You don't say where your son is aiming, and he's just a junior, so the jury is still out. If his grades this year and in his senior year (especially during the first semester) are strong, then his "rising record" will catch the attention of admission committees. Most admission folks are fairly forgiving when it comes to freshman and even sophomore foibles, especially when standardized tests are "stellar" and the applicant has excelled in tough courses in grades 11 and 12.
Of course, if your son is gunning for the Ivies and their hyper-competitive counterparts, he will be up against many others who share his strengths but who also fared well in grades 9 and 10. That doesn't mean he's automatically out of the running, but it will be a steeper slope for him to gain admission. Elite college admission officials are always looking for those special talents or unique accomplishments that make a top student an admitted one, and--in your son's case--he will need some especially distinguishing notches on his belt, should he wish to be Ivy-bound. This is especially so if his high school is one that ranks it students, and your son's rank has been greatly diminished by his previous grades.
For the lion's share of U.S. colleges and universities, however, strong test scores and excellent junior/senior grades should make him a desirable candidate.
You ask how to present his situation to admission committees. Well, his rising record should speak for itself when his application is evaluated. If, however, there are extenuating circumstances behind his lower frosh and soph grades, he can explain them in a supplemental essay or letter to accompany his applications (or his guidance counselor can do so in a recommendation). Be careful, though, to use this approach only if there are significant reasons for his earlier academic struggles. No admission staffer wants to hear about the trials of sharing a bedroom with a noisy older brother or an over-commitment to the skateboard club. Family problems, long-term illness, a major move or change of school, and other similar serious concerns may be worth explaining.
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