Neural Architecture Search as Program Transformation Exploration

Improving the performance of deep neural networks (DNNs) is important to both the compiler and neural architecture search (NAS) communities. Compilers apply program transformations in order to exploit hardware parallelism and memory hierarchy. However, legality concerns mean they fail to exploit the natural robustness of neural networks. In contrast, NAS techniques mutate networks by operations such as the grouping or bottlenecking of convolutions, exploiting the resilience of DNNs. In this work, we express such neural architecture operations as program transformations whose legality depends on a notion of representational capacity. This allows them to be combined with existing transformations into a unified optimization framework. This unification allows us to express existing NAS operations as combinations of simpler transformations. Crucially, it allows us to generate and explore new tensor convolutions. We prototyped the combined framework in TVM and were able to find optimizations across different DNNs, that significantly reduce inference time - over 3$\times$ in the majority of cases. Furthermore, our scheme dramatically reduces NAS search time. Code is available at~\href{https://github.com/jack-willturner/nas-as-program-transformation-exploration}{this https url}

Genomic plasticity of pathogenic Escherichia coli mediates D-serine tolerance via multiple adaptive mechanisms

Significance Pathogens ensure infection of favored sites in the body by responding to chemical signals. One chemical abundant in urine, the amino acid d -Ser, is toxic to EHEC and reduces expression of the machinery used for host cell attachment, making the bladder an unfavorable environment. We observed that under d -Ser stress, EHEC acquires genetic changes that lead to blocking d -Ser uptake into the cell or activating a silent enzyme for degrading d -Ser. This prevents growth inhibition and, critically, inhibits the repression of attachment machinery normally caused by d -Ser. These findings highlight the importance of pathogen evolution in determining how host molecules regulate colonization. These interactions underpin a process known as niche restriction that is important for pathogen success within the host

mlirSynth: Automatic, Retargetable Program Raising in Multi-Level IR using Program Synthesis

MLIR is an emerging compiler infrastructure for modern hardware, but existing programs cannot take advantage of MLIR’s high-performance compilation if they are described in lower-level general purpose languages. Consequently, to avoid programs needing to be rewritten manually, this has led to efforts to automatically raise lower-level to higher-level dialects in MLIR. However, current methods rely on manually-defined raising rules, which limit their applicability and make them challenging to maintain as MLIR dialects evolve. We present mlirSynth – a novel approach which translates programs from lower-level MLIR dialects to high-level ones without manually defined rules. Instead, it uses available dialect definitions to construct a program space and searches it effectively using type constraints and equivalences. We demonstrate its effectiveness by raising C programs to two distinct high-level MLIR dialects, which enables us to use existing high-level dialect specific compilation flows. On Polybench, we show a greater coverage than previous approaches, resulting in geomean speedups of 2.5x (Intel) and 3.4x (AMD) over state-of-the-art compilation flows. mlirSynth also enables retargetability to domain-specific accelerators, resulting in a geomean speedup of 21.6x on a TPU

mlirSynth: Automatic, Retargetable Program Raising in Multi-Level IR using Program Synthesis

MLIR is an emerging compiler infrastructure for modern hardware, but existing programs cannot take advantage of MLIR's high-performance compilation if they are described in lower-level general purpose languages. Consequently, to avoid programs needing to be rewritten manually, this has led to efforts to automatically raise lower-level to higher-level dialects in MLIR. However, current methods rely on manually-defined raising rules, which limit their applicability and make them challenging to maintain as MLIR dialects evolve. We present mlirSynth -- a novel approach which translates programs from lower-level MLIR dialects to high-level ones without manually defined rules. Instead, it uses available dialect definitions to construct a program space and searches it effectively using type constraints and equivalences. We demonstrate its effectiveness \revi{by raising C programs} to two distinct high-level MLIR dialects, which enables us to use existing high-level dialect specific compilation flows. On Polybench, we show a greater coverage than previous approaches, resulting in geomean speedups of 2.5x (Intel) and 3.4x (AMD) over state-of-the-art compilation flows for the C programming language. mlirSynth also enables retargetability to domain-specific accelerators, resulting in a geomean speedup of 21.6x on a TPU

MACiE: a database of enzyme reaction mechanisms.

SUMMARY: MACiE (mechanism, annotation and classification in enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme catalytic mechanisms and also to create a classification system which reflects the actual chemical mechanism (catalytic steps) of an enzyme reaction, not only the overall reaction. AVAILABILITY: http://www-mitchell.ch.cam.ac.uk/macie/.EPSRC (G.L.H. and J.B.O.M.), the BBSRC (G.J.B. and J.M.T.—CASE studentship in association with Roche Products Ltd; N.M.O.B. and J.B.O.M.—grant BB/C51320X/1), the Chilean Government’s Ministerio de Planificacio´n y Cooperacio´n and Cambridge Overseas Trust (D.E.A.) for funding and Unilever for supporting the Centre for Molecular Science Informatics.application note restricted to 2 printed pages web site: http://www-mitchell.ch.cam.ac.uk/macie