small language models (SLMs) have shown promise on various reasoning tasks, their ability to judge the correctness of answers remains unclear compared to large language models (LLMs). Prior work on LLM-as-a-judge frameworks typically relies on comparing candidate answers against ground-truth labels or other candidate answers using predefined metrics like entailment. However, this approach is inherently indirect and difficult to fully automate, offering limited support for fine-grained and scalable evaluation of reasoning outputs. In this work, we propose JudgeBoard, a novel evaluation pipeline that directly queries models to assess the correctness of candidate answers without requiring extra answer comparisons. We focus on two core reasoning domains: mathematical reasoning and science/commonsense reasoning, and construct task-specific evaluation leaderboards using both accuracy-based ranking and an Elo-based rating system across five benchmark datasets, enabling consistent model comparison as judges rather than comparators. To improve judgment performance in lightweight models, we propose MAJ (Multi-Agent Judging), a novel multi-agent evaluation framework that leverages multiple interacting SLMs with distinct reasoning profiles to approximate LLM-level judgment accuracy through collaborative deliberation. Experimental results reveal a significant performance gap between SLMs and LLMs in isolated judging tasks. However, our MAJ framework substantially improves the reliability and consistency of SLMs. On the MATH dataset, MAJ using smaller-sized models as backbones performs comparatively well or even better than their larger-sized counterparts. Our findings highlight that multi-agent SLM systems can potentially match or exceed LLM performance in judgment tasks, with implications for scalable and efficient assessment.
A Scalable NorthPole System with End-to-End Vertical Integration for Low-Latency and Energy-Efficient LLM Inference
DeBole, Michael V., Appuswamy, Rathinakumar, McGlohon, Neil, Taba, Brian, Esser, Steven K., Akopyan, Filipp, Arthur, John V., Amir, Arnon, Andreopoulos, Alexander, Carlson, Peter J., Cassidy, Andrew S., Datta, Pallab, Flickner, Myron D., Gandhasri, Rajamohan, Garreau, Guillaume J., Ito, Megumi, Klamo, Jennifer L., Kusnitz, Jeffrey A., McClatchey, Nathaniel J., McKinstry, Jeffrey L., Nayak, Tapan K., Otero, Carlos Ortega, Penner, Hartmut, Risk, William P., Sawada, Jun, Sivagnaname, Jay, Smith, Daniel F., Sousa, Rafael, Terrizzano, Ignacio, Ueda, Takanori, Gray-Donald, Trent, Cox, David, Modha, Dharmendra S.
Abstract--A vertically integrated, end-to-end, research prototype system combines 288 NorthPole neural inference accelerator cards, offline training algorithms, a high-performance runtime stack, and a containerized inference pipeline to deliver a scalable and efficient cloud inference service. The system delivers 115 peta-ops at 4-bit integer precision and 3.7 PB/s of memory bandwidth across 18 2U servers, while consuming only 30 kW of power and weighing 730 kg in a 0.67 m The system can run 3 simultaneous instances of the 8-billion-parameter open-source IBM Granite-3.3-8b-instruct The system is scalable, modular, and reconfigurable, supporting various model sizes and context lengths, and is ideal for deploying agentic workflows for enterprise AI applications in existing data center (cloud, on-prem) environments. For example, the system can support 18 instances of a 3-billion-parameter model or a single instance of a 70-billion-parameter model. Large language models have become a pervasive form of computing, and while the current paradigm has been to push frontier models for all applications, it is becoming evident that "Faith in God-like large language models is waning" [1]. In fact, by continuing along this trajectory, global energy requirements for AI-focused data centers are projected to reach double-digit percentages of total electricity consumption by 2030, with individual facilities requiring up to 1 gigawatt or more of dedicated power--driving both infrastructure and cooling costs toward potentially unsustainable or unprofitable levels [2] [3]. However, for many business applications, frontier models containing trillions of parameters may prove less useful and cost efficient than much smaller language models with only a tenth or even a hundredth as many parameters [4].
iLTM: Integrated Large Tabular Model
Bonet, David, Cara, Marçal Comajoan, Calafell, Alvaro, Montserrat, Daniel Mas, Ioannidis, Alexander G.
Tabular data underpins decisions across science, industry, and public services. Despite rapid progress, advances in deep learning have not fully carried over to the tabular domain, where gradient-boosted decision trees (GBDTs) remain a default choice in practice. We present iLTM, an integrated Large Tabular Model that unifies tree-derived embeddings, dimensionality-agnostic representations, a meta-trained hypernetwork, multilayer perceptrons (MLPs), and retrieval within a single architecture. Pretrained on more than 1,800 heterogeneous classification datasets, iLTM achieves consistently superior performance across tabular classification and regression tasks, from small datasets to large and high-dimensional tasks. After light fine-tuning, the meta-trained hypernetwork transfers to regression targets, matching or surpassing strong baselines. Extensive experiments show that iLTM outperforms well-tuned GBDTs and leading deep tabular models while requiring less task-specific tuning. By bridging the gap between tree-based and neural methods, iLTM offers a new framework for tabular foundation models for robust, adaptable, and scalable tabular learning.
Gimballed Rotor Mechanism for Omnidirectional Quadrotors
Cristobal, J., Aldeen, A. Z. Zain, Izadi, M., Faieghi, R.
This paper presents the design of a gimballed rotor mechanism as a modular and efficient solution for constructing omnidirectional quadrotors. Unlike conventional quadrotors, which are underactuated, this class of quadrotors achieves full actuation, enabling independent motion in all six degrees of freedom. While existing omnidirectional quadrotor designs often require significant structural modifications, the proposed gimballed rotor system maintains a lightweight and easy-to-integrate design by incorporating servo motors within the rotor platforms, allowing independent tilting of each rotor without major alterations to the central structure of a quadrotor. To accommodate this unconventional design, we develop a new control allocation scheme in PX4 Autopilot and present successful flight tests, validating the effectiveness of the proposed approach.
Unified all-atom molecule generation with neural fields
Kirchmeyer, Matthieu, Pinheiro, Pedro O., Willett, Emma, Martinkus, Karolis, Kleinhenz, Joseph, Makowski, Emily K., Watkins, Andrew M., Gligorijevic, Vladimir, Bonneau, Richard, Saremi, Saeed
Generative models for structure-based drug design are often limited to a specific modality, restricting their broader applicability. To address this challenge, we introduce FuncBind, a framework based on computer vision to generate target-conditioned, all-atom molecules across atomic systems. FuncBind uses neural fields to represent molecules as continuous atomic densities and employs score-based generative models with modern architectures adapted from the computer vision literature. This modality-agnostic representation allows a single unified model to be trained on diverse atomic systems, from small to large molecules, and handle variable atom/residue counts, including non-canonical amino acids. FuncBind achieves competitive in silico performance in generating small molecules, macrocyclic peptides, and antibody complementarity-determining region loops, conditioned on target structures. FuncBind also generated in vitro novel antibody binders via de novo redesign of the complementarity-determining region H3 loop of two chosen co-crystal structures. As a final contribution, we introduce a new dataset and benchmark for structure-conditioned macrocyclic peptide generation. The code is available at https://github.com/prescient-design/funcbind.