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A Flexible Open-Source Framework for FPGA-based Network-Attached Accelerators using SpinalHDL
(2026)
Domain-specific accelerators are increasingly vital in heterogeneous computing systems, driven by the demand for higher computational capacity and especially energy efficiency. Network-attached FPGAs promise a scalable and flexible alternative to closely coupled FPGAs for integrating accelerators into computing environments. While the advantages of specialized hardware implementations are apparent, traditional hardware development and integration remain time-consuming and complex.
We present an open-source framework which combines a hardware shell with supporting software libraries, which enables fast development and deployment of FPGA-based network-attached accelerators. In contrast to traditional approaches using VHDL or Verilog, we leverage generative programming with SpinalHDL, providing a flexible hardware description with multi-level abstractions. This work eases the integration of accelerators into existing network infrastructures and simplifies adaptation to different FPGAs, eliminating complex and lengthy top-level hardware descriptions.
The mutual information (MI) between two random variables is an important
correlation measure in data analysis. The Shannon entropy of a joint probability distri-
bution is the variable part under fixed marginals. We aim to minimize and maximize it
to obtain the largest and smallest MI possible in this case, leading to a scaled MI ratio
for better comparability. We present algorithmic approaches and optimal solutions for
a set of problem instances based on data from molecular evolution. We show that this
allows us to construct a sensible, systematic correction to raw MI values.
We solve the problem of determining the pose of known shapes in R^3 from their unoccluded silhouettes. The pose is determined up to global optimality using a simple yet under-explored property of the area-of-silhouette: its continuity w.r.t trajectories in the rotation space. The proposed method utilises pre-computed silhouette-signatures, modelled as a response surface of the area-of-silhouettes. Querying this silhouette-signature response surface for pose estimation leads to a strong branching of the rotation search space, making resolution-guided candidate search feasible. Additionally, we utilise the aspect ratio of 2D ellipses fitted to projected silhouettes as an auxiliary global shape signature to accelerate the pose search. This combined strategy forms the first method to efficiently estimate globally optimal pose from just the silhouettes, without being guided by correspondences, for any shape, irrespective of its convexity and genus. We validate our method on synthetic and real examples, demonstrating significantly improved accuracy against comparable approaches.
We present a structure-aware parallel presolve framework specialized to arrowhead linear programs (AHLPs) and designed for high-performance computing (HPC) environments, integrated into the parallel interior point solver PIPS-IPM++. Large-scale LPs arising from automated model generation frequently contain redundancies and numerical pathologies that necessitate effective presolve, yet existing presolve techniques are primarily serial or structure-agnostic and can become time-consuming in parallel solution workflows.
Within PIPS-IPM++, AHLPs are stored in distributed memory, and our presolve builds on this to apply a highly parallel, distributed presolve across compute nodes while keeping communication overhead low and preserving the underlying arrowhead structure. We demonstrate the scalability and effectiveness of our approach on a diverse set of AHLPs and compare it against state-of-the-art presolve implementations, including PaPILO and the presolve implemented within Gurobi. Even on a single machine, our presolve significantly outperforms PaPILO by a factor of 18 and Gurobi’s presolve by a factor of 6 in terms of shifted geometric mean runtime, while reducing the problems by a similar amount to PaPILO. Using a distributed compute environment, we outperform Gurobi's presolve by a factor of 13.
Branching decisions play a crucial role in branch-and-bound algorithms for solving combinatorial optimization problems. In this paper, we investigate several branching rules applied to the Quota Steiner Tree Problem with Interference (QSTPI). The Quota Steiner Tree Problem (QSTP) generalizes the classical Steiner Tree Problem (STP) in graphs by seeking a minimum-cost tree that connects a subset of profit-associated vertices whose cumulative profit meets or exceeds a given quota. The QSTPI introduces interference among vertices: Selecting certain vertices simultaneously reduces their individual contributions to the overall profit. This problem arises, for example, in positioning and connecting wind turbines, where turbines possibly shadow other turbines, reducing their energy yield. Unlike classical STP variants, large QSTPI instances require significantly more branching to compute provably optimal solutions. In contrast to branching on variables, we utilize the combinatorial structure of the QSTPI by branching on the graph's vertices. We adapt classical and problem-specific branching rules and present a comprehensive computational study comparing the effectiveness of these branching strategies.
Background: Filopodia are thin and dynamic membrane protrusions that play a crucial role in cell migration, axon guidance, and other processes where cells explore and interact with their surroundings. Historically, filopodial dynamics have been studied in great detail in 2D in cultured cells, and more recently in 3D culture as well as living brains. However, there is a lack of efficient tools to trace and track filopodia in 4D images of complex brain cells.
Results: To address this issue, we have developed a semi-automatic workflow for tracing filopodia in 3D images and tracking the traced filopodia over time. The workflow was developed based on high-resolution data of photoreceptor axon terminals in the in vivo context of normal Drosophila brain development, but devised to be applicable to filopodia in any system, including at different temporal and spatial scales. In contrast to the pre-existing methods, our workflow relies solely on the original intensity images without the requirement for segmentation or complex preprocessing. The workflow was realized in C++ within the Amira software system and consists of two main parts, dataset pre-processing, and geometrical filopodia reconstruction, where each of the two parts comprises multiple steps. In this paper, we provide an extensive workflow description and demonstrate its versatility for two different axo-dendritic morphologies, R7 and Dm8 cells. Finally, we provide an analysis of the time requirements for user input and data processing.
Conclusion: To facilitate simple application within Amira or other frameworks, we share the source code, which is available at https://github.com/zibamira/filopodia-tool.